[English] 日本語
Yorodumi
- EMDB-11875: Cryo-EM structure of Arabidopsis thaliana complex-I (open conform... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11875
TitleCryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
Map data
Sample
  • Complex: Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
    • Protein or peptide: x 46 types
  • Ligand: x 13 types
Function / homology
Function and homology information


anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / NADH dehydrogenase activity ...anther dehiscence / vegetative to reproductive phase transition of meristem / cold acclimation / NADH dehydrogenase complex / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / NADH dehydrogenase activity / respiratory chain complex I / ubiquinone binding / regulation of reactive oxygen species metabolic process / cobalt ion binding / electron transport coupled proton transport / response to osmotic stress / plastid / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / protein homotrimerization / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / response to salt stress / respiratory electron transport chain / chloroplast / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / carbohydrate metabolic process / mitochondrial matrix / copper ion binding / nucleolus / mitochondrion / zinc ion binding / extracellular region / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, plant/fungi / At2g27730-like / NADH-ubiquinone oxidoreductase 11kDa subunit / NADH-ubiquinone oxidoreductase 11 kDa subunit / : / NADH-ubiquinone oxidoreductase, 21kDa subunit, N-terminal / NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / SLBB domain / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / Zinc finger, CHCC-type / Zinc-finger domain / Hexapeptide repeat / GRIM-19 / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / NADH-ubiquinone oxidoreductase B12 subunit family / NDUFA6, LYR domain / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 / NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7) / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Bacterial transferase hexapeptide (six repeats) / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH-quinone oxidoreductase, chain M/4 / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Trimeric LpxA-like superfamily / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / CHCH / NuoE domain / CHCH domain / NADH:ubiquinone oxidoreductase / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter
Similarity search - Domain/homology
NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 ...NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 2 / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A / Acyl carrier protein 2, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A / NADH-ubiquinone oxidoreductase chain 5 / Acyl carrier protein 1, mitochondrial / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial / At4g16450 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Transmembrane protein / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / Excitatory amino acid transporter / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / Gamma carbonic anhydrase 1, mitochondrial / At1g67350 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / At2g31490 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / thale cress (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.72 Å
AuthorsKlusch N / Kuelbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Plant Cell / Year: 2021
Title: A ferredoxin bridge connects the two arms of plant mitochondrial complex I.
Authors: Niklas Klusch / Jennifer Senkler / Özkan Yildiz / Werner Kühlbrandt / Hans-Peter Braun /
Abstract: Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two ...Mitochondrial complex I is the main site for electron transfer to the respiratory chain and generates much of the proton gradient across the inner mitochondrial membrane. Complex I is composed of two arms, which form a conserved L-shape. We report the structures of the intact, 47-subunit mitochondrial complex I from Arabidopsis thaliana and the 51-subunit complex I from the green alga Polytomella sp., both at around 2.9 Å resolution. In both complexes, a heterotrimeric γ-carbonic anhydrase domain is attached to the membrane arm on the matrix side. Two states are resolved in A. thaliana complex I, with different angles between the two arms and different conformations of the ND1 (NADH dehydrogenase subunit 1) loop near the quinol binding site. The angle appears to depend on a bridge domain, which links the peripheral arm to the membrane arm and includes an unusual ferredoxin. We propose that the bridge domain participates in regulating the activity of plant complex I.
History
DepositionOct 23, 2020-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ar7
  • Surface level: 0.011
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11875.png

Downloads & links

-
Map

FileDownload / File: emd_11875.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.837 Å
Density
Contour LevelBy AUTHOR: 0.011 / Movie #1: 0.011
Minimum - Maximum-0.03679776 - 0.11912532
Average (Standard dev.)6.365711e-05 (±0.0010330073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 502.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8370.8370.837
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z502.200502.200502.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0370.1190.000

-
Supplemental data

-
Half map: #2

Fileemd_11875_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11875_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Cryo-EM structure of Arabidopsis thaliana complex-I (open conform...

