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- EMDB-20692: Structure of the membrane-bound sulfane sulfur reductase (MBS), a... -

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Basic information

Entry
Database: EMDB / ID: EMD-20692
TitleStructure of the membrane-bound sulfane sulfur reductase (MBS), an archaeal respiratory membrane complex
Map datastructure of an archaea respiratory membrane complex
Sample
  • Complex: respiratory membrane complex
    • Protein or peptide: x 13 types
  • Ligand: x 1 types
KeywordscryoEM / membrane protein / respiratory system
Function / homology
Function and homology information


NADH dehydrogenase (quinone) / sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / NAD binding ...NADH dehydrogenase (quinone) / sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD ...: / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / : / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) / MBH, subunit D / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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, 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, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 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
Similarity search - Domain/homology
NADH dehydrogenase subunit C / NADH dehydrogenase subunit M / Monovalent cation/H+ antiporter subunit G / NADH dehydrogenase subunit I / Monovalent cation/H+ antiporter subunit B / Monovalent cation/H+ antiporter subunit C / Monovalent cation/H+ antiporter subunit E / NADH dehydrogenase subunit B / NADH dehydrogenase subunit N / Monovalent cation/H+ antiporter subunit F ...NADH dehydrogenase subunit C / NADH dehydrogenase subunit M / Monovalent cation/H+ antiporter subunit G / NADH dehydrogenase subunit I / Monovalent cation/H+ antiporter subunit B / Monovalent cation/H+ antiporter subunit C / Monovalent cation/H+ antiporter subunit E / NADH dehydrogenase subunit B / NADH dehydrogenase subunit N / Monovalent cation/H+ antiporter subunit F / NADH dehydrogenase subunit D / NADH dehydrogenase subunit / MrpA C-terminal/MbhD domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea) / Pyrococcus furiosus COM1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsYu HJ / Li HL
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life.
Authors: Hongjun Yu / Dominik K Haja / Gerrit J Schut / Chang-Hao Wu / Xing Meng / Gongpu Zhao / Huilin Li / Michael W W Adams /
Abstract: Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas- ...Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S)-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.
History
DepositionSep 6, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseSep 9, 2020-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6u8y
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20692.png

Downloads & links

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Map

FileDownload / File: emd_20692.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of an archaea respiratory membrane complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.28 Å		1.03 Å/pix.
x 320 pix.
= 329.28 Å		1.03 Å/pix.
x 320 pix.
= 329.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.029 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.08619391 - 0.26333424
Average (Standard dev.)0.00056844734 (±0.0033783943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.28003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0291.0291.029
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.280329.280329.280
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0860.2630.001

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Supplemental data

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Sample components

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Entire : respiratory membrane complex

EntireName: respiratory membrane complex
Components
  • Complex: respiratory membrane complex
    • Protein or peptide: Monovalent cation/H+ antiporter subunit E
    • Protein or peptide: Monovalent cation/H+ antiporter subunit F
    • Protein or peptide: Monovalent cation/H+ antiporter subunit G
    • Protein or peptide: DUF4040 domain-containing protein
    • Protein or peptide: Monovalent cation/H+ antiporter subunit B
    • Protein or peptide: Monovalent cation/H+ antiporter subunit C
    • Protein or peptide: NADH dehydrogenase subunit N
    • Protein or peptide: NADH dehydrogenase subunit M
    • Protein or peptide: NADH dehydrogenase subunit B
    • Protein or peptide: NADH dehydrogenase subunit C
    • Protein or peptide: NADH dehydrogenase subunit D
    • Protein or peptide: NADH dehydrogenase subunit
    • Protein or peptide: NADH dehydrogenase subunit I
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: respiratory membrane complex

SupramoleculeName: respiratory membrane complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Pyrococcus furiosus (archaea)

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Macromolecule #1: Monovalent cation/H+ antiporter subunit E

MacromoleculeName: Monovalent cation/H+ antiporter subunit E / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 19.134307 KDa
SequenceString:
MEEASSISRY LYTFIVLFII WLFLTASLDP QELTIGALFS AIAALFTYEI FTTRGLANLH PKRVLYFIAY IPYFLWAMIM ANLDVAYRV LHPKRPINPG IVECKTTLTN NVGKMALANS ITLTPGTITL DVDGDKYFIH WIDVKDSSVE GASEHITKPF E KFLRVIFE

