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- EMDB-11040: bovine ATP synthase F1c8-peripheral stalk domain, state 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-11040
Titlebovine ATP synthase F1c8-peripheral stalk domain, state 3
Map dataState 3 half map 1
Sample
  • Complex: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
    • Complex: ATP synthase F1 domain
      • Protein or peptide: x 5 types
    • Complex: ATP synthase peripheral stalk
      • Protein or peptide: x 4 types
    • Complex: ATPase inhibitor, mitochondrial
      • Protein or peptide: x 1 types
  • Ligand: x 4 types
Function / homology
Function and homology information


angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / proton-transporting ATP synthase complex ...angiostatin binding / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / negative regulation of hydrolase activity / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / heme biosynthetic process / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / negative regulation of endothelial cell proliferation / proton motive force-driven mitochondrial ATP synthesis / proton motive force-driven ATP synthesis / proton transmembrane transporter activity / proton-transporting ATP synthase complex, catalytic core F(1) / aerobic respiration / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / proton-transporting ATP synthase activity, rotational mechanism / erythrocyte differentiation / ADP binding / ATPase binding / protein homotetramerization / mitochondrial inner membrane / calmodulin binding / lipid binding / structural molecule activity / cell surface / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B ...Mitochondrial ATPase inhibitor / Mitochondrial ATPase inhibitor, IATP / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / : / Metazoan delta subunit of F1F0-ATP synthase, C-terminal domain / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase, F1 complex, epsilon subunit, mitochondrial / ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial / Mitochondrial ATP synthase epsilon chain / ATPase, OSCP/delta subunit, conserved site / ATP synthase delta (OSCP) subunit signature. / F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily / ATPase, OSCP/delta subunit / ATP synthase delta (OSCP) subunit / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F0 complex, subunit C / F1F0 ATP synthase subunit C superfamily / ATP synthase, F0 complex, subunit C, DCCD-binding site / ATP synthase c subunit signature. / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ATP synthase subunit beta, mitochondrial / ATPase inhibitor, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit delta, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit C2, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit alpha, mitochondrial
Similarity search - Component
Biological speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsSpikes T / Montgomery MG / Walker JE
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009858/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105663150 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the dimeric ATP synthase from bovine mitochondria.
Authors: Tobias E Spikes / Martin G Montgomery / John E Walker /
Abstract: The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial ...The structure of the dimeric ATP synthase from bovine mitochondria determined in three rotational states by electron cryo-microscopy provides evidence that the proton uptake from the mitochondrial matrix via the proton inlet half channel proceeds via a Grotthus mechanism, and a similar mechanism may operate in the exit half channel. The structure has given information about the architecture and mechanical constitution and properties of the peripheral stalk, part of the membrane extrinsic region of the stator, and how the action of the peripheral stalk damps the side-to-side rocking motions that occur in the enzyme complex during the catalytic cycle. It also describes wedge structures in the membrane domains of each monomer, where the skeleton of each wedge is provided by three α-helices in the membrane domains of the b-subunit to which the supernumerary subunits e, f, and g and the membrane domain of subunit A6L are bound. Protein voids in the wedge are filled by three specifically bound cardiolipin molecules and two other phospholipids. The external surfaces of the wedges link the monomeric complexes together into the dimeric structures and provide a pivot to allow the monomer-monomer interfaces to change during catalysis and to accommodate other changes not related directly to catalysis in the monomer-monomer interface that occur in mitochondrial cristae. The structure of the bovine dimer also demonstrates that the structures of dimeric ATP synthases in a tetrameric porcine enzyme have been seriously misinterpreted in the membrane domains.
History
DepositionMay 14, 2020-
Header (metadata) releaseSep 9, 2020-
Map releaseSep 9, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6z1u
  • Surface level: 0.0267
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z1u
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11040.png

Downloads & links

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Map

FileDownload / File: emd_11040.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState 3 half map 1
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.0267 / Movie #1: 0.0267
Minimum - Maximum-0.07156458 - 0.11974778
Average (Standard dev.)-0.00000321631 (±0.00284674)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 524.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z524.000524.000524.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.0720.120-0.000

