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- PDB-8h9s: Human ATP synthase state 1 (combined) -

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Basic information

Entry
Database: PDB / ID: 8h9s
TitleHuman ATP synthase state 1 (combined)
Components
  • (ATP synthase F(0) complex subunit ...) x 2
  • (ATP synthase subunit ...) x 12
  • ATP synthase protein 8
  • ATP synthase-coupling factor 6, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsMEMBRANE PROTEIN / ATP synthase
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / regulation of protein targeting to mitochondrion / estradiol binding / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding ...mitochondrial proton-transporting ATP synthase complex binding / regulation of ATP metabolic process / negative regulation of cell adhesion involved in substrate-bound cell migration / Formation of ATP by chemiosmotic coupling / Cristae formation / regulation of protein targeting to mitochondrion / estradiol binding / positive regulation of proteolysis involved in protein catabolic process / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / ATP biosynthetic process / mitochondrial depolarization / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / positive regulation of type 2 mitophagy / Mitochondrial protein import / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to interleukin-7 / proton channel activity / oxidative phosphorylation / heme biosynthetic process / response to copper ion / response to muscle activity / negative regulation of endothelial cell proliferation / cellular response to cytokine stimulus / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / MHC class I protein binding / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis / proton-transporting ATPase activity, rotational mechanism / enzyme inhibitor activity / positive regulation of blood vessel endothelial cell migration / response to hyperoxia / cellular response to dexamethasone stimulus / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / Mitochondrial protein degradation / substantia nigra development / cellular response to nitric oxide / proton transmembrane transport / reactive oxygen species metabolic process / aerobic respiration / cellular response to cAMP / erythrocyte differentiation / regulation of intracellular pH / generation of precursor metabolites and energy / Transcriptional activation of mitochondrial biogenesis / ADP binding / mitochondrial membrane / lipid metabolic process / fibrillar center / osteoblast differentiation / ATPase binding / protease binding / response to ethanol / angiogenesis / nuclear membrane / calmodulin binding / hydrolase activity / mitochondrial inner membrane / mitochondrial matrix / membrane raft / lipid binding / protein-containing complex binding / structural molecule activity / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals ...ATP synthase subunit ATP5MJ, mitochondrial / Mitochondrial proteolipid / ATP synthase, F0 complex, subunit G, mitochondrial / ATP synthase, F0 complex, subunit E, mitochondrial / Mitochondrial ATP synthase subunit g, animal / Mitochondrial ATP synthase g subunit / ATP synthase E chain / ATP synthase protein 8, metazoa / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial F1F0-ATP synthase, subunit f / 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, F0 complex, subunit B/MI25 / ATP synthase, F0 complex, subunit B / Mitochondrial ATP synthase B chain precursor (ATP-synt_B) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / ATP synthase, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase, F0 complex, subunit D superfamily, mitochondrial / ATP synthase, F0 complex, subunit A, bacterial/mitochondria / 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 / ATP synthase, F0 complex, subunit A / ATP synthase, F0 complex, subunit A, active site / ATP synthase, F0 complex, subunit A superfamily / ATP synthase A chain / ATP synthase a subunit signature. / 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, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / 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 / C-terminal domain of V and A type ATP synthase / 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
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase F(0) complex subunit a / ATP synthase F(0) complex subunit 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase F(1) complex subunit beta, mitochondrial ...1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / CARDIOLIPIN / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase F(0) complex subunit a / ATP synthase F(0) complex subunit 8 / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase F(1) complex subunit beta, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit j, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial / ATPase inhibitor, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsLai, Y. / Zhang, Y. / Liu, F. / Gao, Y. / Gong, H. / Rao, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)813300237 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: Mol Cell / Year: 2023
Title: Structure of the human ATP synthase.
Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / ...Authors: Yuezheng Lai / Yuying Zhang / Shan Zhou / Jinxu Xu / Zhanqiang Du / Ziyan Feng / Long Yu / Ziqing Zhao / Weiwei Wang / Yanting Tang / Xiuna Yang / Luke W Guddat / Fengjiang Liu / Yan Gao / Zihe Rao / Hongri Gong /
Abstract: Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main ...Biological energy currency ATP is produced by FF-ATP synthase. However, the molecular mechanism for human ATP synthase action remains unknown. Here, we present snapshot images for three main rotational states and one substate of human ATP synthase using cryoelectron microscopy. These structures reveal that the release of ADP occurs when the β subunit of FF-ATP synthase is in the open conformation, showing how ADP binding is coordinated during synthesis. The accommodation of the symmetry mismatch between F and F motors is resolved by the torsional flexing of the entire complex, especially the γ subunit, and the rotational substep of the c subunit. Water molecules are identified in the inlet and outlet half-channels, suggesting that the proton transfer in these two half-channels proceed via a Grotthus mechanism. Clinically relevant mutations are mapped to the structure, showing that they are mainly located at the subunit-subunit interfaces, thus causing instability of the complex.
History
DepositionOct 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: ATP synthase F(0) complex subunit B1, mitochondrial
L: ATP synthase-coupling factor 6, mitochondrial
M: ATP synthase subunit d, mitochondrial
A: ATP synthase subunit alpha, mitochondrial
B: ATP synthase subunit alpha, mitochondrial
C: ATP synthase subunit alpha, mitochondrial
E: ATP synthase subunit beta, mitochondrial
F: ATP synthase subunit beta, mitochondrial
D: ATP synthase subunit beta, mitochondrial
G: ATP synthase subunit gamma, mitochondrial
J: ATPase inhibitor, mitochondrial
O: ATP synthase subunit O, mitochondrial
1: ATP synthase F(0) complex subunit C1, mitochondrial
2: ATP synthase F(0) complex subunit C1, mitochondrial
3: ATP synthase F(0) complex subunit C1, mitochondrial
4: ATP synthase F(0) complex subunit C1, mitochondrial
5: ATP synthase F(0) complex subunit C1, mitochondrial
6: ATP synthase F(0) complex subunit C1, mitochondrial
7: ATP synthase F(0) complex subunit C1, mitochondrial
8: ATP synthase F(0) complex subunit C1, mitochondrial
H: ATP synthase subunit delta, mitochondrial
I: ATP synthase subunit epsilon, mitochondrial
N: ATP synthase subunit a
P: ATP synthase subunit ATP5MJ, mitochondrial
Q: ATP synthase protein 8
R: ATP synthase subunit f, mitochondrial
S: ATP synthase subunit g, mitochondrial
T: ATP synthase subunit e, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,00341
Polymers588,87228
Non-polymers6,13113
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase F(0) complex subunit ... , 2 types, 9 molecules K12345678

