[English] 日本語
Yorodumi
- EMDB-15936: Drosophila melanogaster complex I in the Active state (Dm1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15936
TitleDrosophila melanogaster complex I in the Active state (Dm1)
Map dataGlobally sharpened consensus map generated using RELION Postprocess
Sample
  • Complex: Mitochondrial respiratory complex I
    • Protein or peptide: x 42 types
  • Ligand: x 12 types
Function / homology
Function and homology information


Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / regulation of terminal button organization / protein lipoylation / Neutrophil degranulation / cellular respiration / ubiquinone binding ...Mitochondrial protein import / Glyoxylate metabolism and glycine degradation / Respiratory electron transport / Complex I biogenesis / Mitochondrial Fatty Acid Beta-Oxidation / regulation of terminal button organization / protein lipoylation / Neutrophil degranulation / cellular respiration / ubiquinone binding / acyl binding / electron transport coupled proton transport / mitochondrial ATP synthesis coupled electron transport / acyl carrier activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / respiratory electron transport chain / reactive oxygen species metabolic process / response to reactive oxygen species / determination of adult lifespan / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / mitochondrial matrix / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH-ubiquinone oxidoreductase, subunit 10 / NADH-ubiquinone oxidoreductase subunit 10 / Soluble ligand binding domain ...NADH-ubiquinone oxidoreductase flavoprotein 3 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH:ubiquinone oxidoreductase, ESSS subunit / ESSS subunit of NADH:ubiquinone oxidoreductase (complex I) / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1, NDUB1 / MNLL subunit / 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 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, metazoa / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 2, animal type / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NADH dehydrogenase 1 beta subcomplex subunit 2 / NADH dehydrogenase [ubiquinone] 1 subunit C2, NDUC2 / NADH:ubiquinone oxidoreductase, subunit NDUFB4 / NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2) / NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4) / NADH dehydrogenase 1, beta subcomplex, subunit 6 / NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit / NADH:ubiquinone oxidoreductase chain 4, N-terminal / NADH:ubiquinone oxidoreductase, chain 2 / NADH dehydrogenase subunit 2, C-terminal / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH-ubiquinone oxidoreductase chain 4, amino terminus / NADH dehydrogenase subunit 2 C-terminus / NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 / GRIM-19 / NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8) / GRIM-19 protein / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / 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 / NDUFB9, LYR domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / 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 / Deoxynucleoside kinase domain / Deoxynucleoside kinase / 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 dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, F subunit / Complex 1 LYR protein domain / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Complex 1 protein (LYR family) / 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
Similarity search - Domain/homology
FI24283p1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L ...FI24283p1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 / GH23780p / GEO11417p1 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / Acyl carrier protein, mitochondrial / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial / GM23292p / Complex I-49kD / NADH dehydrogenase (ubiquinone) 23 kDa subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH dehydrogenase [ubiquinone] 1 subunit C2 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10 / NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A / LD31474p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 / RH45008p / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1 / NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / fruit fly (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsAgip AA / Chung I / Sanchez-Martinez A / Whitworth AJ / Hirst J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_00015/2 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UU_00028/1 United Kingdom
CitationJournal: Elife / Year: 2023
Title: Cryo-EM structures of mitochondrial respiratory complex I from .
Authors: Ahmed-Noor A Agip / Injae Chung / Alvaro Sanchez-Martinez / Alexander J Whitworth / Judy Hirst /
Abstract: Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a ...Respiratory complex I powers ATP synthesis by oxidative phosphorylation, exploiting the energy from NADH oxidation by ubiquinone to drive protons across an energy-transducing membrane. is a candidate model organism for complex I due to its high evolutionary conservation with the mammalian enzyme, well-developed genetic toolkit, and complex physiology for studies in specific cell types and tissues. Here, we isolate complex I from and determine its structure, revealing a 43-subunit assembly with high structural homology to its 45-subunit mammalian counterpart, including a hitherto unknown homologue to subunit NDUFA3. The major conformational state of the enzyme is the mammalian-type 'ready-to-go' active resting state, with a fully ordered and enclosed ubiquinone-binding site, but a subtly altered global conformation related to changes in subunit ND6. The mammalian-type 'deactive' pronounced resting state is not observed: in two minor states, the ubiquinone-binding site is unchanged, but a deactive-type π-bulge is present in ND6-TMH3. Our detailed structural knowledge of complex I provides a foundation for new approaches to disentangle mechanisms of complex I catalysis and regulation in bioenergetics and physiology.
History
DepositionOct 10, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15936.png

Downloads & links

-
Map

FileDownload / File: emd_15936.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobally sharpened consensus map generated using RELION Postprocess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 450 pix.
= 471.6 Å		1.05 Å/pix.
x 450 pix.
= 471.6 Å		1.05 Å/pix.
x 450 pix.
= 471.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.017511453 - 0.10321252
Average (Standard dev.)-0.00015190923 (±0.0020192822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 471.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15936_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened and unfiltered consensus map generated using RELION...

