[English] 日本語
Yorodumi
- EMDB-11872: Cryo-EM structure of Arabidopsis thaliana Complex-I (membrane core) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11872
TitleCryo-EM structure of Arabidopsis thaliana Complex-I (membrane core)
Map data
Sample
  • Complex: Arabidopsis complex I - membrane core
    • Protein or peptide: x 21 types
  • Ligand: x 9 types
Function / homology
Function and homology information


anther dehiscence / vegetative to reproductive phase transition of meristem / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I ...anther dehiscence / vegetative to reproductive phase transition of meristem / NADH dehydrogenase complex / P450-containing electron transport chain / Lyases; Carbon-oxygen lyases; Hydro-lyases / photorespiration / embryo development ending in seed dormancy / response to abscisic acid / plant-type vacuole / respiratory chain complex I / regulation of reactive oxygen species metabolic process / plastid / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / protein homotrimerization / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / response to salt stress / mitochondrial membrane / carbonate dehydratase activity / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / peroxisome / mitochondrial inner membrane / copper ion binding / nucleolus / mitochondrion / extracellular region / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
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 / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 ...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 / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex subunit 1 / NADH-ubiquinone oxidoreductase MWFE subunit / Hexapeptide repeat / GRIM-19 / GRIM-19 protein / NADH dehydrogenase subunit 5, C-terminal / NADH dehydrogenase subunit 5 C-terminus / NADH:ubiquinone oxidoreductase, NDUFS5-15kDa / Bacterial transferase hexapeptide (six repeats) / NADH:ubiquinone oxidoreductase, iron-sulphur subunit 5 / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 8 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / 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 / 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 / CHCH domain / NADH:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / Coiled coil-helix-coiled coil-helix (CHCH) domain profile. / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
(thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / At4g16450 ...(thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L / (thale cress) hypothetical protein / NADH-ubiquinone oxidoreductase chain 1 / NADH-ubiquinone oxidoreductase chain 4 / NADH-ubiquinone oxidoreductase chain 5 / NADH-ubiquinone oxidoreductase chain 2 / NADH-ubiquinone oxidoreductase chain 3 / At4g16450 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A / Excitatory amino acid transporter / Gamma carbonic anhydrase 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1 / Gamma carbonic anhydrase 1, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B / Gamma carbonic anhydrase-like 2, mitochondrial / At2g46540/F11C10.23 / Uncharacterized protein At2g27730, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Mouse-ear cress (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsKlusch N / Kuehlbrandt W / Yildiz O
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 22, 2020-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateDec 8, 2021-
Current statusDec 8, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7aqq
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11872.png

Downloads & links

-
Map

FileDownload / File: emd_11872.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: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.027493287 - 0.056241017
Average (Standard dev.)3.3608107e-05 (±0.0007588884)
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-0.0270.0560.000

-
Supplemental data

-
Half map: #2

Fileemd_11872_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11872_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Arabidopsis complex I - membrane core

EntireName: Arabidopsis complex I - membrane core
Components
  • Complex: Arabidopsis complex I - membrane core
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 3
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 1
    • Protein or peptide: NADH-ubiquinone oxidoreductase chain 6
    • Protein or peptide: NADH dehydrogenase subunit 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: AT3G07480.1
    • 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: Excitatory amino acid transporter
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
    • Protein or peptide: At4g16450
    • Protein or peptide: P1
    • 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: Ubiquinone-9Coenzyme Q10
  • Ligand: PHOSPHATIDYLETHANOLAMINE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: FE (III) ION
  • Ligand: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE
  • Ligand: ZINC ION
  • 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: Arabidopsis complex I - membrane core

SupramoleculeName: Arabidopsis complex I - membrane core / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
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: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 13.941387 KDa
SequenceString:
MMLEFAPIFI YLVISLLVSL ILLGVPFLFA SNSSTYPEKL SAYECGFDPF GDARSRFDIR FYLVSILFLI FDLEVTFFFP WAVSLNKID LFGFWSMMAF LFILTIGFLY EWKRGALDWE