#1: Protein ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase proton-transporting mitochondrial ...ATP synthase peripheral stalk-membrane subunit b / ATP synthase proton-transporting mitochondrial F(0) complex subunit B1 / ATP synthase subunit b / ATPase subunit b


Mass: 24658.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P24539
#9: Protein
ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase ...ATP synthase lipid-binding protein / ATP synthase membrane subunit c locus 1 / ATP synthase proteolipid P1 / ATP synthase proton-transporting mitochondrial F(0) complex subunit C1 / ATPase protein 9 / ATPase subunit c


Mass: 7610.954 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05496

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Protein , 3 types, 3 molecules LJQ

#2: Protein ATP synthase-coupling factor 6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 12606.499 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18859
#7: Protein ATPase inhibitor, mitochondrial / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 9540.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UII2
#14: Protein ATP synthase protein 8 / A6L / F-ATPase subunit 8


Mass: 8000.634 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P03928

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ATP synthase subunit ... , 12 types, 16 molecules MABCEFDGOHINPRST

#3: Protein ATP synthase subunit d, mitochondrial / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18383.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75947
#4: Protein ATP synthase subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55276.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25705
#5: Protein ATP synthase subunit beta, mitochondrial


Mass: 51821.965 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P06576
#6: Protein ATP synthase subunit gamma, mitochondrial / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 30207.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36542
#8: Protein ATP synthase subunit O, mitochondrial / ATP synthase peripheral stalk subunit OSCP / Oligomycin sensitivity conferral protein / OSCP


Mass: 20904.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48047
#10: Protein ATP synthase subunit delta, mitochondrial / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 15029.817 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P30049
#11: Protein ATP synthase subunit epsilon, mitochondrial / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5790.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56381
#12: Protein ATP synthase subunit a / F-ATPase protein 6


Mass: 24833.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00846
#13: Protein ATP synthase subunit ATP5MJ, mitochondrial / 6.8 kDa mitochondrial proteolipid protein / MLQ / ATP synthase membrane subunit 6.8PL


Mass: 6673.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56378
#15: Protein ATP synthase subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 10804.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56134
#16: Protein ATP synthase subunit g, mitochondrial / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11309.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75964
#17: Protein ATP synthase subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 7947.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56385

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Non-polymers , 5 types, 13 molecules

#18: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#19: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#20: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#22: Chemical ChemComp-3PH / 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE / PHOSPHATIDIC ACID


Mass: 704.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H77O8P / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human ATP synthase / Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightValue: 0.6 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1200 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
8PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68388 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00539565
ELECTRON MICROSCOPYf_angle_d0.56753506
ELECTRON MICROSCOPYf_dihedral_angle_d7.02524078
ELECTRON MICROSCOPYf_chiral_restr0.0446216
ELECTRON MICROSCOPYf_plane_restr0.0056813

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