Fileemd_15936_additional_1.map
AnnotationUnsharpened and unfiltered consensus map generated using RELION Postprocess
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 generated using RELION Postprocess (unsharpened...

Fileemd_15936_half_map_1.map
AnnotationHalf map 1 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 2 generated using RELION Postprocess (unsharpened...

Fileemd_15936_half_map_2.map
AnnotationHalf map 2 generated using RELION Postprocess (unsharpened and unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Mitochondrial respiratory complex I

EntireName: Mitochondrial respiratory complex I
Components
  • Complex: Mitochondrial respiratory complex I
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: LD31474p
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
    • Protein or peptide: Complex I-49kD
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH dehydrogenase (ubiquinone) 23 kDa subunit
    • 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 10, mitochondrial
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
    • 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: Acyl carrier protein, mitochondrial
    • Protein or peptide: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
    • Protein or peptide: RH45008p
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 subunit C2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
    • Protein or peptide: GEO11417p1
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
    • 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
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: CARDIOLIPIN
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: SODIUM IONSodium
  • Ligand: Ubiquinone-9Coenzyme Q10
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: ZINC ION
  • Ligand: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate

+
Supramolecule #1: Mitochondrial respiratory complex I

SupramoleculeName: Mitochondrial respiratory complex I / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#42
Details: Native purification of mitochondrial complex I from Drosophila melanogaster (fruit fly) W1118.
Source (natural)Organism: Drosophila melanogaster (fruit fly) / Strain: W1118
Molecular weightTheoretical: 1 MDa

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 13.572529 KDa
SequenceString:
MFSIIFIALL ILLITTIVMF LASILSKKAL IDREKSSPFE CGFDPKSSSR LPFSLRFFLI TIIFLIFDVE IALILPMIII MKYSNIMIW TITSIIFILI LLIGLYHEWN QGMLNWSN

+
Macromolecule #2: LD31474p

MacromoleculeName: LD31474p / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 20.493963 KDa
SequenceString:
QQTLPVAEVA QNLPKKGYSP FGTKQSSVAE WSLARLDDLL NWGRKGSIWP LTFGLACCAV EMMHIAAPRY DMDRYGVVFR ASPRQADVI IVAGTLTNKM APALRKVYDQ MPEPRWVISM GSCANGGGYY HYSYSVVRGC DRIIPVDIYV PGCPPTAEAL M YGVLQLQK KVKRMKTLQM WYRK

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 24.435604 KDa
SequenceString: DKPTVRQPDA VARSHLSDFG RYVAECLPKY VQKVQLTAGD ELEVLIAPEG VVPVLQFLKD HHQAQFTNLV DIAGVDVPCR KNRFEVVYN LLSLRYNSRI RVKTYTDELT PLDSACEVHK AANWYEREIW DMYGVFFANH PDLRRILTDY GFEGHPQRRD F PLSGYVEL ...String:
DKPTVRQPDA VARSHLSDFG RYVAECLPKY VQKVQLTAGD ELEVLIAPEG VVPVLQFLKD HHQAQFTNLV DIAGVDVPCR KNRFEVVYN LLSLRYNSRI RVKTYTDELT PLDSACEVHK AANWYEREIW DMYGVFFANH PDLRRILTDY GFEGHPQRRD F PLSGYVEL RYDDEKKRVV CEPLELAQEF RKFDLSAPWE QFPNFRNANP P