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Supplemental data

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Mask #1

Fileemd_11040_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 3 half map 2

Fileemd_11040_half_map_1.map
AnnotationState 3 half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: State 3 half map 1

Fileemd_11040_half_map_2.map
AnnotationState 3 half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His

EntireName: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
Components
  • Complex: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
    • Complex: ATP synthase F1 domain
      • Protein or peptide: ATP synthase subunit alpha, mitochondrial
      • Protein or peptide: ATP synthase subunit beta, mitochondrial
      • Protein or peptide: ATP synthase subunit gamma, mitochondrial
      • Protein or peptide: ATP synthase subunit delta, mitochondrial
      • Protein or peptide: ATP synthase subunit epsilon, mitochondrial
    • Complex: ATP synthase peripheral stalk
      • Protein or peptide: ATP synthase F(0) complex subunit C2, mitochondrial
      • Protein or peptide: ATP synthase subunit O, mitochondrial
      • Protein or peptide: ATP synthase F(0) complex subunit B1, mitochondrial
      • Protein or peptide: ATP synthase-coupling factor 6, mitochondrial
    • Complex: ATPase inhibitor, mitochondrial
      • Protein or peptide: ATPase inhibitor, mitochondrial
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His

SupramoleculeName: Bovine ATP synthase F1-peripheral stalk domain with IF1_1-60_6His
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weightTheoretical: 7.441 KDa

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Supramolecule #2: ATP synthase F1 domain

SupramoleculeName: ATP synthase F1 domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#5 / Details: The F1 domain of ATP synthase
Source (natural)Organism: Bos taurus (cattle)

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Supramolecule #3: ATP synthase peripheral stalk

SupramoleculeName: ATP synthase peripheral stalk / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#10 / Details: Part of the stator of the enzyme
Source (natural)Organism: Bos taurus (cattle)

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Supramolecule #4: ATPase inhibitor, mitochondrial

SupramoleculeName: ATPase inhibitor, mitochondrial / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6 / Details: ATPase inhibitor (truncated version of IF1)
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: ATP synthase subunit alpha, mitochondrial

MacromoleculeName: ATP synthase subunit alpha, mitochondrial / type: protein_or_peptide / ID: 1
Details: Chain ABC res 481: Residue 481 in chains A, B, and C in this structure should be GLY. There is no density to support a SER and negative density appears if you try SER. We have seen SER in ...Details: Chain ABC res 481: Residue 481 in chains A, B, and C in this structure should be GLY. There is no density to support a SER and negative density appears if you try SER. We have seen SER in some of our previous structures of bovine F1-ATPAse. We have used the following REMARK in other PDB files: REMARK 999 REFERENCE FOR THE ALPHA SUBUNIT J. E. WALKER, S. J. REMARK 999 POWELL,O. VINAS AND M. J. RUNSWICK, BIOCHEMISTRY,VOL 28,PP REMARK 999 4702-4708, 1989. REMARK 999 REMARK 999 SER 481 GLY IN CHAINS A, B AND C REMARK 999 WAS IDENTIFIED AS A GLY FROM THE PROTEIN REMARK 999 SEQUENCE. IN THE CDNA SEQUENCE, THE CODON FOR THIS REMARK 999 RESIDUE WAS AGC SER IN THREE CLONES WHILE IN TWO REMARK 999 OTHERS IT WAS GGC GLY. THE DIFFERENCE WAS THOUGHT TO REMARK 999 BE DUE TO A MUTATION OCCURRING DURING EITHER PROPAGATION REMARK 999 OF THE CLONES IN THE LIBRARY OR SUBCLONING INTO M13 REMARK 999 VECTORS. THE ELECTRON DENSITY SUGGESTS A GLY IN REMARK 999 THIS POSITION.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 55.302191 KDa
SequenceString: EKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKARRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII ...String:
EKTGTAEVSS ILEERILGAD TSVDLEETGR VLSIGDGIAR VHGLRNVQAE EMVEFSSGLK GMSLNLEPDN VGVVVFGNDK LIKEGDIVK RTGAIVDVPV GEELLGRVVD ALGNAIDGKG PIGSKARRRV GLKAPGIIPR ISVREPMQTG IKAVDSLVPI G RGQRELII GDRQTGKTSI AIDTIINQKR FNDGTDEKKK LYCIYVAIGQ KRSTVAQLVK RLTDADAMKY TIVVSATASD AA PLQYLAP YSGCSMGEYF RDNGKHALII YDDLSKQAVA YRQMSLLLRR PPGREAYPGD VFYLHSRLLE RAAKMNDAFG GGS LTALPV IETQAGDVSA YIPTNVISIT DGQIFLETEL FYKGIRPAIN VGLSVSRVGS AAQTRAMKQV AGTMKLELAQ YREV AAFAQ FGSDLDAATQ QLLSRGVRLT ELLKQGQYSP MAIEEQVAVI YAGVRGYLDK LEPSKITKFE NAFLSHVISQ HQALL GKIR TDGKISEESD AKLKEIVTNF LAGFEA

