[English] 日本語
Yorodumi
- PDB-4b2q: Model of the yeast F1Fo-ATP synthase dimer based on subtomogram a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4b2q
TitleModel of the yeast F1Fo-ATP synthase dimer based on subtomogram average
Components
  • (ATP SYNTHASE SUBUNIT ...) x 11
  • ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
KeywordsHYDROLASE / SUBTOMOGRAM AVERAGE
Function / homology
Function and homology information


mitochondrial proton-transporting ATP synthase, central stalk / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / proton motive force-driven mitochondrial ATP synthesis ...mitochondrial proton-transporting ATP synthase, central stalk / Formation of ATP by chemiosmotic coupling / Cristae formation / mitochondrial proton-transporting ATP synthase, catalytic core / mitochondrial proton-transporting ATP synthase, stator stalk / mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) / mitochondrial proton-transporting ATP synthase complex / mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) / mitochondrial nucleoid / 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) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ADP binding / mitochondrial intermembrane space / mitochondrial inner membrane / lipid binding / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / 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) ...: / Fungal epsilon subunit of F1F0-ATP synthase C-terminal domain / ATP synthase-coupling factor 6, mitochondrial / ATP synthase-coupling factor 6 superfamily, mitochondrial / Mitochondrial ATP synthase coupling factor 6 / 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, F0 complex, subunit D superfamily, mitochondrial / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial ...ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / ATP synthase subunit beta, mitochondrial / ATP synthase-coupling factor 6, mitochondrial / ATP synthase subunit alpha, mitochondrial / ATP synthase F(0) complex subunit B1, mitochondrial / ATP synthase subunit d, mitochondrial / ATP synthase subunit O, mitochondrial / ATP synthase subunit epsilon, mitochondrial / ATP synthase subunit gamma, mitochondrial / ATP synthase subunit 9, mitochondrial / ATP synthase subunit delta, mitochondrial
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
BOS TAURUS (cattle)
MethodELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 37 Å
AuthorsDavies, K.M. / Kuehlbrandt, W.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae.
Authors: Karen M Davies / Claudio Anselmi / Ilka Wittig / José D Faraldo-Gómez / Werner Kühlbrandt /
Abstract: We used electron cryotomography of mitochondrial membranes from wild-type and mutant Saccharomyces cerevisiae to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram ...We used electron cryotomography of mitochondrial membranes from wild-type and mutant Saccharomyces cerevisiae to investigate the structure and organization of ATP synthase dimers in situ. Subtomogram averaging of the dimers to 3.7 nm resolution revealed a V-shaped structure of twofold symmetry, with an angle of 86° between monomers. The central and peripheral stalks are well resolved. The monomers interact within the membrane at the base of the peripheral stalks. In wild-type mitochondria ATP synthase dimers are found in rows along the highly curved cristae ridges, and appear to be crucial for membrane morphology. Strains deficient in the dimer-specific subunits e and g or the first transmembrane helix of subunit 4 lack both dimers and lamellar cristae. Instead, cristae are either absent or balloon-shaped, with ATP synthase monomers distributed randomly in the membrane. Computer simulations indicate that isolated dimers induce a plastic deformation in the lipid bilayer, which is partially relieved by their side-by-side association. We propose that the assembly of ATP synthase dimer rows is driven by the reduction in the membrane elastic energy, rather than by direct protein contacts, and that the dimer rows enable the formation of highly curved ridges in mitochondrial cristae.
History
DepositionJul 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Jul 24, 2013Group: Derived calculations
Revision 1.3Aug 23, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2161
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
B: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
C: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
D: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
E: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
F: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
G: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
H: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
I: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
J: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
K: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
L: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
M: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
N: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
O: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
P: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
Q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
R: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
S: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
T: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
U: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
V: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
W: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
a: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
b: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
c: ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL
d: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
e: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
f: ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL
g: ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL
h: ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL
i: ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL
j: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
k: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
l: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
m: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
n: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
o: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
p: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
q: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
r: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
s: ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL
t: ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL
u: ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL
v: ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL
w: ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)981,27966
Polymers976,28446
Non-polymers4,99520
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

-
ATP SYNTHASE SUBUNIT ... , 11 types, 44 molecules ACacBbDdEFefGgHhIiJKLMNOPQRSjk...