+
Macromolecule #4: Complex I-49kD

MacromoleculeName: Complex I-49kD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 48.880125 KDa
SequenceString: AAKWYPDPEF MKQFSGPVMY PDEVTSLWTV PPWNSKVTPV EKSVRNLTLN FGPQHPAAHG VLRLVLELDG ETVMRADPHI GLLH(2MR)GTEK LIEYKTYTQA LPYFDRLDYV SMMCNEQCYS LAVEKLLNID VPLRAKYIRT LFAEITRILN HIMAVGT HA LDVGALTPFF ...String:
AAKWYPDPEF MKQFSGPVMY PDEVTSLWTV PPWNSKVTPV EKSVRNLTLN FGPQHPAAHG VLRLVLELDG ETVMRADPHI GLLH(2MR)GTEK LIEYKTYTQA LPYFDRLDYV SMMCNEQCYS LAVEKLLNID VPLRAKYIRT LFAEITRILN HIMAVGT HA LDVGALTPFF WLFEEREKMM EFYERVSGAR MHAAYIRPGG VSLDMPLGLM DDIYEFASKF AERLDEVEDV LTTNRIWV Q RTEDIGIVTA EEALNYGFSG VMLRGSGIKW DLRKQQPYDA YNLVNFDVPI GTKGDCYDRY LCRVEEMRQS LRIIDQCLN QMPAGEIKTD DAKVAPPSRS EMKTSMEALI HHFKLFTQGY QVPPGATYTA IEAPKGEFGV YLISDGSSRP YRCKIKAPGF AHLAALEKI GKQHMLADVV AIIGTLDVVF GEIDR

+
Macromolecule #5: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 24 kDa subunit, isoform A
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 23.979373 KDa
SequenceString: DNLFVHRDTP EDNPNIPFEF TAENKKRVEA ILSIYPEGHK RGAMIPLLDL AQRQYGWLPI SAMHKVAEIL QLPNMRVYEV ATFYTMFMR KPTGKYHIQV CTTTPCWLRG SDDILETCKK QLGIGVGDTT KDRKFTISEV ECLGACVNAP MVAINDDYYE D LTSKDMQD ...String:
DNLFVHRDTP EDNPNIPFEF TAENKKRVEA ILSIYPEGHK RGAMIPLLDL AQRQYGWLPI SAMHKVAEIL QLPNMRVYEV ATFYTMFMR KPTGKYHIQV CTTTPCWLRG SDDILETCKK QLGIGVGDTT KDRKFTISEV ECLGACVNAP MVAINDDYYE D LTSKDMQD ILNDLKADKI SPPGPRNGRF ASEPKGEPTS LSEEPKGPGF GLQAGL

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 48.261363 KDa
SequenceString: PPPGTPPPQT KTKFGPLADE DRIFTNLYGR HDWRLKGALK RGDWYKTKEI VLKGADWIVN EIKTSGLRGR GGAGFPSGMK WSFMNKPGD GRPKYLVVNA DEGEPGTCKD REIMRHDPHK LVEGCLIAGR AMGAQAAYIY IRGEFYNEAS NMQLAIAEAY Q AGLIGKNA ...String:
PPPGTPPPQT KTKFGPLADE DRIFTNLYGR HDWRLKGALK RGDWYKTKEI VLKGADWIVN EIKTSGLRGR GGAGFPSGMK WSFMNKPGD GRPKYLVVNA DEGEPGTCKD REIMRHDPHK LVEGCLIAGR AMGAQAAYIY IRGEFYNEAS NMQLAIAEAY Q AGLIGKNA CGTGYDFDVF MHRGAGAYIC GEETALIESL EGKQGKPRLK PPFPADVGVF GCPTTVTNVE TVAVAPTICR RG GVWFASF GRTRNSGTKL FNISGHVNRP CTVEEEMSIP LKELIERHCG GVTGGWDNLL GVIPGGSSTP IIPKNVCDDV IMD FDGLIA AQTSLGTAAI IVMDKSTDVI KAIARLISFY KHESCGQCTP CREGIGWMNK IMTRFVKGDA QPAEIDMLWE ISKQ IEGHT ICALGDGAAW PVQGLIRHFR PEIEKRMQLH AKRVSN