EntireName: Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
Components
  • Complex: Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4L
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 5
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 4
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
    • Protein or peptide: Acyl carrier protein 1, mitochondrial
    • Protein or peptide: Acyl carrier protein 2, mitochondrial
    • Protein or peptide: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
    • Protein or peptide: At2g46540/F11C10.23
    • Protein or peptide: Transmembrane protein
    • Protein or peptide: Excitatory amino acid transporter
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A
    • Protein or peptide: At4g16450
    • Protein or peptide: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
    • Protein or peptide: At1g67350
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: AT2G31490 protein
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
    • Protein or peptide: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
    • Protein or peptide: B14.5a
    • Protein or peptide: unknown
    • Protein or peptide: Uncharacterized protein At2g27730, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase-like 2, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase 2, mitochondrial
    • Protein or peptide: Gamma carbonic anhydrase 1, mitochondrial
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: Ubiquinone-9Coenzyme Q10
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ZINC ION
  • Ligand: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE
  • Ligand: Phosphatidylinositol

+
Supramolecule #1: Cryo-EM structure of Arabidopsis thaliana complex-I (open conform...

SupramoleculeName: Cryo-EM structure of Arabidopsis thaliana complex-I (open conformation)
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#46
Source (natural)Organism: Arabidopsis thaliana (thale cress)

+
Macromolecule #1: NADH-ubiquinone oxidoreductase chain 3

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.941387 KDa
SequenceString:
MMLEFAPIFI YLVISLLVSL ILLGVPFLFA SNSSTYPEKL SAYECGFDPF GDARSRFDIR FYLVSILFLI FDLEVTFFFP WAVSLNKID LFGFWSMMAF LFILTIGFLY EWKRGALDWE

+
Macromolecule #2: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 17.794744 KDa
SequenceString:
SKAAEFVISK VDDLMNWART GSIWPMTFGL ACCAVEMMHT GAARYDLDRF GIIFRPSPRQ SDCMIVAGTL TNKMAPALRK VYDQMPEPR WVISMGSCAN GGGYYHYSYS VVRGCDRIVP VDIYVPGCPP TAEALLYGLL QLQKKINRRK DFLHWWNK

+
Macromolecule #3: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 22.366369 KDa
SequenceString:
MDNQFIFKYS WETLPKKWVK KMERSEHGNR FDTNTDYLFQ LLCFLKLHTY TRVQVLIDIC GVDYPSRKRR FEVVYNLLST RYNSRIRVQ TSADEVTRIS SVVSLFPSAG WWEREVWDMF GVSFINHPDL RRILTDYGFE GHPLRKDFPL SGYVQVRYDD P EKRVVSEP IEMTQEFRYF DFASPWE

+
Macromolecule #4: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 43.889418 KDa
SequenceString: NFTLNFGPQH PAAHGVLRLV LEMNGEVVER AEPHIGLLHR GTEKLIEYKT YLQALPYFDR LDYVSMMAQE HAYSLAVEKL LNCEVPLRA QYIRVLFCEI TRILNHLLAL TTHAMDVGAL TPFLWAFEER EKLLEFYERV SGARMHASFI RPGGVAQDLP L GLCRDIDS ...String:
NFTLNFGPQH PAAHGVLRLV LEMNGEVVER AEPHIGLLHR GTEKLIEYKT YLQALPYFDR LDYVSMMAQE HAYSLAVEKL LNCEVPLRA QYIRVLFCEI TRILNHLLAL TTHAMDVGAL TPFLWAFEER EKLLEFYERV SGARMHASFI RPGGVAQDLP L GLCRDIDS FTQQFASRID ELEEMLTGNR IWKQRLVDIG TVTAQQAKDW GFSGVMLRGS GVCWDLRRAA PYDVYDQLDF DV PVGTRGD CYDRYCIRIE EMRQSLRIIV QCLNQMPSGM IKADDRKLCP PSRCRMKLSM ESLIHHFELY TEGFSVPASS TYT AVEAPK GEFGVFLVSN GSNRPYRCKI RAPGFAHSQG LDFMSKHHML ADVVTIIGTQ DIVFGEVDR

+
Macromolecule #5: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 21.411398 KDa
SequenceString: TALNYHLDSP DNKPDLPWEF SEANQSKVKE ILSYYPSNYK QSAVIPLLDL AQQQNGGWLP VSAMNAVAKV IEVAPIRVYE VATFYSMFN RAKVGKYHLL VCGTTPCMIR GSRDIESALL DHLGVKRGEV TKDGLFSVGE MECMGCCVNA PMITVADYSN G SEGYTYNY ...String:
TALNYHLDSP DNKPDLPWEF SEANQSKVKE ILSYYPSNYK QSAVIPLLDL AQQQNGGWLP VSAMNAVAKV IEVAPIRVYE VATFYSMFN RAKVGKYHLL VCGTTPCMIR GSRDIESALL DHLGVKRGEV TKDGLFSVGE MECMGCCVNA PMITVADYSN G SEGYTYNY FEDVTPEKVV EIVEKLRKGE KPPH