+
Macromolecule #2: NADH-ubiquinone oxidoreductase chain 1

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 36.02007 KDa
SequenceString: MYIAVPAEIL GIILPLLLGV AFLVLAERKV MAFVQRRKGP DVVGSFGLLQ PLADGLKLIL KEPISPSSAN FFLFRMAPVA TFMLSLVAW AVVPFDYGMV LSDLNIGLLY LFAISSLGVY GIIIAGRSSN SKYAFLGALR SAAQMVSYEV SIGLILITVL I CVGSCNLS ...String:
MYIAVPAEIL GIILPLLLGV AFLVLAERKV MAFVQRRKGP DVVGSFGLLQ PLADGLKLIL KEPISPSSAN FFLFRMAPVA TFMLSLVAW AVVPFDYGMV LSDLNIGLLY LFAISSLGVY GIIIAGRSSN SKYAFLGALR SAAQMVSYEV SIGLILITVL I CVGSCNLS EIVMAQKQIW FGIPLFPVLV MFFISCLAET NRAPFDLPEA EAELVAGYNV EYSSMGFALF FLGEYANMIL MS GLCTLFF LGGWLPILDL PIFKKIPGSI WFSIKVLFFL FLYIWVRAAF PRYRYDQLMG LGWKVFLPLS LAWVVSVSGL LVT FQWLP

+
Macromolecule #3: NADH-ubiquinone oxidoreductase chain 6

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Mouse-ear 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 #4: NADH dehydrogenase subunit 4L

MacromoleculeName: NADH dehydrogenase subunit 4L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 11.165549 KDa
SequenceString:
MDLIKYFTFS MIIFILGIWG ILLNRRNILI MLMSIELMLL AVNLNFLVFS VSLDDMMGQV FALLVLTVAA AESAIGLAIF VITFRVRGT IAVEFINSIQ G

+
Macromolecule #5: NADH-ubiquinone oxidoreductase chain 5

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 74.497977 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 SQLQSGFVYH YAFAMLLGLT LFVTFFC MW DSLSSWVDNR LSFILIVSSF YTKSSQE

+
Macromolecule #6: NADH-ubiquinone oxidoreductase chain 4

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 56.055758 KDa
SequenceString: MLEHFCECYF NLSGLILCPV LGSIILLFIP NSRIRLIRLI GLCASLITFL YSLVLWIQFD SSTAKFQFVE SLRWLPYENI NFYLGIDGI SLFFVILTTF LIPICILVGW SGMRSYGKEY IIAFLICEFL MIAVFCMLDL LLFYVFFESV LIPMFIIIGV W GSRQRKIK ...String:
MLEHFCECYF NLSGLILCPV LGSIILLFIP NSRIRLIRLI GLCASLITFL YSLVLWIQFD SSTAKFQFVE SLRWLPYENI NFYLGIDGI SLFFVILTTF LIPICILVGW SGMRSYGKEY IIAFLICEFL MIAVFCMLDL LLFYVFFESV LIPMFIIIGV W GSRQRKIK AAYQFFLYTL LGSLFMLLAI LLILFQTGTT DLQILLTTEF SERRQIFLWI AFFASFAVKV PMVPVHIWLP EA HVEAPTA GSVILAGILL KFGTYGFLRF SIPMFPEATL CFTPFIYTLS AIAIIYTSLT TLRQIDLKKI IAYSSVAHMN LVT IGMFSL NIQGIGGSIL LMLSHGLVSS ALFLCVGVLY DRHKTRLVRY YGGLVSTMPN FFTIFFFFTL ANMSLPGTSS FIGE FLILV GAFQRNSLVA TLAALGMILG AAYSLWLYNR VVSGNLKPDF LHKFSDLNGR EVFIFIPFLV GLVWMGVYPK VFLDC MHTS VSNLVQHGKF H

+
Macromolecule #7: NADH-ubiquinone oxidoreductase chain 2

MacromoleculeName: NADH-ubiquinone oxidoreductase chain 2 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 55.486836 KDa
SequenceString: MKAEFVRILP HMFNLFLAVF PEIFIINATF ILLIHGVVFS TSKKYDYPPL ASNVGWLGLL SVLITLLLLA AGAPLLTIAH LFWNNLFRR DNFTYFCQIF LLLSTAGTIS MCFDFFDQER FDAFEFIVLI LLSTCGMLFM ISAYDLIAMY LAIELQSLCF Y VIAASKRK ...String:
MKAEFVRILP HMFNLFLAVF PEIFIINATF ILLIHGVVFS TSKKYDYPPL ASNVGWLGLL SVLITLLLLA AGAPLLTIAH LFWNNLFRR DNFTYFCQIF LLLSTAGTIS MCFDFFDQER FDAFEFIVLI LLSTCGMLFM ISAYDLIAMY LAIELQSLCF Y VIAASKRK SEFSTEAGLK YLILGAFSSG ILLFGCSMIY GSTGATHFDQ LAKILTGYEI TGARSSGIFM GILFIAVGFL FK ITAVPFH MWAPDIYEGS PTPVTAFLSI APKISIFANI LRVFIYGSYG ATLQQIFFFC SIASMILGAL AAMAQTKVKR LLA YSSIGH VGYICIGFSC GTIEGIQSLL IGIFIYALMT MDAFAIVLAL RQTRVKYIAD LGALAKTNPI LAITFSITMF SYAG IPPLA GFCSKFYLFF AALGCGAYFL ALVGVVTSVI GCFYYIRLVK RMFFDTPRTW ILYEPMDRNK SLLLAMTSFF ITLFL LYPS PLFSVTHQMA LSLYL