UniProtKB: Monovalent cation/H+ antiporter subunit E

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Macromolecule #2: Monovalent cation/H+ antiporter subunit F

MacromoleculeName: Monovalent cation/H+ antiporter subunit F / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 9.328299 KDa
SequenceString:
MIGVNIYLLL IGVATLLSMY RVFRGPTTVD RLVAVDIMTT ITVGLMVLFA LYYRRIIFLD VALVYAILSF AGVIAFARYL EGGL

UniProtKB: Monovalent cation/H+ antiporter subunit F

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Macromolecule #3: Monovalent cation/H+ antiporter subunit G

MacromoleculeName: Monovalent cation/H+ antiporter subunit G / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 13.550896 KDa
SequenceString:
MSVLSLIGEL LVLFGTVFYL LSTLGLIRMP DVYNRMQTAT KSATLGSLGV IIGTGIWALG EGFSVAWLTK AIVIAAFLLL TNPISAHAL IRAAYKSGIP LWEGSVVDKY KEHLERKKKE EGEQE

UniProtKB: Monovalent cation/H+ antiporter subunit G

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Macromolecule #4: DUF4040 domain-containing protein

MacromoleculeName: DUF4040 domain-containing protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 10.56046 KDa
SequenceString:
MNCIVCIEYI IVALMIISAI LAVEWRDLLA STVGMAAVSL FASILFFFLQ APDVAMTEAA IGAALSAAVF IFAIKRTYRY ETEEEEKLG WWVRW

UniProtKB: MrpA C-terminal/MbhD domain-containing protein

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Macromolecule #5: Monovalent cation/H+ antiporter subunit B

MacromoleculeName: Monovalent cation/H+ antiporter subunit B / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 25.691111 KDa
SequenceString: MLKRVLAILT ILVIGYWLAQ GLADVPFGQD KMVVGKYYLE HVKEETGAVN AVTAVVVNYR GLDTLGEVTV LFIASTGVAA LLWKKKRER TAKTEGSVVL TTGARLLFPF IALFGMYIFI HGHLTPGGGF PGGATIATAF LLMYLAFTIY EIPHRGFEVT E GLAGMGYV ...String:
MLKRVLAILT ILVIGYWLAQ GLADVPFGQD KMVVGKYYLE HVKEETGAVN AVTAVVVNYR GLDTLGEVTV LFIASTGVAA LLWKKKRER TAKTEGSVVL TTGARLLFPF IALFGMYIFI HGHLTPGGGF PGGATIATAF LLMYLAFTIY EIPHRGFEVT E GLAGMGYV ITGLIGLAIG GYFLFDWIWQ TWGWGHENIG RLFSGGFIPI IYTLIGIKVG TELSGIVDNM LKEEVKE

UniProtKB: Monovalent cation/H+ antiporter subunit B

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Macromolecule #6: Monovalent cation/H+ antiporter subunit C

MacromoleculeName: Monovalent cation/H+ antiporter subunit C / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 12.073443 KDa
SequenceString:
MISSYYFGAI SLILIGLYAV LVKKNLLKIL IGLSIMETGV NLLLISIGYV SGKSAPILSE GVTASNAVDP IPQALVLTAI VIGVATTAM ALSVAILLYE KYGTLNIEEI RRLRG

UniProtKB: Monovalent cation/H+ antiporter subunit C

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Macromolecule #7: NADH dehydrogenase subunit N

MacromoleculeName: NADH dehydrogenase subunit N / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 53.019332 KDa
SequenceString: MSQVAALLIA LPLISAFFVP VLKQIGKSLI KPFLVIITLL QTLIASWAFV QVYSTGKPII IYAGGWKPPI GINLYIGHFA ALFILVIAV VSFLMALFNF KAVTVEPIDK YAMLFLLLLL GATGMIATGD IFNLFVFMEI TAISAYALTA YNKTGEAAEA S MKYIVLGG ...String:
MSQVAALLIA LPLISAFFVP VLKQIGKSLI KPFLVIITLL QTLIASWAFV QVYSTGKPII IYAGGWKPPI GINLYIGHFA ALFILVIAV VSFLMALFNF KAVTVEPIDK YAMLFLLLLL GATGMIATGD IFNLFVFMEI TAISAYALTA YNKTGEAAEA S MKYIVLGG IGSSFFLVGV ALIYGATGTL NMAHLAMLAN DINPTVVQVG LALIIFGLAV EAELFPLNAW APDAYQAAPH PI TVMFSAF VVKAGLYAMA RILYLFKDVS GWSSLTKLLI AMATLTVVFA ELSALRQKNV KRMIAYSSIG QVGLIALALS LGT QEGVSA GVFHMLNHAI VKTMMFMAIG YVGITLGGTM IENFEGLGKR MPLTSLSLTI GGIATVGVPL FNVFWSKLRI ILAA AHEGN LWPVALVLFA SVVEAVYYFR LIHTMWFKGK SGERIPEGAI AIVLLLLAML IIVIGVYPTP FWNLVTKAGS DIVEV SKYV ANVLPGVKL