+
Macromolecule #6: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 48.087199 KDa
SequenceString: EKTHFGGLKD EDRIFTNLYG LHDPFLKGAM KRGDWHRTKD LVLKGTDWIV NEMKKSGLRG RGGAGFPSGL KWSFMPKVSD GRPSYLVVN ADESEPGTCK DREIMRHDPH KLLEGCLIAG VGMRASAAYI YIRGEYVNER LNLEKARREA YAAGLLGKNA C GSGYDFEV ...String:
EKTHFGGLKD EDRIFTNLYG LHDPFLKGAM KRGDWHRTKD LVLKGTDWIV NEMKKSGLRG RGGAGFPSGL KWSFMPKVSD GRPSYLVVN ADESEPGTCK DREIMRHDPH KLLEGCLIAG VGMRASAAYI YIRGEYVNER LNLEKARREA YAAGLLGKNA C GSGYDFEV YIHFGAGAYI CGEETALLES LEGKQGKPRL KPPFPANAGL YGCPTTVTNV ETVAVSPTIL RRGPEWFSSF GR KNNAGTK LFCISGHVNK PCTVEEEMSI PLKELIERHC GGVRGGWDNL LAIIPGGSSV PLIPKNICED VLMDFDALKA VQS GLGTAA VIVMDKSTDV VDAIARLSYF YKHESCGQCT PCREGTGWLW MIMERMKVGN AKLEEIDMLQ EVTKQIEGHT ICAL GDAAA WPVQGLIRHF RPELERRIRE RAERELLQA

+
Macromolecule #7: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 1, mitochondrial
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 75.10082 KDa
SequenceString: RNPVGGARVH FSNPEDAIEV FVDGYAVKVP KGFTVLQACE VAGVDIPRFC YHSRLSIAGN CRMCLVEVEK SPKPVASCAM PALPGMKIK TDTPIAKKAR EGVMEFLLMN HPLDCPICDQ GGECDLQDQS MAFGSDRGRF TEMKRSVVDK NLGPLVKTVM T RCIQCTRC ...String:
RNPVGGARVH FSNPEDAIEV FVDGYAVKVP KGFTVLQACE VAGVDIPRFC YHSRLSIAGN CRMCLVEVEK SPKPVASCAM PALPGMKIK TDTPIAKKAR EGVMEFLLMN HPLDCPICDQ GGECDLQDQS MAFGSDRGRF TEMKRSVVDK NLGPLVKTVM T RCIQCTRC VRFASEVAGV QDLGILGRGS GEEIGTYVEK LMTSELSGNV IDICPVGALT SKPFAFKARN WELKATETID VS DAVGSNI RVDSRGPEVM RIIPRLNEDI NEEWISDKTR FCYDGLKRQR LSDPMIRDSD GRFKAVSWRD ALAVVGDIIH QVK PDEIVG VAGQLSDAES MMVLKDFVNR MGSDNVWCEG TAAGVDADLR YSYLMNTSIS GLENADLFLL IGTQPRVEAA MVNA RICKT VRASNAKVGY VGPPAEFNYD CKHLGTGPDT LKEIAEGRHP FCTALKNAKN PAIIVGAGLF NRTDKNAILS SVESI AQAN NVVRPDWNGL NFLLQYAAQA AALDLGLIQQ SAKALESAKF VYLMGADDVN VDKIPKDAFV VYQGHHGDKA VYRANV ILP ASAFTEKEGT YENTEGFTQQ TVPAVPTVGD ARDDWKIVRA LSEVSGVKLP YNSIEGVRSR IKSVAPNLVH TDEREPA AF GPSLKPECKE AMSTTPFQTV VENFYMTNSI TRASKIMAQC SAVLLK

