[English] 日本語
Yorodumi
- EMDB-13291: Respiratory complex I from Escherichia coli solubilized in LMNG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13291
TitleRespiratory complex I from Escherichia coli solubilized in LMNG
Map data
Sample
  • Complex: Respiratory complex I from Escherichia coli solubilized in LMNG
    • Protein or peptide: x 13 types
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / endomembrane system / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. ...NADH dehydrogenase, subunit CD / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin oxidoreductase Fe4S4 domain / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / : / NADH-quinone oxidoreductase subunit 3, ferredoxin-like domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / 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-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH:ubiquinone oxidoreductase, subunit G / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 3. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 2. / NADH ubiquinone oxidoreductase, F subunit / Aspartate decarboxylase-like domain superfamily / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / : / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / NADH-ubiquinone oxidoreductase-G iron-sulfur binding region / 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. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 1. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH-quinone oxidoreductase subunit E-like / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-quinone oxidoreductase subunit E, N-terminal / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Nuo51 FMN-binding domain / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N ...NADH-quinone oxidoreductase subunit L / NADH-quinone oxidoreductase subunit A / NADH-quinone oxidoreductase subunit B / NADH-quinone oxidoreductase subunit E / NADH-quinone oxidoreductase subunit H / NADH-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NADH-quinone oxidoreductase subunit K / NADH-quinone oxidoreductase subunit M / NADH-quinone oxidoreductase subunit N / NADH-quinone oxidoreductase subunit F / NADH-quinone oxidoreductase subunit C/D / NADH-quinone oxidoreductase subunit G
Similarity search - Component
Biological speciesEscherichia coli B (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsKolata P / Efremov RG
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)00281ROEFEuropean Union
CitationJournal: Elife / Year: 2021
Title: Structure of respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation.
Authors: Piotr Kolata / Rouslan G Efremov /
Abstract: Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I ...Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from is among the best functionally characterized complexes, but its structure remains unknown, hindering further studies to understand the enzyme coupling mechanism. Here, we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data, we suggest a new simple hypothetical coupling mechanism for the molecular machine.
History
DepositionAug 2, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0872
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0872
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13291.png

Downloads & links

-
Map

FileDownload / File: emd_13291.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.3 Å/pix.
x 160 pix.
= 367.68 Å		2.3 Å/pix.
x 160 pix.
= 367.68 Å		2.3 Å/pix.
x 160 pix.
= 367.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.298 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0872 / Movie #1: 0.0872
Minimum - Maximum-0.16804877 - 0.6467492
Average (Standard dev.)-7.336295e-05 (±0.013501473)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 367.68002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2982.2982.298
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z367.680367.680367.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ332332332
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.1680.647-0.000

-
Supplemental data

-
Half map: #1

Fileemd_13291_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13291_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Respiratory complex I from Escherichia coli solubilized in LMNG

EntireName: Respiratory complex I from Escherichia coli solubilized in LMNG
Components
  • Complex: Respiratory complex I from Escherichia coli solubilized in LMNG
    • Protein or peptide: NADH-quinone oxidoreductase subunit B
    • Protein or peptide: NADH-quinone oxidoreductase subunit C/D
    • Protein or peptide: NADH-quinone oxidoreductase subunit E
    • Protein or peptide: NADH-quinone oxidoreductase subunit F
    • Protein or peptide: NADH-quinone oxidoreductase subunit G
    • Protein or peptide: NADH-quinone oxidoreductase subunit I
    • Protein or peptide: NADH-quinone oxidoreductase subunit K
    • Protein or peptide: NADH-quinone oxidoreductase subunit J
    • Protein or peptide: NADH-quinone oxidoreductase subunit A
    • Protein or peptide: NADH-quinone oxidoreductase subunit H
    • Protein or peptide: NADH-quinone oxidoreductase subunit L
    • Protein or peptide: NADH-quinone oxidoreductase subunit M
    • Protein or peptide: NADH-quinone oxidoreductase subunit N

+
Supramolecule #1: Respiratory complex I from Escherichia coli solubilized in LMNG

SupramoleculeName: Respiratory complex I from Escherichia coli solubilized in LMNG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli B (bacteria) / Strain: BL21(AI) / Location in cell: cell membrane
Molecular weightTheoretical: 550 KDa

