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- EMDB-4480: CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2 -

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Basic information

Entry
Database: EMDB / ID: EMD-4480
TitleCI Peripheral Arm focused refinement from Ovine respiratory SC I+III2
Map dataFocused refinement around complex I peripheral arm
Sample
  • Complex: Ovine mitochondrial SC I+III2
    • Protein or peptide: x 18 types
  • Ligand: x 6 types
Function / homology
Function and homology information


NADH dehydrogenase activity / respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport ...NADH dehydrogenase activity / respiratory chain complex I / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / apoptotic mitochondrial changes / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / electron transport chain / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / respirasome / ATP metabolic process / reactive oxygen species metabolic process / respiratory electron transport chain / regulation of mitochondrial membrane potential / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / circadian rhythm / fatty acid biosynthetic process / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / response to oxidative stress / oxidoreductase activity / mitochondrial matrix / protein-containing complex binding / metal ion binding
Similarity search - Function
Complex1_LYR-like / Soluble ligand binding domain / SLBB domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 ...Complex1_LYR-like / Soluble ligand binding domain / SLBB domain / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) / NDUFA6, LYR domain / NADH dehydrogenase ubiquinone Fe-S protein 4-like superfamily / NADH dehydrogenase ubiquinone Fe-S protein 4 / NADH dehydrogenase ubiquinone Fe-S protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 2 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / NADH ubiquinone oxidoreductase subunit NDUFA12 / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / ETC complex I subunit conserved region / NADH dehydrogenase [ubiquinone] (complex I), alpha subcomplex, subunit 6 / NADH-quinone oxidoreductase, chain G, C-terminal / NADH-ubiquinone oxidoreductase subunit G, C-terminal / 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 / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory-chain NADH dehydrogenase 75 Kd subunit signature 1. / NADH:ubiquinone oxidoreductase, 75kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / 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. / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / Thioredoxin-like [2Fe-2S] ferredoxin / NADH-quinone oxidoreductase subunit E, N-terminal / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / NADH:ubiquinone oxidoreductase, 51kDa subunit, conserved site / Respiratory-chain NADH dehydrogenase 51 Kd subunit signature 2. / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain / NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain superfamily / NADH-ubiquinone oxidoreductase 51kDa subunit, FMN-binding domain superfamily / Respiratory-chain NADH dehydrogenase 51 Kd subunit / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / NADH-ubiquinone oxidoreductase-F iron-sulfur binding region / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Acyl carrier protein (ACP) / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Thioredoxin-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 ...NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 / Acyl carrier protein / NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 / NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial / NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5 / NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 / NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial / NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6
Similarity search - Component
Biological speciesOvis aries (sheep) / Sheep (sheep)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLetts JA / Sazanov LA
Funding support Austria, 1 items
OrganizationGrant numberCountry
European Research Council701309 Austria
CitationJournal: Mol Cell / Year: 2019
Title: Structures of Respiratory Supercomplex I+III Reveal Functional and Conformational Crosstalk.
Authors: James A Letts / Karol Fiedorczuk / Gianluca Degliesposti / Mark Skehel / Leonid A Sazanov /
Abstract: The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We ...The mitochondrial electron transport chain complexes are organized into supercomplexes (SCs) of defined stoichiometry, which have been proposed to regulate electron flux via substrate channeling. We demonstrate that CoQ trapping in the isolated SC I+III limits complex (C)I turnover, arguing against channeling. The SC structure, resolved at up to 3.8 Å in four distinct states, suggests that CoQ oxidation may be rate limiting because of unequal access of CoQ to the active sites of CIII. CI shows a transition between "closed" and "open" conformations, accompanied by the striking rotation of a key transmembrane helix. Furthermore, the state of CI affects the conformational flexibility within CIII, demonstrating crosstalk between the enzymes. CoQ was identified at only three of the four binding sites in CIII, suggesting that interaction with CI disrupts CIII symmetry in a functionally relevant manner. Together, these observations indicate a more nuanced functional role for the SCs.
History
DepositionDec 18, 2018-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 21, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6q9d
  • Surface level: 0.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4480.png

Downloads & links

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Map

FileDownload / File: emd_4480.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement around complex I peripheral arm
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.36786753 - 1.4292165
Average (Standard dev.)-0.00002810240 (±0.014591322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 560.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z560.000560.000560.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.3681.429-0.000

