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- PDB-9w2r: Cryo-EM structure of FoF1-ATPase monomer state 1 on the bovine he... -

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Basic information

Entry
Database: PDB / ID: 9w2r
TitleCryo-EM structure of FoF1-ATPase monomer state 1 on the bovine heart submitochondrial particles (FoF1-1)
Components
  • (ATP synthase F(0) complex subunit ...) x 8
  • (ATP synthase F(1) complex subunit ...) x 4
  • (ATP synthase peripheral stalk subunit ...) x 4
  • ATP synthase F(1) complex catalytic subunit beta, mitochondrial
  • ATPase inhibitor, mitochondrial
KeywordsMOTOR PROTEIN / ATP synthase / FoF1-ATPase / submitochondrial particles
Function / homology
Function and homology information


Mitochondrial protein import / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial translation termination ...Mitochondrial protein import / negative regulation of mitochondrial ATP synthesis coupled proton transport / angiostatin binding / negative regulation of hydrolase activity / Formation of ATP by chemiosmotic coupling / Cristae formation / ATPase inhibitor activity / mitochondrial proton-transporting ATP synthase complex assembly / mitochondrial envelope / Mitochondrial translation termination / proton channel activity / heme biosynthetic process / Mitochondrial protein degradation / negative regulation of endothelial cell proliferation / proton transmembrane transporter activity / proton motive force-driven ATP synthesis / proton-transporting two-sector ATPase complex, proton-transporting domain / proton motive force-driven mitochondrial ATP synthesis / H+-transporting two-sector ATPase / proton-transporting ATP synthase complex / proton-transporting ATP synthase activity, rotational mechanism / proton transmembrane transport / aerobic respiration / erythrocyte differentiation / ADP binding / mitochondrial membrane / ATPase binding / protein homotetramerization / calmodulin binding / mitochondrial inner membrane / lipid binding / structural molecule activity / cell surface / protein homodimerization activity / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
ATP synthase membrane subunit K / ATP synthase regulation / 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 ...ATP synthase membrane subunit K / ATP synthase regulation / 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 ATPase inhibitor / Mitochondrial F1-F0 ATP synthase subunit F, predicted / ATP synthase protein 8, mammals / ATP synthase protein 8 / Mitochondrial ATPase inhibitor, IATP / Mitochondrial F1F0-ATP synthase, subunit f / 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, F0 complex, subunit D, mitochondrial / ATP synthase D chain, mitochondrial (ATP5H) / ATP synthase delta/epsilon subunit, C-terminal domain superfamily / 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, alpha subunit nucleotide-binding domain / 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 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(0) complex subunit a / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F(0) complex subunit a / ATPase inhibitor, mitochondrial / ATP synthase peripheral stalk subunit F6, mitochondrial / ATP synthase F(0) complex subunit 8 / ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F(1) complex subunit epsilon, mitochondrial / ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase peripheral stalk subunit d, mitochondrial / ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase F(0) complex subunit j, mitochondrial / ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F(0) complex subunit C1, mitochondrial / ATP synthase F(0) complex subunit e, mitochondrial / ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase F(0) complex subunit g, mitochondrial / ATP synthase F(0) complex subunit k, mitochondrial