+
Macromolecule #1: NADH-quinone oxidoreductase subunit B

MacromoleculeName: NADH-quinone oxidoreductase subunit B / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MDYTLTRIDP NGENDRYPLQ KQEIVTDPLE QEVNKNVFMG KLNDMVNWGR KNSIWPYNFG LSCCYVEMVT SFTAVHDVAR FGAEVLRASP RQADLMVVAG TCFTKMAPVI QRLYDQMLEP KWVISMGACA NSGGMYDIYS VVQGVDKFIP VDVYIPGCPP RPEAYMQALM ...String:
MDYTLTRIDP NGENDRYPLQ KQEIVTDPLE QEVNKNVFMG KLNDMVNWGR KNSIWPYNFG LSCCYVEMVT SFTAVHDVAR FGAEVLRASP RQADLMVVAG TCFTKMAPVI QRLYDQMLEP KWVISMGACA NSGGMYDIYS VVQGVDKFIP VDVYIPGCPP RPEAYMQALM LLQESIGKER RPLSWVVGDQ GVYRANMQSE RERKRGERIA VTNLRTPDEI

+
Macromolecule #2: NADH-quinone oxidoreductase subunit C/D

MacromoleculeName: NADH-quinone oxidoreductase subunit C/D / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MTDLTAQEPA WQTRDHLDDP VIGELRNRFG PDAFTVQATR TGVPVVWIKR EQLLEVGDFL KKLPKPYVML FDLHGMDERL RTHREGLPAA DFSVFYHLIS IDRNRDIMLK VALAENDLHV PTFTKLFPNA NWYERETWDL FGITFDGHPN LRRIMMPQTW KGHPLRKDYP ...String:
MTDLTAQEPA WQTRDHLDDP VIGELRNRFG PDAFTVQATR TGVPVVWIKR EQLLEVGDFL KKLPKPYVML FDLHGMDERL RTHREGLPAA DFSVFYHLIS IDRNRDIMLK VALAENDLHV PTFTKLFPNA NWYERETWDL FGITFDGHPN LRRIMMPQTW KGHPLRKDYP ARATEFSPFE LTKAKQDLEM EALTFKPEEW GMKRGTENED FMFLNLGPNH PSAHGAFRIV LQLDGEEIVD CVPDIGYHHR GAEKMGERQS WHSYIPYTDR IEYLGGCVNE MPYVLAVEKL AGITVPDRVN VIRVMLSELF RINSHLLYIS TFIQDVGAMT PVFFAFTDRQ KIYDLVEAIT GFRMHPAWFR IGGVAHDLPR GWDRLLREFL DWMPKRLASY EKAALQNTIL KGRSQGVAAY GAKEALEWGT TGAGLRATGI DFDVRKARPY SGYENFDFEI PVGGGVSDCY TRVMLKVEEL RQSLRILEQC LNNMPEGPFK ADHPLTTPPP KERTLQHIET LITHFLQVSW GPVMPANESF QMIEATKGIN SYYLTSDGST MSYRTRVRTP SFAHLQQIPA AIRGSLVSDL IVYLGSIDFV MSDVDR

+
Macromolecule #3: NADH-quinone oxidoreductase subunit E

MacromoleculeName: NADH-quinone oxidoreductase subunit E / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString:
MHENQQPQTE AFELSAAERE AIEHEMHHYE DPRAASIEAL KIVQKQRGWV PDGAIHAIAD VLGIPASDVE GVATFYSQIF RQPVGRHVIR YCDSVVCHIN GYQGIQAALE KKLNIKPGQT TFDGRFTLLP TCCLGNCDKG PNMMIDEDTH AHLTPEAIPE LLERYK

+
Macromolecule #4: NADH-quinone oxidoreductase subunit F

MacromoleculeName: NADH-quinone oxidoreductase subunit F / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MKNIIRTPET HPLTWRLRDD KQPVWLDEYR SKNGYEGARK ALTGLSPDEI VNQVKDAGLK GRGGAGFSTG LKWSLMPKDE SMNIRYLLCN ADEMEPGTYK DRLLMEQLPH LLVEGMLISA FALKAYRGYI FLRGEYIEAA VNLRRAIAEA TEAGLLGKNI MGTGFDFELF ...String:
MKNIIRTPET HPLTWRLRDD KQPVWLDEYR SKNGYEGARK ALTGLSPDEI VNQVKDAGLK GRGGAGFSTG LKWSLMPKDE SMNIRYLLCN ADEMEPGTYK DRLLMEQLPH LLVEGMLISA FALKAYRGYI FLRGEYIEAA VNLRRAIAEA TEAGLLGKNI MGTGFDFELF VHTGAGRYIC GEETALINSL EGRRANPRSK PPFPATSGAW GKPTCVNNVE TLCNVPAILA NGVEWYQNIS KSKDAGTKLM GFSGRVKNPG LWELPFGTTA REILEDYAGG MRDGLKFKAW QPGGAGTDFL TEAHLDLPME FESIGKAGSR LGTALAMAVD HEINMVSLVR NLEEFFARES CGWCTPCRDG LPWSVKILRA LERGEGQPGD IETLEQLCRF LGPGKTFCAH APGAVEPLQS AIKYFREEFE AGIKQPFSNT HLINGIQPNL LKERW