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Supplemental data

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Mask #1

Fileemd_4480_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused refinement around complex I peripheral arm. Half map 1

Fileemd_4480_half_map_1.map
AnnotationFocused refinement around complex I peripheral arm. Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Focused refinement around complex I peripheral arm. Half map 2

Fileemd_4480_half_map_2.map
AnnotationFocused refinement around complex I peripheral arm. Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ovine mitochondrial SC I+III2

EntireName: Ovine mitochondrial SC I+III2
Components
  • Complex: Ovine mitochondrial SC I+III2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
    • Protein or peptide: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
    • Protein or peptide: NADH:ubiquinone oxidoreductase core subunit S1
    • Protein or peptide: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
    • Protein or peptide: NADH:ubiquinone oxidoreductase core subunit S3
    • Protein or peptide: NADH:ubiquinone oxidoreductase core subunit S7
    • Protein or peptide: NADH:ubiquinone oxidoreductase core subunit S8
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit V3
    • Protein or peptide: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit S4
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit A9
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
    • Protein or peptide: NADH:ubiquinone oxidoreductase subunit A6
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
    • Protein or peptide: Acyl carrier protein
    • Protein or peptide: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: FLAVIN MONONUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: ZINC ION
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

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Supramolecule #1: Ovine mitochondrial SC I+III2

SupramoleculeName: Ovine mitochondrial SC I+III2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Details: Complex I membrane arm focused refinement from ovine respiratory SC I+III2
Source (natural)Organism: Ovis aries (sheep) / Organ: Heart / Tissue: Cardiac / Organelle: Mitochondria / Location in cell: Mitochondrial inner membrane
Molecular weightTheoretical: 1.4 MDa

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: NADH dehydrogenase
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 48.678281 KDa
SequenceString: FSGDTTAPKK TSFGSLKDED RIFTNLYGRH DWRLKGAQSR GDWYKTKEIL LKGPDWILGE VKTSGLRGRG GAGFPTGLKW SFMNKPSDG RPKYLVVNAD EGEPGTCKDR EIIRHDPHKL VEGCLVGGRA MGARAAYIYI RGEFYNEASN LQVAIREAYE A GLIGKNAC ...String:
FSGDTTAPKK TSFGSLKDED RIFTNLYGRH DWRLKGAQSR GDWYKTKEIL LKGPDWILGE VKTSGLRGRG GAGFPTGLKW SFMNKPSDG RPKYLVVNAD EGEPGTCKDR EIIRHDPHKL VEGCLVGGRA MGARAAYIYI RGEFYNEASN LQVAIREAYE A GLIGKNAC GSGYDFDVFV VRGAGAYICG EETALIESIE GKQGKPRLKP PFPADVGVFG CPTTVANVET VAVSPTICRR GG AWFASFG RERNSGTKLF NISGHVNNPC TVEEEMSVPL KELIEKHAGG VTGGWDNLLA VIPGGSSTPL IPKSVCETVL MDF DALIQA QTGLGTAAVI VMDRSTDIVK AIARLIEFYK HESCGQCTPC REGVDWMNKV MARFVRGDAR PAEIDSLWEI SKQI EGHTI CALGDGAAWP VQGLIRHFRP ELEERMQRFA QQHQARQAAS

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

MacromoleculeName: NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 23.840428 KDa
SequenceString: GAGGALFVHR DTPKNNPETP FDFTPENYKR IEAIVKNYPE GHKAAAVLPV LDLAQRQNGW LPISAMNKVA EILQVPPMRV YEVATFYTM YNRKPVGKYH IQVCTTTPCM LRNSDSILEA IQKKLGIKVG ETTPDKLFTL IEVECLGACV NAPMVQINDN Y YEDLTPKD ...String:
GAGGALFVHR DTPKNNPETP FDFTPENYKR IEAIVKNYPE GHKAAAVLPV LDLAQRQNGW LPISAMNKVA EILQVPPMRV YEVATFYTM YNRKPVGKYH IQVCTTTPCM LRNSDSILEA IQKKLGIKVG ETTPDKLFTL IEVECLGACV NAPMVQINDN Y YEDLTPKD IEEIIDELKA GKIPKPGPRS GRFSCEPAGG LTSLTEPPKG PGFGVQAGL

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Macromolecule #3: NADH:ubiquinone oxidoreductase core subunit S1