UniProtKB: NADH dehydrogenase subunit N

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Macromolecule #8: NADH dehydrogenase subunit M

MacromoleculeName: NADH dehydrogenase subunit M / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 67.561906 KDa
SequenceString: MNELPIILLS PLIGGALAWL IRVKGIREAI GVVSSAIPLY FLIKLYPALE GEPIRYSLNV GGFELTLALS HISWIFAMIA AVVGLSAVL GLVSTAKDSN EWLFALMSLA GALGVFLAND FVVFFLSWEI MTFASFMMVF KYNRHASLKY FVLSIAGAYA M LLAIGIIY ...String:
MNELPIILLS PLIGGALAWL IRVKGIREAI GVVSSAIPLY FLIKLYPALE GEPIRYSLNV GGFELTLALS HISWIFAMIA AVVGLSAVL GLVSTAKDSN EWLFALMSLA GALGVFLAND FVVFFLSWEI MTFASFMMVF KYNRHASLKY FVLSIAGAYA M LLAIGIIY AKTGSLSFPE ISAIFRQDAM MGMMGGGGVF TKTETLLIYA LFLVAFGVKA GMFPLHVWAP DAYSETNQSY TA MFSGVLS KTGVYGFFLL YLLMYGKLAI TLGNVRSAPT FGYIIAFLGG LTIMVGGILA ALQEDIRKLF AYSSISQIGY ILI GLGIGT PLGIAAATYH AISHALFKGL FFLIVATIIY RTGKTEFKDY GGLAEKMPIT FAMAFVAILS LAGIPPMAGF ASKW LIFEA VISRNLPILG AMVFFGSAIG FVYLIRFTYA VWFGQRPSDL EDVKDAPLPL AIGMGILAIL NVIFGVAPGL VAREL NKLF SNPPIGGTIW ELDLGFGRYN GLLLSIWLVI GLIIAAILYF MGAGVRKVPV TDTYQSGNPV TMEYNLTIRR NFFLPL KEA MAFWLKMSFD RLYHDIWKAI EELADLARSY VYNGNIQAYA WYLAIILLIL VAMGV

UniProtKB: NADH dehydrogenase subunit M

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Macromolecule #9: NADH dehydrogenase subunit B

MacromoleculeName: NADH dehydrogenase subunit B / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 22.731473 KDa
SequenceString: MVDWRLFEPL FNWARKKSLW IVAFCTGCGG IEMPPLMTAR YDLERFGIMP DPSPRQYDLF LITGYVTPKT LKRIIITYEM APDPKYVLA HGSCPINGGI YWDAYNAIKQ LDKYIPVDVY IAGCMPRPEA VMDGIKKLME MIENGEADGW KRYKENYEWY R KNQDELLG ...String:
MVDWRLFEPL FNWARKKSLW IVAFCTGCGG IEMPPLMTAR YDLERFGIMP DPSPRQYDLF LITGYVTPKT LKRIIITYEM APDPKYVLA HGSCPINGGI YWDAYNAIKQ LDKYIPVDVY IAGCMPRPEA VMDGIKKLME MIENGEADGW KRYKENYEWY R KNQDELLG EGWREKEARK WIPWLMDKRK EVKE

UniProtKB: NADH dehydrogenase subunit B

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Macromolecule #10: NADH dehydrogenase subunit C

MacromoleculeName: NADH dehydrogenase subunit C / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 20.966279 KDa
SequenceString:
MTWEKGEEIV KQILEKAPYA EGKVRRERRL EFRVPADKIR DFLRIMKESN FPLMLQITAV DWPKEGEIEL VYHLINVELG THAMVKTRI PRDLDKARMP TVKDIYPAAE TYERDVHDFF GVYFEGNEKM EMPWILDDPE RGLYPHRKDF DMLAYVKKKY K ILDRFDED KDKYVI