+
Macromolecule #8: AT3G07480.1

MacromoleculeName: AT3G07480.1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 17.626197 KDa
SequenceString:
MATTLQKLSS QIHRLSPFTR SLIVRTSATS APSPSLGSKK VSDRIVKLSA IDPDGYKQDI IGLSGQTLLR ALTHTGLIDP ASHRLDDIE ACSAECEVQI AEEWLEKLPP RTYDEEYVLK RSSRSRILNK HSRLGCQVVL TQELQGMVVA VPEAKPWDIP

+
Macromolecule #9: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8-B
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 11.985954 KDa
SequenceString:
MSSAVDATGN PIPTSAVLTA SAKHIGMRCM PENVAFLKCK KNDPNPEKCL DKGRDVTRCV LGLLKDLHQK CQKEMDDYVG CMYYYTNEF DLCRKEQEAF EKVCPLK

+
Macromolecule #10: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13-A
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 16.145584 KDa
SequenceString:
MTEAMIRNKP GMASVKDMPL LQDGPPPGGF APVRYARRIS NTGPSAMAMF LAVSGAFAWG MYQVGQGNKI RRALKEEKYA ARRTILPIL QAEEDERFVS EWKKYLEYEA DVMKDVPGWK VGENVYNSGR WMPPATGELR PDVW

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 7.349628 KDa
SequenceString:
MSLVWLEAML PLGIIGGMLC IMGNSQYYIH KAYHGRPKHI GHDEWDVAME RRDKKVVEKA AAPSS

+
Macromolecule #12: At2g46540/F11C10.23

MacromoleculeName: At2g46540/F11C10.23 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 6.810177 KDa
SequenceString:
MPVMEKLRMF VAQEPVVAAS CLIGGVGLFL PAVVRPILDS LEASKQVKAP PLTDVIAGVT GKKQS

+
Macromolecule #13: Excitatory amino acid transporter

MacromoleculeName: Excitatory amino acid transporter / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 9.220749 KDa
SequenceString:
MPISATMVGA LLGLGTQMYS NALRKLPYMR HPWEHVVGMG LGAVFANQLV KWDVKLKEDL DVMLAKARAA NERRYFDEDR D

+
Macromolecule #14: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 5-B
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 9.914133 KDa
SequenceString:
MASGWGITGN KGRCYDFWMD FSECMSHCRE PKDCTLLRED YLECLHHSKE FQRRNRIYKE EQRKLRAASR KGEETGDGTH THH

+
Macromolecule #15: At4g16450

MacromoleculeName: At4g16450 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 11.355008 KDa
SequenceString:
MNTDITALEK AQYPVVDRNP AFTKVVGNFS TLDYLRFSTI TGISVTVGYL SGIKPGIKGP SMVTGGLIGL MGGFMYAYQN SAGRLMGFF PNDGEVASYQ KRGGFSK

+
Macromolecule #16: P1

MacromoleculeName: P1 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 11.808244 KDa
SequenceString:
MGFIMEFAEN LVLRLMENPE ERDRKAREHI YEMHERCKKI KEMWALPIRP YGFWTFERHN AQLRWDPQIS QVAGRRDPYD DLLEDNYTP PSSSSSSSD

+
Macromolecule #17: unknown

MacromoleculeName: unknown / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear 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 #18: Uncharacterized protein At2g27730, mitochondrial

MacromoleculeName: Uncharacterized protein At2g27730, mitochondrial / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 11.96552 KDa
SequenceString:
MATRNALRIV SRRFSSGKVL SEEERAAENV FIKKMEQEKL QKLARQGPGE QAAGSASEAK VAGATASASA ESGPKVSEDK NRNYAVVAG VVAIVGSIGW YLKAGGKKQP EVQE