MacromoleculeName: NADH:ubiquinone oxidoreductase core subunit S1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 77.031156 KDa
SequenceString: TATAASNLIE VFVDGQSVMV EPGTTVLQAC EKVGMQIPRF CYHERLSVAG NCRMCLVEIE KAPKVVAACA MPVMKGWNIL TNSEKTKKA REGVMEFLLA NHPLDCPICD QGGECDLQDQ SMMFGSDRSR FLEGKRAVED KNIGPLVKTI MTRCIQCTRC I RFASEIAG ...String:
TATAASNLIE VFVDGQSVMV EPGTTVLQAC EKVGMQIPRF CYHERLSVAG NCRMCLVEIE KAPKVVAACA MPVMKGWNIL TNSEKTKKA REGVMEFLLA NHPLDCPICD QGGECDLQDQ SMMFGSDRSR FLEGKRAVED KNIGPLVKTI MTRCIQCTRC I RFASEIAG VDDLGTTGRG NDMQVGTYIE KMFMSELSGN IIDICPVGAL TSKPYAFTAR PWETRKTESI DVMDAVGSNI VV STRTGEV MRILPRMHED INEEWISDKT RFAYDGLKRQ RLTEPMVRNE KGLLTHTTWE DALSRVAGML QSCQGNDVAA IAG GLVDAE ALIALKDLLN RVDSDTLCTE EVFPTAGAGT DLRSNYLLNT TIAGVEEADV VLLVGTNPRF EAPLFNARIR KSWL HNDLK VALIGSPVDL TYRYDHLGDS PKILQDIASG SHPFSQVLQE AKKPMVVLGS SALQRNDGAA ILAAVSNIAQ KIRTS SGVT GDWKVMNILH RIASQVAALD LGYKPGVEAI RKNPPKMLFL LGADGGCVTR QDLPKDCFIV YQGHHGDVGA PIADVI LPG AAYTEKSATY VNTEGRAQQT KVAVMPPGLA REDWKIIRAL SEIAGMTLPY DTLDQVRNRL EEVSPNLVRY DDVEGAN YF QQASELSKLV NQQLLADPLV PPQLTIKDFY MTDSISRASQ TMAKCVKAVT EGAHAVEEPS IC

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Macromolecule #4: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone ox...

MacromoleculeName: NADH:ubiquinone oxidoreductase core subunit S2,NADH:ubiquinone oxidoreductase core subunit S2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 49.193273 KDa
SequenceString: ARQWQPDVEW AEQYGGAVMY PTKETAHWKP PPWNDVDPPK DTLVSNLTLN FGPQHPAAHG VLRLVMELSG EMVRKCDPHI GLLHRGTEK LIEYKTYLQA LPYFDRLDYV SMMCNEQAYS LAVEKLLNIQ PPPRAQWIRV LFGEITRLLN HIMAVTTHAL D IGAMTPFF ...String:
ARQWQPDVEW AEQYGGAVMY PTKETAHWKP PPWNDVDPPK DTLVSNLTLN FGPQHPAAHG VLRLVMELSG EMVRKCDPHI GLLHRGTEK LIEYKTYLQA LPYFDRLDYV SMMCNEQAYS LAVEKLLNIQ PPPRAQWIRV LFGEITRLLN HIMAVTTHAL D IGAMTPFF WMFEEREKMF EFYERVSGAR MHAAYVRPGG VHQDLPLGLM DDIYEFSKNF SLRIDELEEM LTNNRIWRNR TV DIGVVTA EDALNYGFSG VMLRGSGIQW DLRKTQPYDV YDQVEFDVPI GSRGDCYDRY LCRVEEMRQS IRIISQCLNK MPP GEIKVD DAKVSPPKRA EMKTSMESLI HHFKLYTEGY QVPPGATYTA IEAPKGEFGV YLVSDGSSRP YRCKIKAPGF AHLA GLDKM SKGHMLADVV AIIGTQDIVF GEVDR

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Macromolecule #5: NADH:ubiquinone oxidoreductase core subunit S3