+
Macromolecule #8: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 35.888875 KDa
SequenceString: YIAVPAEILG IILPLLLGVA FLVLAERKVM AFVQRRKGPD VVGSFGLLQP LADGLKLILK EPISPSSANF FLFRMAPVAT FMLSLVAWA VVPFDYGMVL SDLNIGLLYL FAISSLGVYG IIIAGRSSNS KYAFLGALRS AAQMVSYEVS IGLILITVLI C VGSCNLSE ...String:
YIAVPAEILG IILPLLLGVA FLVLAERKVM AFVQRRKGPD VVGSFGLLQP LADGLKLILK EPISPSSANF FLFRMAPVAT FMLSLVAWA VVPFDYGMVL SDLNIGLLYL FAISSLGVYG IIIAGRSSNS KYAFLGALRS AAQMVSYEVS IGLILITVLI C VGSCNLSE IVMAQKQIWF GIPLFPVLVM FFISCLAETN RAPFDLPEAE AELVAGYNVE YSSMGFALFF LGEYANMILM SG LCTLFFL GGWLPILDLP IFKKIPGSIW FSIKVLFFLF LYIWVRAAFP RYRYDQLMGL GWKVFLPLSL AWVVSVSGLL VTF QWLP

+
Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 8-A, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 19.72327 KDa
SequenceString:
KEISKDWNTV FERSINTLFL TEMVRGLSLT LKYFFDPKVT INYPFEKGPL SPRFRGEHAL RRYPTGEERC IACKLCEAVC PAQAITIEA EEREDGSRRT TRYDIDMTKC IYCGFCQEAC PVDAIVEGPN FEFATETHEE LLYDKEKLLE NGDRWETEIA E NLRSESLY R

+
Macromolecule #10: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 23.690385 KDa
SequenceString: MILSVLSSLA LVSGLMVVRA KNPVHSVLFF ILVFCDTSGL LLLLGLDFFA MIFLVVYIGA IAVLFLFVVM MFHIQIAEIH EEVLRYLPV SGIIGLIFWW EMFFILDNES IPLLPTQRNT TSLRYTVYAG KVRSWTNLET LGNLLYTYYF VWFLVSSLIL L VAMIGAIV ...String:
MILSVLSSLA LVSGLMVVRA KNPVHSVLFF ILVFCDTSGL LLLLGLDFFA MIFLVVYIGA IAVLFLFVVM MFHIQIAEIH EEVLRYLPV SGIIGLIFWW EMFFILDNES IPLLPTQRNT TSLRYTVYAG KVRSWTNLET LGNLLYTYYF VWFLVSSLIL L VAMIGAIV LTMHRTTKVK RQDVFRRNAI DFRRTIMRRT TDPLTIY

+
Macromolecule #11: NADH-ubiquinone oxidoreductase chain 4L

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4L / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.892114 KDa
SequenceString:
MDLIKYFTFS MIIFILGIWG ILLNRRNILI MLMSIELMLL AVNLNFLVFS VSLDDMMGQV FALLVLTVAA AESAIGLAIF VITFRVRG

+
Macromolecule #12: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 68.21475 KDa
SequenceString: MYLLIVFLPL LGSSVAGFFG RFLGSEGSAI MTTTCVSFSS ILSLIAFYEV ALGASACYLR IAPWISSEMF DASWGFLFDS LTVVMLIVV TFISSLVHLY SISYMSEDPH SPRFMCYLSI FTFFMLMLVT GDNFLQLFLG WEGVGLASYL LIHFWFTRLQ A DKAAIKAM ...String:
MYLLIVFLPL LGSSVAGFFG RFLGSEGSAI MTTTCVSFSS ILSLIAFYEV ALGASACYLR IAPWISSEMF DASWGFLFDS LTVVMLIVV TFISSLVHLY SISYMSEDPH SPRFMCYLSI FTFFMLMLVT GDNFLQLFLG WEGVGLASYL LIHFWFTRLQ A DKAAIKAM LVNRVGDFGL ALGILGCFTL FQTVDFSTIF ACASVPRNSW IFCNMRLNAI SLICILLFIG AVGKSAQIGL HT WLPDAME GPTPVSALIH AATMVTAGVF MIARCSPLFE YSPTALIVIT FAGAMTSFLA ATTGILQNDL KRVIAYSTCS QLG YMIFAC GISNYSVSVF HLMNHAFFKA LLFLSAGSVI HAMSDEQDMR KMGGLASSFP LTYAMMLIGS LSLIGFPFLT GFYS KDVIL ELAYTKYTIS GNFAFWLGSV SVLFTSYYSF RLLFLTFLVP TNSFGRDISR CHDAPIPMAI PLILLALGSL FVGYL AKDM MIGLGTNFWA NSLLVLPKNE ILAESEFAAP TIIKLIPILF STLGAFVAYN VNLVADQFQR AFQTSTFCNR LYSFFN KRW FFDQVLNDFL VRSFLRFGYE VSFEALDKGA IEILGPYGIS YTFRRLAERI SQ