+
Macromolecule #5: NADH-quinone oxidoreductase subunit G

MacromoleculeName: NADH-quinone oxidoreductase subunit G / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MATIHVDGKE YEVNGADNLL EACLSLGLDI PYFCWHPALG SVGACRQCAV KQYQNAEDTR GRLVMSCMTP ASDGTFISID DEEAKQFRES VVEWLMTNHP HDCPVCEEGG NCHLQDMTVM TGHSFRRYRF TKRTHRNQDL GPFISHEMNR CIACYRCVRY YKDYADGTDL ...String:
MATIHVDGKE YEVNGADNLL EACLSLGLDI PYFCWHPALG SVGACRQCAV KQYQNAEDTR GRLVMSCMTP ASDGTFISID DEEAKQFRES VVEWLMTNHP HDCPVCEEGG NCHLQDMTVM TGHSFRRYRF TKRTHRNQDL GPFISHEMNR CIACYRCVRY YKDYADGTDL GVYGAHDNVY FGRPEDGTLE SEFSGNLVEI CPTGVFTDKT HSERYNRKWD MQFAPSICQQ CSIGCNISPG ERYGELRRIE NRYNGTVNHY FLCDRGRFGY GYVNLKDRPR QPVQRRGDDF ITLNAEQAMQ GAADILRQSK KVIGIGSPRA SVESNFALRE LVGEENFYTG IAHGEQERLQ LALKVLREGG IYTPALREIE SYDAVLVLGE DVTQTGARVA LAVRQAVKGK AREMAAAQKV ADWQIAAILN IGQRAKHPLF VTNVDDTRLD DIAAWTYRAP VEDQARLGFA IAHALDNSAP AVDGIEPELQ SKIDVIVQAL AGAKKPLIIS GTNAGSLEVI QAAANVAKAL KGRGADVGIT MIARSVNSMG LGIMGGGSLE EALTELETGR ADAVVVLEND LHRHASAIRV NAALAKAPLV MVVDHQRTAI MENAHLVLSA ASFAESDGTV INNEGRAQRF FQVYDPAYYD SKTVMLESWR WLHSLHSTLL SREVDWTQLD HVIDAVVAKI PELAGIKDAA PDATFRIRGQ KLAREPHRYS GRTAMRANIS VHEPRQPQDI DTMFTFSMEG NNQPTAHRSQ VPFAWAPGWN SPQAWNKFQD EVGGKLRFGD PGVRLFETSE NGLDYFTSVP ARFQPQDGKW RIAPYYHLFG SDELSQRAPV FQSRMPQPYI KLNPADAAKL GVNAGTRVSF SYDGNTVTLP VEIAEGLTAG QVGLPMGMSG IAPVLAGAHL EDLKEAQQ

+
Macromolecule #6: NADH-quinone oxidoreductase subunit I

MacromoleculeName: NADH-quinone oxidoreductase subunit I / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString:
MTLKELLVGF GTQVRSIWMI GLHAFAKRET RMYPEEPVYL PPRYRGRIVL TRDPDGEERC VACNLCAVAC PVGCISLQKA ETKDGRWYPE FFRINFSRCI FCGLCEEACP TTAIQLTPDF EMGEYKRQDL VYEKEDLLIS GPGKYPEYNF YRMAGMAIDG KDKGEAENEA KPIDVKSLLP

+
Macromolecule #7: NADH-quinone oxidoreductase subunit K

MacromoleculeName: NADH-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 7 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString:
MIPLQHGLIL AAILFVLGLT GLVIRRNLLF MLIGLEIMIN ASALAFVVAG SYWGQTDGQV MYILAISLAA AEASIGLALL LQLHRRRQNL NIDSVSEMRG