MacromoleculeName: NADH:ubiquinone oxidoreductase core subunit S3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 26.441793 KDa
SequenceString: ESASADTRPT VRPRNDVAHK QLSAFGEYVA EILPKYVQQV QVSCFSELEI CIHPDGVIPV LTFLRDHSNA QFKSLADLTA VDIPTRQNR FEIVYNLLSL RFNSRIRVKT YTDELTPVES SVSVYKAANW YEREIWDMFG VFFANHPDLR RILTDYGFEG H PFRKDFPL ...String:
ESASADTRPT VRPRNDVAHK QLSAFGEYVA EILPKYVQQV QVSCFSELEI CIHPDGVIPV LTFLRDHSNA QFKSLADLTA VDIPTRQNR FEIVYNLLSL RFNSRIRVKT YTDELTPVES SVSVYKAANW YEREIWDMFG VFFANHPDLR RILTDYGFEG H PFRKDFPL SGYVELRYDD EVKRVVAEPV ELAQEFRKFD LNSPWEAFPA YRQPPESLKL EAGDKKPEAK

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Macromolecule #6: NADH:ubiquinone oxidoreductase core subunit S7

MacromoleculeName: NADH:ubiquinone oxidoreductase core subunit S7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 20.104531 KDa
SequenceString:
PSSTQPAVSQ ARAVVPKPAA LPSSRGEYVV AKLDDLINWA RRSSLWPMTF GLACCAVEMM HMAAPRYDMD RFGVVFRASP RQSDVMIVA GTLTNKMAPA LRKVYDQMPE PRYVVSMGSC ANGGGYYHYS YSVVRGCDRI VPVDIYVPGC PPTAEALLYG I LQLQKKIK REKRLRIWYR R

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Macromolecule #7: NADH:ubiquinone oxidoreductase core subunit S8

MacromoleculeName: NADH:ubiquinone oxidoreductase core subunit S8 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 20.219947 KDa
SequenceString:
TYKYVNLREP SMDMKSVTDR AAQTLLWTEL IRGLGMTLSY LFREPATINY PFEKGPLSPR FRGEHALRRY PSGEERCIAC KLCEAVCPA QAITIEAEPR ADGSRRTTRY DIDMTKCIYC GFCQEACPVD AIVEGPNFEF STETHEELLY NKEKLLNNGD K WEAEIAAN IQADYLYR

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Macromolecule #8: NADH:ubiquinone oxidoreductase subunit V3

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit V3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 8.423314 KDa
SequenceString:
SAESGKNEKG LPPNPKKQSP PKKPASAAPT EPFDNTTYKN LQHHDYSTYT FLDLNLDLSK FRMPQPSSGR ESPRH

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Macromolecule #9: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial

MacromoleculeName: NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 10.651796 KDa
SequenceString:
GVRTSPTGEK VTHTGQVYDD EDYRRVRFVG RQKEVNENFA IDLIAEQPVS QVGSRVISCD GGGGALGHPR VYINLDKETK TGTCGYCGL QFRQQHH

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Macromolecule #10: NADH:ubiquinone oxidoreductase subunit S4

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit S4 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 15.3753 KDa
SequenceString:
AQDQTRDTQL ITVDEKLDIT TLTGVPEEHI KTRKARIFVP ARNNMQSGVN NTKKWKMEFD TRERWENPLM GWASTADPLS NLVLTFSTK EDAIAFAEKN GWSYDVEERK VPKPKSKSYG ANFSWNKRTR VSTK

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Macromolecule #11: NADH:ubiquinone oxidoreductase subunit A9

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit A9 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 38.660488 KDa
SequenceString: LHHAVIPHGK GGRSSVSGIV ATVFGATGFL GRYLVNHLGR MGSQVIVPYR CEPYDTMHLR PMGDLGQIIF MDWNGRDKDS IRRAVEHSN VVINLVGREW ETKNFDFEDV FVKIPQAIAQ VSKEAGVEKF IHISHLNADI KSSSKYLRNK AVGEKEVRET F PEATIIKP ...String:
LHHAVIPHGK GGRSSVSGIV ATVFGATGFL GRYLVNHLGR MGSQVIVPYR CEPYDTMHLR PMGDLGQIIF MDWNGRDKDS IRRAVEHSN VVINLVGREW ETKNFDFEDV FVKIPQAIAQ VSKEAGVEKF IHISHLNADI KSSSKYLRNK AVGEKEVRET F PEATIIKP ADIFGREDRF LNYFANIRWF GGVPLISLGK KTVKQPVYIV DVTKGIINAI KDPDARGKTF AFVGPNRYLL FD LVQYVFA VAHRPFLPYP MPHFAYRWIG RLFEISPFEP WTTRDKVERI HTTDRTLPHL PGLEDLGVQA TPLELKAIEV LRR HRTYRW LSSEIEDVQP AK