+
Macromolecule #13: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 55.001484 KDa
SequenceString: YFNLSGLILC PVLGSIILLF IPNSRIRLIR LIGLCASLIT FLYSLVLWIQ FDSSTAKFQF VESLRWLPYE NINFYLGIDG ISLFFVILT TFLIPICILV GWSGMRSYGK EYIIAFLICE FLMIAVFCML DLLLFYVFFE SVLIPMFIII GVWGSRQRKI K AAYQFFLY ...String:
YFNLSGLILC PVLGSIILLF IPNSRIRLIR LIGLCASLIT FLYSLVLWIQ FDSSTAKFQF VESLRWLPYE NINFYLGIDG ISLFFVILT TFLIPICILV GWSGMRSYGK EYIIAFLICE FLMIAVFCML DLLLFYVFFE SVLIPMFIII GVWGSRQRKI K AAYQFFLY TLLGSLFMLL AILLILFQTG TTDLQILLTT EFSERRQIFL WIAFFASFAV KVPMVPVHIW LPEAHVEAPT AG SVILAGI LLKFGTYGFL RFSIPMFPEA TLCFTPFIYT LSAIAIIYTS LTTLRQIDLK KIIAYSSVAH MNLVTIGMFS LNI QGIGGS ILLMLSHGLV SSALFLCVGV LYDRHKTRLV RYYGGLVSTM PNFSTIFFFF TLANMSLPGT SSFIGEFLIL VGAF QRNSL VATLAALGMI LGAAYSLWLY NRVVSGNLKP DFLHKFSDLN GREVFIFIPF LVGLVWMGVY PKVFLDCMHT SVSNL VQHG KFH

+
Macromolecule #14: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 54.161207 KDa
SequenceString: MFNLFLAVFP EIFIINATFI LLIHGVVFST SKKYDYPPLA SNVGWLGLLS VLITLLLLAA GAPLLTIAHL FWNNLFRRDN FTYFCQIFL LLSTAGTISM CFDFFDQERF DAFEFIVLIL LSTCGMLFMI SAYDLIAMYL AIELQSLCFY VIAASKRKSE F STEAGLKY ...String:
MFNLFLAVFP EIFIINATFI LLIHGVVFST SKKYDYPPLA SNVGWLGLLS VLITLLLLAA GAPLLTIAHL FWNNLFRRDN FTYFCQIFL LLSTAGTISM CFDFFDQERF DAFEFIVLIL LSTCGMLFMI SAYDLIAMYL AIELQSLCFY VIAASKRKSE F STEAGLKY LILGAFSSGI LLFGCSMIYG STGATHFDQL AKILTGYEIT GARSSGIFMG ILFIAVGFLF KITAVPFHMW AP DIYEGSP TPVTAFLSIA PKISIFANIL RVFIYGSYGA TLQQIFFFCS IASMILGALA AMAQTKVKRL LAYSSIGHVG YIC IGFSCG TIEGIQSLLI GIFIYALMTM DAFAIVLALR QTRVKYIADL GALAKTNPIL AITFSITMFS YAGIPPLAGF CSKF YLFFA ALGCGAYFLA LVGVVTSVIG CFYYIRLVKR MFFDTPRTWI LYEPMDRNKS LLLAMTSFFI TLFLLYPSPL FSVTH QMAL SLYL

+
Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mit...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 36.400199 KDa
SequenceString: VGHLARKGTG GRSSVSGIVA TVFGATGFLG RYLVQQLAKM GSQVLVPFRG SEDSPRHLKL MGDLGQVVPM KFDPRDEDSI KAVMAKANV VINLIGREYE TRNFSFEDAN HHIAEKLALV AKEHGGIMRY IQVSCLGASV SSPSRMLRAK AAAEEAVLNA L PEATIMRP ...String:
VGHLARKGTG GRSSVSGIVA TVFGATGFLG RYLVQQLAKM GSQVLVPFRG SEDSPRHLKL MGDLGQVVPM KFDPRDEDSI KAVMAKANV VINLIGREYE TRNFSFEDAN HHIAEKLALV AKEHGGIMRY IQVSCLGASV SSPSRMLRAK AAAEEAVLNA L PEATIMRP ATMIGTEDRI LNPWSMFVKK YGFLPLIGGG TTKFQPVYVV DVAAAIVAAL KDDGSSMGKT YELGGPDVFT TH ELAEIMY DMIREWPRYV KLPFPIAKAM AAPRDFMVNK VPFPLPSPQI FNLDQINALT TDTLVSDNAL KFQDLDLVPH KLK GYPVEF LIQYR