+
Macromolecule #7: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial

MacromoleculeName: NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 78.72425 KDa
SequenceString: MIRAPLVKAL GALGSPTHQM ASRAVRTSAM VAQTPAKAPE KIEVFVDDIP VQVVPGTTVL QAAAQIGVEI PRFCYHERLA VAGNCRMCL VEVEKSPKPV AACAMPVMKG WRIKTNSDLT RKAREGVMEF LLMNHPLDCP ICDQGGECDL QDQAMAFGSD R SRFTDINY ...String:
MIRAPLVKAL GALGSPTHQM ASRAVRTSAM VAQTPAKAPE KIEVFVDDIP VQVVPGTTVL QAAAQIGVEI PRFCYHERLA VAGNCRMCL VEVEKSPKPV AACAMPVMKG WRIKTNSDLT RKAREGVMEF LLMNHPLDCP ICDQGGECDL QDQAMAFGSD R SRFTDINY TGKRAVEDKD IGPLVKTIMT RCIHCTRCVR FASEIAGVDD LGTTGRGNDM QIGTYVEKLF LTELSGNVID LC PVGALTN KPYSFVARPW EIRKVSSIDV LDAVGSNIVV STRTNEVLRI LPRENEDVNE EWLADKSRFA CDGLKRQRLV APM VRMPNG ELQAVEWEGA LIAVAKAIKA AGGQIAGISG QLADLEAQVA LKDLLNRLGS EVVATEQGFI AGGTDNRANY LLNS TIAGL EEADAVLLVG TNPRYEAPLV NTRLRKAYVH NELQIASIGP KIDLSYDHEN LGADAALVKD VCSGAHAFSK VLEGA KKPA IIIGADLLER ADGAAIHATV AEYCKKLKKP NWNPFNVLQT NAAQVGALDV GYKAGAQTAV KAQPKVLFLL NADAGK VTR EQLPKDCFVV YIGSHGDNGA SIADAVLPGA AYTEKQGIYV NTEGRPQQTL PGVSPPGMAR EDWKILRALS EVVGKPL PY DNLDELRNRL EDVAPHLTRL GQLEPAGDAG AAGTISKSIG GGAIDIKLKE LRDYFMTDAI SRASPTMAKC ISAVNKQQ R ENEAKQSVAI

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 36.38352 KDa
SequenceString: MFYMEFILSL IGSLLLIICV LVSVAFLTLL ERKVLGYIQI RKGPNKVGLM GIPQPFCDAI KLFTKEQTYP LLSNYLSYYI SPIFSLFLS LFVWMCMPFF VKLYSFNLGG LFFLCCTSLG VYTVMVAGWS SNSNYALLGG LRAVAQTISY EVSLALILLS F IFLIGSYN ...String:
MFYMEFILSL IGSLLLIICV LVSVAFLTLL ERKVLGYIQI RKGPNKVGLM GIPQPFCDAI KLFTKEQTYP LLSNYLSYYI SPIFSLFLS LFVWMCMPFF VKLYSFNLGG LFFLCCTSLG VYTVMVAGWS SNSNYALLGG LRAVAQTISY EVSLALILLS F IFLIGSYN MIYFFFYQVY MWFLIILFPM ALVWVSISLA ETNRTPFDFA EGESELVSGF NVEYSSGGFA LIFMAEYASI LF MSMLFCV IFLGCDVFNL LFYMKLTFIS FVFIWVRGTL PRFRYDKLMY LAWKCFLSFS LNYLLFFIGF KILLFSLL

+
Macromolecule #9: NADH dehydrogenase (ubiquinone) 23 kDa subunit

MacromoleculeName: NADH dehydrogenase (ubiquinone) 23 kDa subunit / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 21.202973 KDa
SequenceString:
EPKDIVEVPK GYVYVNNKEL SMEFADITDR AASTMFFGEL LRGFAVTLAH IFKEPATINY PFEKGPLSPR FRGEHALRRY PSGEERCIA CKLCEAICPA QAITIEAEER ADGSRRTTRY DIDMTKCIYC GFCQEACPVD AIVEGPNFEF STETHEELLY N KEKLLCNG DKWESEIASN LQADHLYR

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 19.996514 KDa
SequenceString:
MIQLMLYSLI ITTSIIFLNM IHPLALGLTL LIQTIFVCLL TGLMTKSFWY SYILFLIFLG GMLVLFIYVT SLASNEMFNL SMKLTLFSS LILIFMLILS FIMDKTSSSL FLMNNDMQSI INMNSYFMEN SLSLNKLYNF PTNFITILLM NYLLITLIVI V KITKLFKG PIRMM

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 11.363853 KDa
SequenceString:
MIMILYWSLP MILFILGLFC FVSNRKHLLS MLLSLEFIVL MLFFMLFIYL NMLNYESYFS MMFLTFSVCE GALGLSILVS MIRTHGNDY FQSFSIM