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Macromolecule #12: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 10.966627 KDa
SequenceString:
AAAAAIRGVR GKLGLREIRI HLCQRSPGSQ GVRDFIEKRY VELKKANPDL PILIRECSDV QPKLWARYAF GQEKNVSLNN FSADQVTRA LENVLSSKA

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Macromolecule #13: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 5
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 13.156311 KDa
SequenceString:
AGLLKKTTGL VGLAVCETPH ERLKILYTKI LDVLGHIPKN AAYRKYTEQI TNEKLSIVKA EPDVKKLEEQ LQGGQIEEVI LQAENELSL ARKMIQWKPW EPLVEEPPAS QWKWPI

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Macromolecule #14: NADH:ubiquinone oxidoreductase subunit A6

MacromoleculeName: NADH:ubiquinone oxidoreductase subunit A6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 14.923245 KDa
SequenceString:
AASGLRQAAV AASTSVKPIF SRDMNEAKRR VRELYRAWYR EVPNTVHLFQ LDISVKQGRD KVREMFKKNA HVTDPRVVDL LVIKGKMEL EETINVWKQR THVMRFFHET EAPRPKDFLS KFYVGHDP

+
Macromolecule #15: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 12.399201 KDa
SequenceString:
ASATRLIQGL RNWASGRDLQ AKLQLRYQEI SKRTQPPPKL PVGPSHRLSN NYYCARDGRR EAMPPSIVMS SQKVLVAGKP AESSAVAAS EKKAVSPAPP IKRWELSQDE PYL

+
Macromolecule #16: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 17.115508 KDa
SequenceString:
MELLQVLKRG LQQVSGHGGL RGYLRVLFRA NDVRVGTLVG EDKYGNKYYE DNKQFFGRHR WVIYTTEMNG KNTFWDVDGS MVPPEWHRW LHCMTDDPPT VKPPTARKFI WTNHKFNLSG TPQQYVPYST TRKKIQEWVP PSTPYK

+
Macromolecule #17: Acyl carrier protein

MacromoleculeName: Acyl carrier protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 10.119541 KDa
SequenceString:
SDAPPLTLEG IKDRVLYVLK LYDKIDPEKL SVNSHFMKDL GLDSLDQVEI IMAMEDEFGF EIPDIDAEKL MCPQEIVDYI ADKKDVYE

+
Macromolecule #18: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13

MacromoleculeName: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 13
type: protein_or_peptide / ID: 18
Details: This is a focused refinement so only the N-terminal part of this subunit is present in the map.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sheep (sheep) / Organ: Heart / Tissue: Cardiac
Molecular weightTheoretical: 16.635264 KDa
SequenceString:
AASKVKQDMP PVGGYGPIDY KRNLPRRGLS GYSMFAVGIG ALLFGYWSMM RWNRERRRLQ IEDFEARIAL MPLLQAEKDR RVLQMLREN LEEEATIMKD VPGWKVGESV FHTTRWVTPM MGELYGLRTG EEILSSTYGF IWYT

+
Macromolecule #19: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 19 / Number of copies: 6 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

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

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Macromolecule #20: FLAVIN MONONUCLEOTIDE

MacromoleculeName: FLAVIN MONONUCLEOTIDE / type: ligand / ID: 20 / Number of copies: 1 / Formula: FMN
Molecular weightTheoretical: 456.344 Da
Chemical component information

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

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Macromolecule #21: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 21 / Number of copies: 2 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

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

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Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #23: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 23 / 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 #24: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-b...

MacromoleculeName: S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate
type: ligand / ID: 24 / Number of copies: 1 / Formula: ZMP
Molecular weightTheoretical: 568.704 Da
Chemical component information

ChemComp-ZMP:
S-[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] tetradecanethioate

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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

Concentration2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.25 MNaClSodium chloridesodium chloride
0.02 MHEPES
0.02 %Brij-35

Details: 250 mM NaCl, 20 mM HEPES, pH 7.7, 0.02% Brij-35
VitrificationCryogen name: PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: blotting for 30 seconds at 4 degrees Celsius, 95% humidity and flash freezing.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Number grids imaged: 1 / Number real images: 1854 / Average exposure time: 2.0 sec. / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 400000
CTF correctionSoftware - Name: Gctf
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5lnk

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 178121
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1lnk

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 90
Output model

PDB-6q9d:
CI Peripheral Arm focused refinement from Ovine respiratory SC I+III2

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