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Macromolecule #2: ATP synthase subunit beta, mitochondrial

MacromoleculeName: ATP synthase subunit beta, mitochondrial / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: H+-transporting two-sector ATPase
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 51.757836 KDa
SequenceString: AAQASPSPKA GATTGRIVAV IGAVVDVQFD EGLPPILNAL EVQGRETRLV LEVAQHLGES TVRTIAMDGT EGLVRGQKVL DSGAPIRIP VGPETLGRIM NVIGEPIDER GPIKTKQFAA IHAEAPEFVE MSVEQEILVT GIKVVDLLAP YAKGGKIGLF G GAGVGKTV ...String:
AAQASPSPKA GATTGRIVAV IGAVVDVQFD EGLPPILNAL EVQGRETRLV LEVAQHLGES TVRTIAMDGT EGLVRGQKVL DSGAPIRIP VGPETLGRIM NVIGEPIDER GPIKTKQFAA IHAEAPEFVE MSVEQEILVT GIKVVDLLAP YAKGGKIGLF G GAGVGKTV LIMELINNVA KAHGGYSVFA GVGERTREGN DLYHEMIESG VINLKDATSK VALVYGQMNE PPGARARVAL TG LTVAEYF RDQEGQDVLL FIDNIFRFTQ AGSEVSALLG RIPSAVGYQP TLATDMGTMQ ERITTTKKGS ITSVQAIYVP ADD LTDPAP ATTFAHLDAT TVLSRAIAEL GIYPAVDPLD STSRIMDPNI VGSEHYDVAR GVQKILQDYK SLQDIIAILG MDEL SEEDK LTVSRARKIQ RFLSQPFQVA EVFTGHLGKL VPLKETIKGF QQILAGEYDH LPEQAFYMVG PIEEAVAKAD KLAEE HS

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Macromolecule #3: ATP synthase subunit gamma, mitochondrial

MacromoleculeName: ATP synthase subunit gamma, mitochondrial / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 30.30076 KDa
SequenceString: ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ...String:
ATLKDITRRL KSIKNIQKIT KSMKMVAAAK YARAERELKP ARVYGVGSLA LYEKADIKTP EDKKKHLIIG VSSDRGLCGA IHSSVAKQM KSEAANLAAA GKEVKIIGVG DKIRSILHRT HSDQFLVTFK EVGRRPPTFG DASVIALELL NSGYEFDEGS I IFNRFRSV ISYKTEEKPI FSLDTISSAE SMSIYDDIDA DVLRNYQEYS LANIIYYSLK ESTTSEQSAR MTAMDNASKN AS EMIDKLT LTFNRTRQAV ITKELIEIIS GAAALD

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Macromolecule #4: ATP synthase subunit delta, mitochondrial

MacromoleculeName: ATP synthase subunit delta, mitochondrial / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 15.074813 KDa
SequenceString:
AEAAAAQAPA AGPGQMSFTF ASPTQVFFNS ANVRQVDVPT QTGAFGILAA HVPTLQVLRP GLVVVHAEDG TTSKYFVSSG SVTVNADSS VQLLAEEAVT LDMLDLGAAK ANLEKAQSEL LGAADEATRA EIQIRIEANE ALVKALE