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsNakano, A. / Masuya, T. / Akisada, S. / Ishikawa-Fukuda, M. / Mitsuoka, K. / Miyoshi, H. / Murai, M. / Yokoyama, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23H02453 Japan
Japan Society for the Promotion of Science (JSPS)25K01958 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: Nat Commun / Year: 2026
Title: Structures of respiratory supercomplexes and ATP synthase oligomers in mammalian mitochondrial inner membrane.
Authors: Atsuki Nakano / Takahiro Masuya / Shinsuke Akisada / Moe Ishikawa-Fukuda / Kaoru Mitsuoka / Hideto Miyoshi / Masatoshi Murai / Ken Yokoyama /
Abstract: Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the ...Understanding the functional mechanisms of membrane protein complexes requires structural analysis within their native membrane environment. Here, we applied cryo-electron microscopy to determine the structures of FF ATP synthase and respiratory supercomplexes (SCs) on sub-mitochondrial particles (SMPs) isolated from bovine heart mitochondria. Most FF complexes were observed as dimers stabilized by the regulatory factor IF₁, and a tetrameric assembly comprising two FF-IF₁ dimers arranged linearly was also identified. This finding indicates that the tetrameric units of FF are present in the mitochondrial inner membrane and contribute to shaping cristae tips in mammalian mitochondria. F domain maps resolve the e-subunit- c₈-ring interface and show no discrete density for a tightly bound lipid within the c₈-ring. In addition to the previously reported SCs compositions CI₁CIII₂CIV₁ and CI₁CIII₂CIV₂, our analysis identified an additional assembly with the composition CI₁CIII₂CIV₃, as well as a CI₂CIII₂CIV₆ mega-complex. This approach enables rapid structural determination of FF ATP synthase and SCs from minimal membrane fractions, providing a foundation for elucidating the molecular basis of metabolic disorders and mitochondrial diseases at the level of higher-order architecture.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
8: ATP synthase F(0) complex subunit 8
A: ATP synthase F(1) complex subunit alpha, mitochondrial
B: ATP synthase F(1) complex subunit alpha, mitochondrial
C: ATP synthase F(1) complex subunit alpha, mitochondrial
D: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
E: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
F: ATP synthase F(1) complex catalytic subunit beta, mitochondrial
G: ATP synthase F(1) complex subunit gamma, mitochondrial
H: ATP synthase F(1) complex subunit delta, mitochondrial
I: ATP synthase F(1) complex subunit epsilon, mitochondrial
J: ATPase inhibitor, mitochondrial
K: ATP synthase F(0) complex subunit C1, mitochondrial
L: ATP synthase F(0) complex subunit C1, mitochondrial
M: ATP synthase F(0) complex subunit C1, mitochondrial
N: ATP synthase F(0) complex subunit C1, mitochondrial
O: ATP synthase F(0) complex subunit C1, mitochondrial
P: ATP synthase F(0) complex subunit C1, mitochondrial
Q: ATP synthase F(0) complex subunit C1, mitochondrial
R: ATP synthase F(0) complex subunit C1, mitochondrial
S: ATP synthase peripheral stalk subunit OSCP, mitochondrial
a: ATP synthase F(0) complex subunit a
b: ATP synthase peripheral stalk subunit b, mitochondrial
d: ATP synthase peripheral stalk subunit d, mitochondrial
e: ATP synthase F(0) complex subunit e, mitochondrial
f: ATP synthase F(0) complex subunit f, mitochondrial
g: ATP synthase F(0) complex subunit g, mitochondrial
h: ATP synthase peripheral stalk subunit F6, mitochondrial
j: ATP synthase F(0) complex subunit j, mitochondrial
k: ATP synthase F(0) complex subunit k, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,55539
Polymers588,97729
Non-polymers2,57710
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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ATP synthase F(0) complex subunit ... , 8 types, 15 molecules 8KLMNOPQRaefgjk