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 65.777867 KDa
SequenceString: MKYLSICSIS FVNLISMSLS CFLLSLYFLL NDMIYFIEWE LVSLNSMSIV MTFLFDWMSL LFMSFVLMIS SLVIFYSKEY MMNDNHINR FIMLVLMFVL SMMLLIISPN LISILLGWDG LGLVSYCLVI YFQNIKSYNA GMLTALSNRI GDVALLLSIA W MLNYGSWN ...String:
MKYLSICSIS FVNLISMSLS CFLLSLYFLL NDMIYFIEWE LVSLNSMSIV MTFLFDWMSL LFMSFVLMIS SLVIFYSKEY MMNDNHINR FIMLVLMFVL SMMLLIISPN LISILLGWDG LGLVSYCLVI YFQNIKSYNA GMLTALSNRI GDVALLLSIA W MLNYGSWN YIFYLEIMQN EFEMLMIGSL VMLAAMTKSA QIPFSSWLPA AMAAPTPVSA LVHSSTLVTA GVYLLIRFNI IL STSWLGQ LMLLLSGLTM FMAGLGANFE FDLKKIIALS TLSQLGLMMS ILSMGFLKLA MFHLLTHALF KALLFMCAGA IIH NMNNSQ DIRLMGGLSI HMPLTSACFN VSNLALCGMP FLAGFYSKDM ILEIVSISNV NMFSFFLYYF STGLTVSYSF RLVY YSMTG DLNCGSLNML NDESWIMLRG MMGLLIMSII GGSMLNWLIF PFPYMICLPI YMKLLTLFVC IVGGLFGYLI SLSNL FFLN KSLFMYNLST FLGSMWFMPY ISTYGMIFYP LNYGQLVVKS FDQGWSEYFG GQHLYQKLSM YSKTLFLMHN NSLKIY LLL FVFWILILLI LLFL

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 51.473168 KDa
SequenceString: MLKIIFFLLF LIPFCFINNM YWMVQIMMFF ISFIFLLMNN FMNYWSEISY FLGCDMLSYG LILLSLWICS LMLLASEMIN KHNNYKNLF LLNIIILLLL LILTFSSMSL FMFYLFFESS LIPTLFLILG WGYQPERLQA GLYLLFYTLL VSLPMLIGIF Y LMNKIGSM ...String:
MLKIIFFLLF LIPFCFINNM YWMVQIMMFF ISFIFLLMNN FMNYWSEISY FLGCDMLSYG LILLSLWICS LMLLASEMIN KHNNYKNLF LLNIIILLLL LILTFSSMSL FMFYLFFESS LIPTLFLILG WGYQPERLQA GLYLLFYTLL VSLPMLIGIF Y LMNKIGSM NFYLMNNFMF NYDLLYFCLL CAFLVKMPMF LVHLWLPKAH VEAPVSGSMI LAGIMLKLGG YGMLRVISFL QL MNLKYSF VWISISLVGG VLVSLVCLRQ TDLKALIAYS SVAHMGIVLS GLLTMTYWGL CGSYTLMIAH GLCSSGLFCL ANV SYERLG SRSMLINKGL LNFMPSMTLW WFLLSSANMA APPTLNLLGE IYLLNSIVSW SWISMILLSF LSFFSAAYTL YLYS FSQHG KLFSGVYSFS SGKIREYLLM LLHWLPLNLL ILKSESFMLW L

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 39.839887 KDa
SequenceString: MFNNSSKILF ITIMIIGTLI TVTSNSWLGA WMGLEINLLS FIPLLSDNNN LMSTEASLKY FLTQVLASTV LLFSSILLML KNNMNNEIN ESFTSMIIMS ALLLKSGAAP FHFWFPNMME GLTWMNALML MTWQKIAPLM LISYLNIKYL LLISVILSVI I GAIGGLNQ ...String:
MFNNSSKILF ITIMIIGTLI TVTSNSWLGA WMGLEINLLS FIPLLSDNNN LMSTEASLKY FLTQVLASTV LLFSSILLML KNNMNNEIN ESFTSMIIMS ALLLKSGAAP FHFWFPNMME GLTWMNALML MTWQKIAPLM LISYLNIKYL LLISVILSVI I GAIGGLNQ TSLRKLMAFS SINHLGWMLS SLMISESIWL IYFFFYSFLS FVLTFMFNIF KLFHLNQLFS WFVNSKILKF TL FMNFLSL GGLPPFLGFL PKWLVIQQLT LCNQYFMLTL MMMSTLITLF FYLRICYSAF MMNYFENNWI MKMNMNSINY NMY MIMTFF SIFGLFLISL FYFMF

+
Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mi...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 42.724574 KDa
SequenceString: ISGKTMRGGP RVPKAAPYPY KTKKYSVFNA IFDKTSKRFD ENSKVICVEG PIAAGKSKFA KELAEELDME YYPAVDLDLI YINSYGYDM RKLDPQLPPS CRSYDVRNFC LDPSHDLAAQ FQIRMYMLRY SQYIDALQHV LSTGQGVVLE RSPYSDFVFM E AMFRQGYL ...String:
ISGKTMRGGP RVPKAAPYPY KTKKYSVFNA IFDKTSKRFD ENSKVICVEG PIAAGKSKFA KELAEELDME YYPAVDLDLI YINSYGYDM RKLDPQLPPS CRSYDVRNFC LDPSHDLAAQ FQIRMYMLRY SQYIDALQHV LSTGQGVVLE RSPYSDFVFM E AMFRQGYL SRGARSVYNE LRQNTIGELL KPHLVIYLDL PVDAVKKQIK ARNVDYEVQS KVFSDAYLSD LEQLYKQQYL KD ISTHAEL LIYDWTAGGE TEVVVEDIER IDFNQFEADI HNKKMLDWRF PLEAEWCEAR IKYCHEKPDL MNYFNVPRFD VPE LVRSAD DGKVWRDVWF NAPGMKYRPG YNADMGDEGL LTKTKIGINQ GI