+
Macromolecule #8: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / type: protein_or_peptide / ID: 8 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString:
MEFAFYICGL IAILATLRVI THTNPVHALL YLIISLLAIS GVFFSLGAYF AGALEIIVYA GAIMVLFVFV VMMLNLGGSE IEQERQWLKP QVWIGPAILS AIMLVVIVYA ILGVNDQGID GTPISAKAVG ITLFGPYVLA VELASMLLLA GLVVAFHVGR EERAGEVLSN RKDDSAKRKT EEHA

+
Macromolecule #9: NADH-quinone oxidoreductase subunit A

MacromoleculeName: NADH-quinone oxidoreductase subunit A / type: protein_or_peptide / ID: 9 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString:
MSMSTSTEVI AHHWAFAIFL IVAIGLCCLM LVGGWFLGGR ARARSKNVPF ESGIDSVGSA RLRLSAKFYL VAMFFVIFDV EALYLFAWST SIRESGWVGF VEAAIFIFVL LAGLVYLVRI GALDWTPARS RRERMNPETN SIANRQR

+
Macromolecule #10: NADH-quinone oxidoreductase subunit H

MacromoleculeName: NADH-quinone oxidoreductase subunit H / type: protein_or_peptide / ID: 10 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MSWISPELIE ILLTILKAVV ILLVVVTCGA FMSFGERRLL GLFQNRYGPN RVGWGGSLQL VADMIKMFFK EDWIPKFSDR VIFTLAPMIA FTSLLLAFAI VPVSPGWVVA DLNIGILFFL MMAGLAVYAV LFAGWSSNNK YSLLGAMRAS AQTLSYEVFL GLSLMGVVAQ ...String:
MSWISPELIE ILLTILKAVV ILLVVVTCGA FMSFGERRLL GLFQNRYGPN RVGWGGSLQL VADMIKMFFK EDWIPKFSDR VIFTLAPMIA FTSLLLAFAI VPVSPGWVVA DLNIGILFFL MMAGLAVYAV LFAGWSSNNK YSLLGAMRAS AQTLSYEVFL GLSLMGVVAQ AGSFNMTDIV NSQAHVWNVI PQFFGFITFA IAGVAVCHRH PFDQPEAEQE LADGYHIEYS GMKFGLFFVG EYIGIVTISA LMVTLFFGGW QGPLLPPFIW FALKTAFFMM MFILIRASLP RPRYDQVMSF GWKICLPLTL INLLVTAAVI LWQAQ

+
Macromolecule #11: NADH-quinone oxidoreductase subunit L

MacromoleculeName: NADH-quinone oxidoreductase subunit L / type: protein_or_peptide / ID: 11 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MNMLALTIIL PLIGFVLLAF SRGRWSENVS AIVGVGSVGL AALVTAFIGV DFFANGEQTY SQPLWTWMSV GDFNIGFNLV LDGLSLTMLS VVTGVGFLIH MYASWYMRGE EGYSRFFAYT NLFIASMVVL VLADNLLLMY LGWEGVGLCS YLLIGFYYTD PKNGAAAMKA ...String:
MNMLALTIIL PLIGFVLLAF SRGRWSENVS AIVGVGSVGL AALVTAFIGV DFFANGEQTY SQPLWTWMSV GDFNIGFNLV LDGLSLTMLS VVTGVGFLIH MYASWYMRGE EGYSRFFAYT NLFIASMVVL VLADNLLLMY LGWEGVGLCS YLLIGFYYTD PKNGAAAMKA FVVTRVGDVF LAFALFILYN ELGTLNFREM VELAPAHFAD GNNMLMWATL MLLGGAVGKS AQLPLQTWLA DAMAGPTPVS ALIHAATMVT AGVYLIARTH GLFLMTPEVL HLVGIVGAVT LLLAGFAALV QTDIKRVLAY STMSQIGYMF LALGVQAWDA AIFHLMTHAF FKALLFLASG SVILACHHEQ NIFKMGGLRK SIPLVYLCFL VGGAALSALP LVTAGFFSKD EILAGAMANG HINLMVAGLV GAFMTSLYTF RMIFIVFHGK EQIHAHAVKG VTHSLPLIVL LILSTFVGAL IVPPLQGVLP QTTELAHGSM LTLEITSGVV AVVGILLAAW LWLGKRTLVT SIANSAPGRL LGTWWYNAWG FDWLYDKVFV KPFLGIAWLL KRDPLNSMMN IPAVLSRFAG KGLLLSENGY LRWYVASMSI GAVVVLALLM VLR