UniProtKB: NADH dehydrogenase subunit C

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Macromolecule #11: NADH dehydrogenase subunit D

MacromoleculeName: NADH dehydrogenase subunit D / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 44.756504 KDa
SequenceString: MVSQEELIRE ARQNGMELYP IDKDTYELFF GPQHMATENF SIILKMDGNR VVKAIANPGF LHRGFEKLAE YRPWYTNIAL LLRICVPEP DVPEAIYSMA VDEIIGWEVP ERAQWIRTLV LEMARVTAYL FWIMGLSFKL GVYTAGQWAA AYRERFMALF E QLTGARVY ...String:
MVSQEELIRE ARQNGMELYP IDKDTYELFF GPQHMATENF SIILKMDGNR VVKAIANPGF LHRGFEKLAE YRPWYTNIAL LLRICVPEP DVPEAIYSMA VDEIIGWEVP ERAQWIRTLV LEMARVTAYL FWIMGLSFKL GVYTAGQWAA AYRERFMALF E QLTGARVY HIYTIPGGVR RDIPGDKWLR QVRDTVEYLK DKLKDFDNVL FENYITYKRL EGIGVMDKKF ALEEGVTGPN LR ATGVAYD VRKSDPYLLY PELDFEIPVL KEGDALARVL VRRYELEQDL YIIEQLLDMG PPSGPYKVQD PKLKNLPRFK VPP GEAFAH VEATKGDFGA YVVSDGGHKP YRVHIRGPSI AHGVRVLEQL LVGARLADVP AILMSLDNCP PDIDR

UniProtKB: NADH dehydrogenase subunit D

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Macromolecule #12: NADH dehydrogenase subunit

MacromoleculeName: NADH dehydrogenase subunit / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 33.67757 KDa
SequenceString: MIGVFLRALL IIIYATFVGF IFMGIIRKVT ARIHRRIGPP IYQPIIDTLK FFGKKENITH GLIYDFGIIY AVGATILALM FIPLGPISV LRAYGDLILV TFLLEIPMLG IMFAAMSSGN PYAGIGAQRA LLTLLAIQVP LGLAIIAVAE YYGTFSTYEI V MAQQKMGW ...String:
MIGVFLRALL IIIYATFVGF IFMGIIRKVT ARIHRRIGPP IYQPIIDTLK FFGKKENITH GLIYDFGIIY AVGATILALM FIPLGPISV LRAYGDLILV TFLLEIPMLG IMFAAMSSGN PYAGIGAQRA LLTLLAIQVP LGLAIIAVAE YYGTFSTYEI V MAQQKMGW SIFHLPLLLA AIAYDIVLQA MFGKEPFDIM IAPGEISLGP MVEFGGKHMG MLQIQHAMAL FAETLFFSNI FL GGGVVTA FGSPLLNTLA SLAVLLVKQI AVLLIAIFVG AIFPRFTIDQ AAKFYWKWPT IIAAIGAIMA SL

UniProtKB: NADH dehydrogenase subunit

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Macromolecule #13: NADH dehydrogenase subunit I

MacromoleculeName: NADH dehydrogenase subunit I / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO / EC number: NADH dehydrogenase (quinone)
Source (natural)Organism: Pyrococcus furiosus COM1 (archaea)
Molecular weightTheoretical: 24.746895 KDa
SequenceString: MEEVTFRIAP EEKVKKKPSF LKPWFGLKYL FKKPVTIKIP YEFIEPAPRY RGFHTLDWKK CIGCNMCGQI CPARAIEMTW IEGEKRPHP KIDYGRCTFC QFCVDVCPTG ALGFIETYML TTTWREEELL LYDWVPIEPE KFKEIQEKFK DYKFPVEKIE F NKETKEVT ...String:
MEEVTFRIAP EEKVKKKPSF LKPWFGLKYL FKKPVTIKIP YEFIEPAPRY RGFHTLDWKK CIGCNMCGQI CPARAIEMTW IEGEKRPHP KIDYGRCTFC QFCVDVCPTG ALGFIETYML TTTWREEELL LYDWVPIEPE KFKEIQEKFK DYKFPVEKIE F NKETKEVT YYLRDGTTFK FKILGYGLKP PVKPQPTTKQ QEEEKKESGQ

UniProtKB: NADH dehydrogenase subunit I

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Macromolecule #14: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 14 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 203673
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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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

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