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Macromolecule #5: ATP synthase subunit epsilon, mitochondrial

MacromoleculeName: ATP synthase subunit epsilon, mitochondrial / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 5.662693 KDa
SequenceString:
VAYWRQAGLS YIRYSQICAK AVRDALKTEF KANAMKTSGS TIKIVKVKKE

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Macromolecule #6: ATPase inhibitor, mitochondrial

MacromoleculeName: ATPase inhibitor, mitochondrial / type: protein_or_peptide / ID: 6
Details: ATP synthase inhibitor protein IF1 residues 1-60 with a 6HIS affinity tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 7.462098 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSESGDNVRS SAGAVRDAGG AFGKREQAEE ERYFRARAKE QLAALKKHHE NEISHHAKEI HHHHHH

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Macromolecule #7: ATP synthase F(0) complex subunit C2, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit C2, mitochondrial / type: protein_or_peptide / ID: 7 / Details: Trimethyl-lysine at position 43 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 7.653034 KDa
SequenceString:
DIDTAAKFIG AGAATVGVAG SGAGIGTVFG SLIIGYARNP SL(M3L)QQLFSYA ILGFALSEAM GLFCLMVAFL ILFAM

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Macromolecule #8: ATP synthase subunit O, mitochondrial

MacromoleculeName: ATP synthase subunit O, mitochondrial / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 20.959777 KDa
SequenceString:
FAKLVRPPVQ IYGIEGRYAT ALYSAASKQN KLEQVEKELL RVGQILKEPK MAASLLNPYV KRSVKVKSLS DMTAKEKFSP LTSNLINLL AENGRLTNTP AVISAFSTMM SVHRGEVPCT VTTASALDEA TLTELKTVLK SFLSKGQVLK LEVKIDPSIM G GMIVRIGE KYVDMSAKTK IQKLSRAMRE IL

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Macromolecule #9: ATP synthase F(0) complex subunit B1, mitochondrial

MacromoleculeName: ATP synthase F(0) complex subunit B1, mitochondrial / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 24.702709 KDa
SequenceString: PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK ...String:
PVPPLPEHGG KVRFGLIPEE FFQFLYPKTG VTGPYVLGTG LILYLLSKEI YVITPETFSA ISTIGFLVYI VKKYGASVGE FADKLNEQK IAQLEEVKQA SIKQIQDAID MEKSQQALVQ KRHYLFDVQR NNIAMALEVT YRERLHRVYR EVKNRLDYHI S VQNMMRQK EQEHMINWVE KRVVQSISAQ QEKETIAKCI ADLKLLSKKA QAQPVM

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Macromolecule #10: ATP synthase-coupling factor 6, mitochondrial

MacromoleculeName: ATP synthase-coupling factor 6, mitochondrial / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 8.971079 KDa
SequenceString:
NKELDPVQKL FVDKIREYRT KRQTSGGPVD AGPEYQQDLD RELFKLKQMY GKADMNTFPN FTFEDPKFEV VEKPQS

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Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 13 / Number of copies: 3 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #14: water

MacromoleculeName: water / type: ligand / ID: 14 / Number of copies: 17 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

Concentration4.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK IV
Details: The sample was allowed to penetrate through the holey support and to distribute to both sides of the grid surface for ca. 15 sec. Then the grids were blotted with filter paper for 8-10 sec before blotting..
DetailsNickel affinity purified filled by gel filtration

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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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 12.0 sec. / Average electron dose: 4.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware: (Name: RELION (ver. 3.1), CTFFIND (ver. 4.1))
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2v7q

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 61458
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2v7q

chain_id: A

2v7q

chain_id: B

2v7q

chain_id: C

2v7q

chain_id: D

2v7q

chain_id: E

2v7q

chain_id: F

2v7q

chain_id: G

2v7q

chain_id: H

2v7q

chain_id: I

2v7q

chain_id: J

2cly

chain_id: A

2cly

chain_id: B

2cly

chain_id: C

2xnd

chain_id: M
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6z1u:
bovine ATP synthase F1c8-peripheral stalk domain, state 3

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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

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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

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