+
Macromolecule #16: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 13.290985 KDa
SequenceString:
KRGEIGKVSG IPEEHLSRKV IIYSPARTAT QSGSGKLGKW KINFVSTLKW ENPLMGWTST GDPYANVGDS ALAFDSEEAA KSFAERHGW DYKVKKPNTP LLKVKSYSDN FKWKGNPQPE

+
Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 6.928023 KDa
SequenceString:
RSKKSPMELI SEVPPIKVDG RIVACEGDTN PALGHPIEFI CLDLNEPAIC KYCGLRYVQD HH

+
Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 10.433207 KDa
SequenceString:
AWRGSISKSM KELRILLCQS SPASAPTRTF VEKNYKDLKS LNPKLPILIR ECSGVQPQMW ARYDMGVERC VNLDGLTEPQ ILKALENLV KSGA

+
Macromolecule #19: Acyl carrier protein 1, mitochondrial

MacromoleculeName: Acyl carrier protein 1, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.526669 KDa
SequenceString:
DDHLSREAVV DRVLDVVKSF PKVDPSKVTP EVHFQNDLGL DSLDTVEIVM AIEEEFKLEI PDKEADKIDS CSLAIEYVYN HPMS

+
Macromolecule #20: Acyl carrier protein 2, mitochondrial

MacromoleculeName: Acyl carrier protein 2, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.232275 KDa
SequenceString:
FLDKSEVTDR VLSVVKNFQK VDPSKVTPKA NFQNDLGLDS LDSVEVVMAL EEEFGFEIPD NEADKIQSID LAVDFIASHP QAK

+
Macromolecule #21: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subun...

MacromoleculeName: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5, mitochondrial
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 16.006163 KDa
SequenceString:
AKVKQTTGIV GLDVVPNARA VLIDLYSKTL KEIQAVPEDE GYRKAVESFT RQRLNVCKEE EDWEMIEKRL GCGQVEELIE EARDELTLI GKMIEWDPWG VPDDYECEVI ENDAPIPKHV PQHRPGPLPE QFYKTLEGLI A

+
Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 15.102261 KDa
SequenceString:
MAAPFALRKI GVPPNSANLT EARRRVFDFF RAACRSIPTI MDIYNLQDVV APSQLRYAIS AQIRNNAHIT DPKVIDLLIF KGMEELTDI VDHAKQRHHI IGQYVVGEGL VQNTGNKDQG KTDFLKNFYT SNYF

+
Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.036894 KDa
SequenceString:
NPIPTSAVLT ASAKHIGMRC MPENVAFLKC KKNDPNPEKC LDKGRDVTRC VLGLLKDLHQ KCQKEMDDYV GCMYYYTNEF DLCRKEQEA FEKVCPL

+
Macromolecule #24: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 14.150146 KDa
SequenceString:
PLLQDGPPPG GFAPVRYARR ISNTGPSAMA MFLAVSGAFA WGMYQVGQGN KIRRALKEEK YAARRTILPI LQAEEDERFV SEWKKYLEY EADVMKDVPG WKVGENVYNS GRWMPPATGE LRPDVW

+
Macromolecule #25: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 6.717929 KDa
SequenceString:
LVWLEAMLPL GIIGGMLCIM GNSQYYIHKA YHGRPKHIGH DEWDVAMERR DKKVVEKA

+
Macromolecule #26: At2g46540/F11C10.23

MacromoleculeName: At2g46540/F11C10.23 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 4.240167 KDa
SequenceString:
PVMEKLRMFV AQEPVVAASC LIGGVGLFLP AVVRPILDSL

+
Macromolecule #27: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.811344 KDa
SequenceString:
GDFRAKVWSM TGGPNCRPKH WRRNTAIAMF GVFLVCIPIA KLSAKLEQRP HMPVRPIPSQ IWCKNFGTKD DYEKEH

+
Macromolecule #28: Excitatory amino acid transporter

MacromoleculeName: Excitatory amino acid transporter / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.457983 KDa
SequenceString:
PISATMVGAL LGLGTQMYSN ALRKLPYMRH PWEHVVGMGL GAVFANQLVK WDVKLKEDLD VMLAKARAAN ERRYF

+
Macromolecule #29: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-A
type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 7.847912 KDa
SequenceString:
ASGWGITGNK GRCYDFWMDF SECMSHCREP KDCTLLREDY LECLHHSKEF QRRNRIYKEE QRKL