+
Macromolecule #16: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 39 kDa subunit, isoform A
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 42.994168 KDa
SequenceString: PRPLKTTNPA AMKRGTGGRS SFNGIVATVF GATGFVGRYV CNKLGKSGTQ MILPYRGDDS DVIRLKVTGD LGQVLFHFYN LEDPASIRD AVKHSNVVIN LVGRDFETKN FKFKDVHVNG AERIARIARE AGVERFIHLS SLNVEANPKD LYVKGGSEWL K SKYEGELR ...String:
PRPLKTTNPA AMKRGTGGRS SFNGIVATVF GATGFVGRYV CNKLGKSGTQ MILPYRGDDS DVIRLKVTGD LGQVLFHFYN LEDPASIRD AVKHSNVVIN LVGRDFETKN FKFKDVHVNG AERIARIARE AGVERFIHLS SLNVEANPKD LYVKGGSEWL K SKYEGELR VRDAFPNATI IRPADIYGSE DRFLRYYAHI WRRQFRSMPL WHKGEKTVKQ PVYVSDVAQA IINAAKDPDS AG RIYQAVG PKRYQLSELV DWFHRLMRKD QKRWGYMRYD MRWDPTFLLK AKLNSFICPG TPIGGLHPAR IEREAVTDKV LTG VPTLED LGVTLTTMEQ QVPWELRPYR AALYYDAELG EFETPSPPKC IEARDELRLF A

+
Macromolecule #17: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 17.239344 KDa
SequenceString:
TDGGPLDPKT ALARPEELEQ RNKLSGKITV PTAVNLSPIS GVPEEHIRER RVRIHIPPKN AMQSGTDNVN TWQIEFDNRE RWENPLMGW ASSGDPLSNM NVQFGSPEEA ITFCERNGWR WYVDGAAKPK KERVKNYGIN FAWNKRTRVS TK

+
Macromolecule #18: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 10.197637 KDa
SequenceString:
RGDIEKVTHT GQVFDKEDYR NARFVNAKRY VNENWGIKLI EEVPPKECTE RVVFCDGGDG PLGHPKVYIN LDKPGNHICG YCGLRFVKK

+
Macromolecule #19: Acyl carrier protein, mitochondrial

MacromoleculeName: Acyl carrier protein, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 9.725121 KDa
SequenceString:
PPLSLKLINE RVLLVLKLYD KIDPSKLNVE SHFINDLGLD SLDHVEVIMA MEDEFGFEIP DSDAEKLLKP ADIIKYVADK EDVYE

+
Macromolecule #20: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit

MacromoleculeName: NADH dehydrogenase (Ubiquinone) 13 kDa B subunit / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.135179 KDa
SequenceString:
IKASTGLTGL AVSTNPHHTL SALYGKILRA VSKMPQDASY RKYTEQLVKQ RADSVAQHKD ITALEKAVGC GQVEELIVQA ENELILARK MLGWKPWEKL VQAAPAKQWD WPPAQIMEP

+
Macromolecule #21: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 13.805113 KDa
SequenceString:
AVQQVRPILS VDREEARKRA LNLYKAWYRQ IPYIVMDYDI PMTVEQCRDK LREEFVKHRN VTDIRVIDML VIKGQMELKE SVEIWKQKG HIMRYWKESQ DPKPTDFLSK FIQGV

+
Macromolecule #22: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8
type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 19.742227 KDa
SequenceString:
VITNNTTLPE ESELNVQELN LSSAALRAGA FHLGKQCEQA NNEFMLCRQE LDDPRACLAE GKAVTSCALD FFRKVKKTCH EEFTQYATC LDKSSGTMAF SHCRKTQGVF DKCIKDNFDW DRPSYGYFSR AKVIQSAREA PKKEEKVSYP DATPGLPEDY P KPPAKYGS RFHWLE