#1: Protein ATP synthase F(0) complex subunit 8 / A6L / F-ATPase subunit 8 / ATP synthase subunit A6L


Mass: 7944.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P03929
#8: 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 / ATPase protein 9 / ATPase subunit c / Proton-conducting channel / ATP synthase F(0) complex subunit c


Mass: 7653.034 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P32876
#10: Protein ATP synthase F(0) complex subunit a / ATP synthase subunit a / F-ATPase protein 6 / Proton-conducting channel / ATP synthase F(0) complex subunit a


Mass: 24801.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00847
#13: Protein ATP synthase F(0) complex subunit e, mitochondrial / ATPase subunit e / ATP synthase membrane subunit e


Mass: 8205.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q00361
#14: Protein ATP synthase F(0) complex subunit f, mitochondrial / ATP synthase membrane subunit f


Mass: 10184.011 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28851
#15: Protein ATP synthase F(0) complex subunit g, mitochondrial / ATPase subunit g / ATP synthase membrane subunit g


Mass: 11298.196 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q28852
#17: Protein ATP synthase F(0) complex subunit j, mitochondrial / ATP synthase subunit 6.8PL (subunit j) / 6.8 kDa mitochondrial proteolipid / 6.8 kDa mitochondrial ...ATP synthase subunit 6.8PL (subunit j) / 6.8 kDa mitochondrial proteolipid / 6.8 kDa mitochondrial proteolipid protein / MLQ


Mass: 6846.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P14790
#18: Protein ATP synthase F(0) complex subunit k, mitochondrial / ATP synthase membrane subunit DAPIT / mitochondrial / Diabetes-associated protein in insulin- ...ATP synthase membrane subunit DAPIT / mitochondrial / Diabetes-associated protein in insulin-sensitive tissues / Up-regulated during skeletal muscle growth protein 5


Mass: 6312.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: Q3ZBI7

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ATP synthase F(1) complex subunit ... , 4 types, 6 molecules ABCGHI

#2: Protein ATP synthase F(1) complex subunit alpha, mitochondrial / ATP synthase F1 subunit alpha


Mass: 55331.234 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P19483
#4: Protein ATP synthase F(1) complex subunit gamma, mitochondrial / ATP synthase F1 subunit gamma / F-ATPase gamma subunit


Mass: 30300.760 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05631
#5: Protein ATP synthase F(1) complex subunit delta, mitochondrial / ATP synthase F1 subunit delta / F-ATPase delta subunit


Mass: 15074.813 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05630
#6: Protein/peptide ATP synthase F(1) complex subunit epsilon, mitochondrial / ATPase subunit epsilon / ATP synthase F1 subunit epsilon


Mass: 5662.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P05632

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Protein , 2 types, 4 molecules DEFJ

#3: Protein ATP synthase F(1) complex catalytic subunit beta, mitochondrial / ATP synthase F1 subunit beta


Mass: 51757.836 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle)
References: UniProt: P00829, H+-transporting two-sector ATPase
#7: Protein ATPase inhibitor, mitochondrial / ATP synthase F1 subunit epsilon / Inhibitor of F(1)F(o)-ATPase / IF(1) / IF1


Mass: 6633.216 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01096

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ATP synthase peripheral stalk subunit ... , 4 types, 4 molecules Sbdh

#9: Protein ATP synthase peripheral stalk subunit OSCP, mitochondrial / ATP synthase subunit O / Oligomycin sensitivity conferral protein / OSCP


Mass: 20959.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13621
#11: Protein ATP synthase peripheral stalk subunit b, mitochondrial / ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane ...ATP synthase F(0) complex subunit B1 / mitochondrial / ATP synthase peripheral stalk-membrane subunit b / ATP synthase subunit b / ATPase subunit b


Mass: 24702.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13619
#12: Protein ATP synthase peripheral stalk subunit d, mitochondrial / ATPase subunit d / ATP synthase peripheral stalk subunit d


Mass: 18588.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P13620
#16: Protein ATP synthase peripheral stalk subunit F6, mitochondrial / ATPase subunit F6 / ATP synthase peripheral stalk subunit F6


Mass: 8971.079 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02721

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Non-polymers , 3 types, 10 molecules

#19: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / 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.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: FoF1-ATPase on the bovine heart submitochondrial particles
Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Molecular weightValue: 0.60 MDa / Experimental value: YES
Source (natural)Organism: Bos taurus (domestic cattle)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
7Coot0.9.8.95model fitting
8ISOLDE1.9model fitting
10PHENIX1.21.2_5419model refinement
14cryoSPARC4.73D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 30421492
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 328822 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6ZPO

6zpo


Accession code: 6ZPO / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00439689
ELECTRON MICROSCOPYf_angle_d0.71353701
ELECTRON MICROSCOPYf_dihedral_angle_d15.51414690
ELECTRON MICROSCOPYf_chiral_restr0.0446274
ELECTRON MICROSCOPYf_plane_restr0.0046853

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