+
Macromolecule #12: NADH-quinone oxidoreductase subunit M

MacromoleculeName: NADH-quinone oxidoreductase subunit M / type: protein_or_peptide / ID: 12 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MLLPWLILIP FIGGFLCWQT ERFGVKVPRW IALITMGLTL ALSLQLWLQG GYSLTQSAGI PQWQSEFDMP WIPRFGISIH LAIDGLSLLM VVLTGLLGVL AVLCSWKEIE KYQGFFHLNL MWILGGVIGV FLAIDMFLFF FFWEMMLVPM YFLIALWGHK ASDGKTRITA ...String:
MLLPWLILIP FIGGFLCWQT ERFGVKVPRW IALITMGLTL ALSLQLWLQG GYSLTQSAGI PQWQSEFDMP WIPRFGISIH LAIDGLSLLM VVLTGLLGVL AVLCSWKEIE KYQGFFHLNL MWILGGVIGV FLAIDMFLFF FFWEMMLVPM YFLIALWGHK ASDGKTRITA ATKFFIYTQA SGLVMLIAIL ALVFVHYNAT GVWTFNYEEL LNTPMSSGVE YLLMLGFFIA FAVKMPVVPL HGWLPDAHSQ APTAGSVDLA GILLKTAAYG LLRFSLPLFP NASAEFAPIA MWLGVIGIFY GAWMAFAQTD IKRLIAYTSV SHMGFVLIAI YTGSQLAYQG AVIQMIAHGL SAAGLFILCG QLYERIHTRD MRMMGGLWSK MKWLPALSLF FAVATLGMPG TGNFVGEFMI LFGSFQVVPV ITVISTFGLV FASVYSLAML HRAYFGKAKS QIASQELPGM SLRELFMILL LVVLLVLLGF YPQPILDTSH SAIGNIQQWF VNSVTTTRP

+
Macromolecule #13: NADH-quinone oxidoreductase subunit N

MacromoleculeName: NADH-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 13 / Enantiomer: LEVO / EC number: NADH:ubiquinone reductase (H+-translocating)
Source (natural)Organism: Escherichia coli B (bacteria)
SequenceString: MTITPQNLIA LLPLLIVGLT VVVVMLSIAW RRNHFLNATL SVIGLNAALV SLWFVGQAGA MDVTPLMRVD GFAMLYTGLV LLASLATCTF AYPWLEGYND NKDEFYLLVL IAALGGILLA NANHLASLFL GIELISLPLF GLVGYAFRQK RSLEASIKYT ILSAAASSFL ...String:
MTITPQNLIA LLPLLIVGLT VVVVMLSIAW RRNHFLNATL SVIGLNAALV SLWFVGQAGA MDVTPLMRVD GFAMLYTGLV LLASLATCTF AYPWLEGYND NKDEFYLLVL IAALGGILLA NANHLASLFL GIELISLPLF GLVGYAFRQK RSLEASIKYT ILSAAASSFL LFGMALVYAQ SGDLSFVALG KNLGDGMLNE PLLLAGFGLM IVGLGFKLSL VPFHLWTPDV YQGAPAPVST FLATASKIAI FGVVMRLFLY APVGDSEAIR VVLAIIAFAS IIFGNLMALS QTNIKRLLGY SSISHLGYLL VALIALQTGE MSMEAVGVYL AGYLFSSLGA FGVVSLMSSP YRGPDADSLF SYRGLFWHRP ILAAVMTVMM LSLAGIPMTL GFIGKFYVLA VGVQAHLWWL VGAVVVGSAI GLYYYLRVAV SLYLHAPEQP GRDAPSNWQY SAGGIVVLIS ALLVLVLGVW PQPLISIVRL AMPLM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
20.0 mMC8H19NO5Bis-Tris
200.0 mMNaClSodium chloride
2.0 mMCaCl2Calcium chloride
0.003 % (w/v)C47H88O22LMNG

Details: The buffer was used for gel filtration of protein solubilized in LMNG
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.028 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 97 % / Chamber temperature: 296 K / Instrument: GATAN CRYOPLUNGE 3

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 13084 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 1469948
CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionNumber classes used: 15 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), PHENIX (ver. 1.18.2)) / Number images used: 7962
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 15 / Avg.num./class: 7000 / Software - Name: RELION (ver. 3.1)
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