+
Macromolecule #23: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11
type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 18.101697 KDa
SequenceString:
LRSKYYDHPD GEDAFGKIVA TNKYAVSAGV AWSMFDVLTL SKPQGYLPTL GRFAYNTGPL MGMATAFTLT TLVATNARGK DDKINYLIG GFAAGGVFGA WKHNHVAGLC AGLFLGIAGV IKKMSIEQGW EFFPNTPIKQ YGGLNIAGND WTIMADPPKN W TTEKPKE

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 16.961572 KDa
SequenceString:
PPKQDLPPPG GYKKIPFARV PPKSYFTGFT TIGTYVVVTA VGLGIYYLTA KKVKRDEIEM RSAQNVIFPI LVAERDREFL RQLRRNRDE EAELMKNVPG WEVGTWYGEP VFKTLPEDTL VTPIFKEFYA HSDWKSYAKR AHLKLWS

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 8.587994 KDa
SequenceString:
MWFEILPGAV IITTLLSVPI YAMYGLDKLM IGNAFRRNMD ERFSRVMYQR DFRLTDNPYK MNGLDAIPDE KTN

+
Macromolecule #26: RH45008p

MacromoleculeName: RH45008p / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 7.376355 KDa
SequenceString:
SLLKRAWNEI PDIVGGSALA LAGIVMATIG VANYYAKDGD NRRYKLGYVV YRHDDPRALK VRNDED

+
Macromolecule #27: NADH dehydrogenase [ubiquinone] 1 subunit C2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 subunit C2 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.794606 KDa
SequenceString:
SAVNDPLELL TNKGTHEPSF LSPIWNPIAC GVAGVGAAIF INWGFRKPVF SGIQKHIAFG AIGVGAGAYF DQKRNEYLAK RDAVLRHYI ELHPDDFPVK ERKTYGQVLE SWVPVR

+
Macromolecule #28: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 11.884772 KDa
SequenceString:
SLTPFLRLPL TDLTGCLINH QTYDKCGKFE MKMMECFEAY GLERGKRECA DLISDFQECV GMQKQLMRFH AMRNERYKQW LKGERKGQE FFADPPRVDA Y

+
Macromolecule #29: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 1
type: protein_or_peptide / ID: 29 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 6.101111 KDa
SequenceString:
VLGLDKRALW GALPLLGFAI GHFLDKKETE RMTMFRDKSA LYGRPAGSEG KAPSW

+
Macromolecule #30: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mit...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial
type: protein_or_peptide / ID: 30 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.475763 KDa
SequenceString:
TSLTTEDFAN PSPKNWQSYG FDYKDQVEDR KATKSTFFVT VTLCLVWGSF YWAYLPDTQF RNWAQREGFL ELRRRELAGV DLVSPNYVD PASITLPSDE DLGDTEIII

+
Macromolecule #31: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mito...

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial
type: protein_or_peptide / ID: 31 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 17.45177 KDa
SequenceString:
GHHQMIIKPS RFQWDKFKDL LHFYVMLGVI PVTALVLYAN IFVGPAQLAE IPEGYEPKHW EYEKHPISRF ISRYILNSDQ QNYEKSLHY LYEENEKAQI RLLEDEVRRK MSERNDYQAY YYRPSVAKYH RISKEAADEL EALRGD

+
Macromolecule #32: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 6
type: protein_or_peptide / ID: 32 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 18.467168 KDa
SequenceString:
GASETGGVKP MVIAGRMVRE RERLIGMSPE ERAWRKQWLK DQELHHGPRK VPALELELNN PIKRFYRAPL DKVCNVLEPV LGFQRAYTV RFWTGKALLA LTGIYAGAYY FKYNQNDWTR KGGWRVIHSR KQCVPGDEGY PKVSDRSAPS DYAARGFNES P L

+
Macromolecule #33: GEO11417p1

MacromoleculeName: GEO11417p1 / type: protein_or_peptide / ID: 33 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 7.618564 KDa
SequenceString:
KSHVVSYRNG PPPHSKATKI GALTVGGAMW WWVIWHLWHE PDHITGEFDY PNSRKWSNTE LGVPKD

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3
type: protein_or_peptide / ID: 34 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 9.480889 KDa
SequenceString:
EPYTVPHAST YKVESVPQLV EVKEALGRQG LKDPWLRNEV WRYEPKAFGT HRSRLNTFLF RGLGVGFCAF LATVAVEYAL GIGK

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 17.136066 KDa
SequenceString:
AGWNKDYKPG PYPQTEKERL AAAKKYYLLP EEYKPYADDG LGYGDYPKLG YGLGVEAKDS YYPWDYPEHK RNQHEPISAD HDLYSEDRW SQAEPPRYSN AYYFACFLGV MSGCLALYYW LDDKKMYRPV AAKQYPSPGV KHYTFEK