+
Macromolecule #30: At4g16450

MacromoleculeName: At4g16450 / type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 10.720277 KDa
SequenceString:
MNTDITALEK AQYPVVDRNP AFTKVVGNFS TLDYLRFSTI TGISVTVGYL SGIKPGIKGP SMVTGGLIGL MGGFMYAYQN SAGRLMGFF PNDGEVASYQ K

+
Macromolecule #31: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein

MacromoleculeName: ESSS subunit of NADH:ubiquinone oxidoreductase (Complex I) protein
type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.319505 KDa
SequenceString:
WATPGHEERP KGYFMNRTPP APGQSRKWED WELPCYITSF LTIVILGVGL NAKPDLSIET WAHQKALERL EM

+
Macromolecule #32: At1g67350

MacromoleculeName: At1g67350 / type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 10.493911 KDa
SequenceString:
GFIMEFAENL VLRLMENPEE RDRKAREHIY EMHERCKKIK EMWALPIRPY GFWTFERHNA QLRWDPQISQ VAGRRDPYDD LLEDN

+
Macromolecule #33: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2
type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 5.878873 KDa
SequenceString:
GITYKGVTVH TPKTWHTVTG KGLCAVMWFW ILYRAKQDGP VVMGWRHPWD G

+
Macromolecule #34: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3-A
type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 5.337173 KDa
SequenceString:
PLGTTGEFFR RRDEWRKHPM LSNQMRHALP GIGIGVGAFC VYLVGEQ

+
Macromolecule #35: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
type: protein_or_peptide / ID: 35 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 5.074872 KDa
SequenceString:
YEALAWLSGG LGFFVGLGLL AVLNDKASKV PFTPRVYPYD NLRVEL

+
Macromolecule #36: AT2G31490 protein

MacromoleculeName: AT2G31490 protein / type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 8.003188 KDa
SequenceString:
METNKNKFIE DWGSARENLE HNFRWTRRNF ALIGIFGIAL PIIVYKGIVK DFHMQDEDAG RPHRKFL

+
Macromolecule #37: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9
type: protein_or_peptide / ID: 37 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 12.86448 KDa
SequenceString:
AAYFARRAAQ KERVRILYRR ALKDTLNWAV HRHIFYRDAS DLREKFNVNQ DVEDVDRIDK LIAHGEAEYN KWRHPDPYIV PWAPGGSKF CRNPTPPAGI EIVYNYGLED

+
Macromolecule #38: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7
type: protein_or_peptide / ID: 38 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 9.509255 KDa
SequenceString:
KKMIATQEEM SAAKIALGSR DMCAHLLIPL NKCRQAEFYL PWKCEDERHV YEKCEYELVM ERMLAMKKIR EEEALAKQNK

+
Macromolecule #39: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10-B
type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 11.070687 KDa
SequenceString:
GRKKGLPEFE ESAPDGFDPE NPYKDPVAMV EMREHIVREK WIQIEKAKIL REKVKWCYRV EGVNHYQKCR HLVQQYLDST RGVGWGKDH RPIS

+
Macromolecule #40: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

MacromoleculeName: Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 7.325027 KDa
SequenceString:
GATLVGVDKF GNKYYQKLGD TQYGRHRWVE YASKDRYNAS QVPAEWHGWL HFITDHTGDE LLS

+
Macromolecule #41: B14.5a

MacromoleculeName: B14.5a / type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 1.245536 KDa
SequenceString:
PPIRRYVLTK

+
Macromolecule #42: unknown

MacromoleculeName: unknown / type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 2.571161 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

+
Macromolecule #43: Uncharacterized protein At2g27730, mitochondrial

MacromoleculeName: Uncharacterized protein At2g27730, mitochondrial / type: protein_or_peptide / ID: 43 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 3.208709 KDa
SequenceString:
PKVSEDKNRN YAVVAGVVAI VGSIGWYLKA

+
Macromolecule #44: Gamma carbonic anhydrase-like 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase-like 2, mitochondrial / type: protein_or_peptide / ID: 44 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 23.542941 KDa
SequenceString: PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVTV WDGSSVWNGA VLRGDLNKIT VGFCSNVQER CVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE CIIGQHSILM EGSLVETRSI LEAGSVLPPG RRIPSGELWG G NPARFIRT ...String:
PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVTV WDGSSVWNGA VLRGDLNKIT VGFCSNVQER CVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE CIIGQHSILM EGSLVETRSI LEAGSVLPPG RRIPSGELWG G NPARFIRT LTNEETLEIP KLAVAINHLS GDYFSEFLPY STIYLEVEKF KKSLGI