+
Macromolecule #19: Gamma carbonic anhydrase-like 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase-like 2, mitochondrial / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 27.985113 KDa
SequenceString: MATSLARISK RSITSAVSSN LIRRYFAAEA VAVATTETPK PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVT VWDGSSVWNG AVLRGDLNKI TVGFCSNVQE RCVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE C IIGQHSIL ...String:
MATSLARISK RSITSAVSSN LIRRYFAAEA VAVATTETPK PKSQVTPSPD RVKWDYRGQR QIIPLGQWLP KVAVDAYVAP NVVLAGQVT VWDGSSVWNG AVLRGDLNKI TVGFCSNVQE RCVVHAAWSS PTGLPAQTLI DRYVTVGAYS LLRSCTIEPE C IIGQHSIL MEGSLVETRS ILEAGSVLPP GRRIPSGELW GGNPARFIRT LTNEETLEIP KLAVAINHLS GDYFSEFLPY ST IYLEVEK FKKSLGIAI

+
Macromolecule #20: Gamma carbonic anhydrase 2, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 2, mitochondrial / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 30.102207 KDa
SequenceString: MGTLGRAIYT VGNWIRGTGQ ALDRVGSLLQ GSHRIEEHLS RHRTLMNVFD KSPLVDKDVF VAPSASVIGD VQIGKGSSIW YGCVLRGDV NNISVGSGTN IQDNTLVHVA KTNISGKVLP TLIGDNVTVG HSAVIHGCTV EDDAFVGMGA TLLDGVVVEK H AMVAAGSL ...String:
MGTLGRAIYT VGNWIRGTGQ ALDRVGSLLQ GSHRIEEHLS RHRTLMNVFD KSPLVDKDVF VAPSASVIGD VQIGKGSSIW YGCVLRGDV NNISVGSGTN IQDNTLVHVA KTNISGKVLP TLIGDNVTVG HSAVIHGCTV EDDAFVGMGA TLLDGVVVEK H AMVAAGSL VKQNTRIPSG EVWGGNPAKF MRKLTDEEIV YISQSAKNYI NLAQIHASEN SKSFEQIEVE RALRKKYARK DE DYDSMLG ITRETPPELI LPDNVLPGGK PVAKVPSTQY F

+
Macromolecule #21: Gamma carbonic anhydrase 1, mitochondrial

MacromoleculeName: Gamma carbonic anhydrase 1, mitochondrial / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases; Carbon-oxygen lyases; Hydro-lyases
Source (natural)Organism: Mouse-ear cress (thale cress)
Molecular weightTheoretical: 30.010039 KDa
SequenceString: MGTLGRAFYS VGFWIRETGQ ALDRLGCRLQ GKNYFREQLS RHRTLMNVFD KAPIVDKEAF VAPSASVIGD VHIGRGSSIW YGCVLRGDV NTVSVGSGTN IQDNSLVHVA KSNLSGKVHP TIIGDNVTIG HSAVLHGCTV EDETFIGMGA TLLDGVVVEK H GMVAAGAL ...String:
MGTLGRAFYS VGFWIRETGQ ALDRLGCRLQ GKNYFREQLS RHRTLMNVFD KAPIVDKEAF VAPSASVIGD VHIGRGSSIW YGCVLRGDV NTVSVGSGTN IQDNSLVHVA KSNLSGKVHP TIIGDNVTIG HSAVLHGCTV EDETFIGMGA TLLDGVVVEK H GMVAAGAL VRQNTRIPSG EVWGGNPARF LRKLTDEEIA FISQSATNYS NLAQAHAAEN AKPLNVIEFE KVLRKKHALK DE EYDSMLG IVRETPPELN LPNNILPDKE TKRPSNVN

+
Macromolecule #22: Ubiquinone-9

MacromoleculeName: Ubiquinone-9 / type: ligand / ID: 22 / Number of copies: 1 / Formula: UQ9
Molecular weightTheoretical: 795.226 Da
Chemical component information

ChemComp-UQ9:
Ubiquinone-9

+
Macromolecule #23: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 23 / Number of copies: 2 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM / Phosphatidylethanolamine

+
Macromolecule #24: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 24 / Number of copies: 1 / Formula: LMN
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

+
Macromolecule #25: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 25 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #26: (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: 26 / Number of copies: 1 / 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 #27: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 27 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #28: (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: 28 / 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 #29: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE

MacromoleculeName: 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE / type: ligand / ID: 29 / 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 #30: Phosphatidylinositol

MacromoleculeName: Phosphatidylinositol / type: ligand / ID: 30 / 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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 459177
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