+
Macromolecule #36: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4
type: protein_or_peptide / ID: 36 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 12.61235 KDa
SequenceString:
EEQEFIKRKH EATLKLRQEF LKQSSNPYRH ATGEGGTVFD AGLARFQAMR VSNYEHFKPT GKSFRTGLFA VVLPIALYAW ALKAERDGR EEKYRTGQVA YKDRQFKFI

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 16.285512 KDa
SequenceString:
AQVPLAIVSH KRQVCSLYKR ALRNLESWYD RRNVYRYRAV QLRARFDENR SKDLGEGIRL LACGQRELFE TRHFQPRNFA NSAGGCAFE REVIPPDWVL DYWHPLEKAQ YPEYFAKREQ RKKEFVTWWE KQYGK

+
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: fruit fly (fruit fly)
Molecular weightTheoretical: 13.388468 KDa
SequenceString:
GNALTHYMKP DVMPGPDVVP TFDPLLGFKS RKERVMIATQ EEMESAKLPL EFRDYCAHLA IAYQACRSDT FPFVYKCAHQ KHEYLTCEY EDYVLRMKEF ERERRLLERQ KRL

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10
type: protein_or_peptide / ID: 39 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 18.050463 KDa
SequenceString:
PRSPMASFAE SVLNVIDGPI TWFRESIVEP NQQKQNWYHQ RFRRVPTIDQ CYTDDAVCRF EADQQFRRDR MVDNEIVNIL RQRFEDCTL YEAPDHMVKC RPLMDQYEKA TENWFIKYGD LGGYANAKTA YMKQKHRLIW ERRHGPVGSG MK

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
type: protein_or_peptide / ID: 40 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 15.812925 KDa
SequenceString:
INRLTKLFQM VREAGGLKQA YLKLYRNDDL KIGTLVGIDK YGNKYFENPY YFYGRNRWIE FAPHVNMDYD GSMIPAEWYG WMHYKTDLP PIRDGCRPKY KWIADHSENL SGTKEAYYPY STTPNKVEAW EPKA

+
Macromolecule #41: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
type: protein_or_peptide / ID: 41 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly) / Strain: W1118
Molecular weightTheoretical: 11.562093 KDa
SequenceString:
MSALRRDVSP LIQRIRAFLL GREHNLALRF EDGLADRTQP QPEIPDGPSH LLSANYYCQR DGRREVLPPI DLVEQQKQLA AEGEAAKAP SSKLPTPGKV YAWD

+
Macromolecule #42: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial
type: protein_or_peptide / ID: 42 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: fruit fly (fruit fly)
Molecular weightTheoretical: 6.512273 KDa
SequenceString:
SSPSVVGLTS NCVKPSSGPV GPGASATGGY KVPEYYSFNR FSYAEAEVEM AKYRCPQPSA LK

+
Macromolecule #43: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 43 / Number of copies: 3 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM / Phosphatidylcholine

+
Macromolecule #44: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 44 / Number of copies: 16 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #45: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 45 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

+
Macromolecule #46: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 46 / Number of copies: 4 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*YM / Cardiolipin

+
Macromolecule #47: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 47 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

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

+
Macromolecule #48: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 48 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

+
Macromolecule #49: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 49 / Number of copies: 1
Molecular weightTheoretical: 22.99 Da

+
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: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 51 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosine triphosphate

+
Macromolecule #52: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 52 / 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 #53: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 53 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #54: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butan...

MacromoleculeName: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
type: ligand / ID: 54 / Number of copies: 2 / Formula: EHZ
Molecular weightTheoretical: 584.703 Da
Chemical component information

ChemComp-EHZ:
~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.4 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTrisTRIZMA base
150.0 mMNaClSodium chloridesodium chloride
0.05 %DDMn-Dodecyl beta-D-maltoside
GridModel: UltrAuFoil / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ...Details: Following glow discharge for 90 s at 20 mA, the grid was treated for 7 days in an anaerobic glovebox in ethanol containing 5 mM 11-mercaptoundecyl hexaethyleneglycol, washed three times in ethanol and dried prior to blotting
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 10 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3082 / Average exposure time: 10.0 sec. / Average electron dose: 41.88 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 194538
Startup modelType of model: EMDB MAP
EMDB ID:

4345

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 37608
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6zr2

RefinementSpace: REAL
Output model

PDB-8b9z:
Drosophila melanogaster complex I in the Active state (Dm1)

+
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