+
Macromolecule #45: Gamma carbonic anhydrase 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 2, mitochondrial / type: protein_or_peptide / ID: 45 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 28.947855 KDa
SequenceString: GTLGRAIYTV GNWIRGTGQA LDRVGSLLQG SHRIEEHLSR HRTLMNVFDK SPLVDKDVFV APSASVIGDV QIGKGSSIWY GCVLRGDVN NISVGSGTNI QDNTLVHVAK TNISGKVLPT LIGDNVTVGH SAVIHGCTVE DDAFVGMGAT LLDGVVVEKH A MVAAGSLV ...String:
GTLGRAIYTV GNWIRGTGQA LDRVGSLLQG SHRIEEHLSR HRTLMNVFDK SPLVDKDVFV APSASVIGDV QIGKGSSIWY GCVLRGDVN NISVGSGTNI QDNTLVHVAK TNISGKVLPT LIGDNVTVGH SAVIHGCTVE DDAFVGMGAT LLDGVVVEKH A MVAAGSLV KQNTRIPSGE VWGGNPAKFM RKLTDEEIVY ISQSAKNYIN LAQIHASENS KSFEQIEVER ALRKKYARKD ED YDSMLGI TRETPPELIL PDNVLPGGKP V

+
Macromolecule #46: Gamma carbonic anhydrase 1, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 1, mitochondrial / type: protein_or_peptide / ID: 46 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: thale cress (thale cress)
Molecular weightTheoretical: 25.202623 KDa
SequenceString: GTLGRAFYSV GFWIRETGQA LDRLGCRLQG KNYFREQLSR HRTLMNVFDK APIVDKEAFV APSASVIGDV HIGRGSSIWY GCVLRGDVN TVSVGSGTNI QDNSLVHVAK SNLSGKVHPT IIGDNVTIGH SAVLHGCTVE DETFIGMGAT LLDGVVVEKH G MVAAGALV ...String:
GTLGRAFYSV GFWIRETGQA LDRLGCRLQG KNYFREQLSR HRTLMNVFDK APIVDKEAFV APSASVIGDV HIGRGSSIWY GCVLRGDVN TVSVGSGTNI QDNSLVHVAK SNLSGKVHPT IIGDNVTIGH SAVLHGCTVE DETFIGMGAT LLDGVVVEKH G MVAAGALV RQNTRIPSGE VWGGNPARFL RKLTDEEIAF ISQSATNYSN LAQAHAAENA KPLNVIEFEK VLRKK

+
Macromolecule #47: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 47 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

+
Macromolecule #48: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 48 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

+
Macromolecule #49: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 49 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

+
Macromolecule #50: Ubiquinone-9

MacromoleculeName: Ubiquinone-9 / type: ligand / ID: 50 / Number of copies: 1 / Formula: UQ9
Molecular weightTheoretical: 795.226 Da
Chemical component information

ChemComp-UQ9:
Ubiquinone-9

+
Macromolecule #51: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 51 / Number of copies: 3 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #52: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5...

MacromoleculeName: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
type: ligand / ID: 52 / Number of copies: 2 / Formula: PC7
Molecular weightTheoretical: 763.1 Da
Chemical component information

ChemComp-PC7:
(7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE / phospholipid*YM / Phosphatidylcholine

+
Macromolecule #53: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 53 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

+
Macromolecule #54: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 54 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate

+
Macromolecule #55: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 55 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #56: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
type: ligand / ID: 56 / Number of copies: 2 / Formula: 8Q1
Molecular weightTheoretical: 540.651 Da
Chemical component information

ChemComp-8Q1:
S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate

+
Macromolecule #57: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 57 / Number of copies: 1 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #58: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

MacromoleculeName: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / type: ligand / ID: 58 / Number of copies: 1 / Formula: PSF
Molecular weightTheoretical: 455.437 Da
Chemical component information

ChemComp-PSF:
1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / Phosphatidylserine

+
Macromolecule #59: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 59 / Number of copies: 1 / Formula: T7X
Molecular weightTheoretical: 887.128 Da
Chemical component information

ChemComp-T7X:
Phosphatidylinositol / Phosphatidylinositol

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48933
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more