#1: Protein
ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL /


Mass: 52376.539 Da / Num. of mol.: 4 / Fragment: RESIDUES 61-545 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: P07251
#2: Protein ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL /


Mass: 52447.617 Da / Num. of mol.: 2 / Fragment: RESIDUES 60-545 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: P07251
#3: Protein ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL /


Mass: 50438.348 Da / Num. of mol.: 2 / Fragment: RESIDUES 39-508 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A
References: UniProt: P00830, H+-transporting two-sector ATPase
#4: Protein
ATP SYNTHASE SUBUNIT BETA, MITOCHONDRIAL /


Mass: 50752.641 Da / Num. of mol.: 4 / Fragment: RESIDUES 39-511 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A
References: UniProt: P00830, H+-transporting two-sector ATPase
#5: Protein ATP SYNTHASE SUBUNIT GAMMA, MITOCHONDRIAL / / F-ATPASE GAMMA SUBUNIT


Mass: 30657.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 34-311 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: P38077
#6: Protein ATP SYNTHASE SUBUNIT DELTA, MITOCHONDRIAL / / F-ATPASE DELTA SUBUNIT


Mass: 14080.876 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-160 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: Q12165
#7: Protein ATP SYNTHASE SUBUNIT EPSILON, MITOCHONDRIAL / / ATPASE SUBUNIT EPSILON


Mass: 6388.076 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-60 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: P21306
#8: Protein
ATP SYNTHASE SUBUNIT 9, MITOCHONDRIAL / / LIPID-BINDING PROTEIN / OLIGOMYCIN RESISTANCE PROTEIN 1


Mass: 7762.375 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / Organ: MITOCHONDRIAMitochondrion / Strain: D273-10B/A / References: UniProt: P61829
#9: Protein ATP SYNTHASE SUBUNIT B, MITOCHONDRIAL / / ATPASE SUBUNIT B


Mass: 15408.768 Da / Num. of mol.: 2 / Fragment: RESIDUES 121-249 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIAMitochondrion
References: UniProt: P13619, H+-transporting two-sector ATPase
#10: Protein ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL / / ATPASE SUBUNIT D


Mass: 13768.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 5-124 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIAMitochondrion / References: UniProt: P13620
#12: Protein ATP SYNTHASE SUBUNIT O, MITOCHONDRIAL / / OLIGOMYCIN SENSITIVITY CONFERRAL PROTEIN / OSCP


Mass: 13240.513 Da / Num. of mol.: 2 / Fragment: RESIDUES 24-143 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIAMitochondrion
References: UniProt: P13621, H+-transporting two-sector ATPase

-
Protein , 1 types, 2 molecules Vv

#11: Protein ATP SYNTHASE-COUPLING FACTOR 6, MITOCHONDRIAL / ATPASE SUBUNIT F6


Mass: 7829.806 Da / Num. of mol.: 2 / Fragment: RESIDUES 36-101 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: MITOCHONDRIAMitochondrion / References: UniProt: P02721

-
Non-polymers , 3 types, 20 molecules

#13: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#14: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#15: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: electron tomography

-
Sample preparation

ComponentName: ATP SYNTHASE DIMER FROM MITOCHONDRIA OF SACCHAROMYCES CEREVISIAE
Type: CELL
Buffer solutionName: 250MM TREHALOSE 10NM TRIS- HCL PH7.4 / pH: 7.4 / Details: 250MM TREHALOSE 10NM TRIS- HCL PH7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 100, INSTRUMENT- HOMEMADE PLUNGER, METHOD- SINGLE SIDE MANUAL BLOTTING FOR 5 SECONDS.,

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Date: Mar 11, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 41000 X / Calibrated magnification: 24500 X / Nominal defocus max: 7500 nm / Nominal defocus min: 6500 nm / Cs: 2 mm
Specimen holderTemperature: 80 K / Tilt angle max: 60 ° / Tilt angle min: -50 °
Image recordingElectron dose: 160 e/Å2 / Film or detector model: GATAN ULTRASCAN 1000 (2k x 2k)
Image scansNum. digital images: 75
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2IMOD3D reconstruction
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: WEIGHTED BACK-PROJECTION / Resolution: 37 Å / Num. of particles: 121 / Actual pixel size: 5.76 Å
Details: MODEL BASED ON PDBS 2WPD,2CLY AND 2BO5. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2161. (DEPOSITION ID: 10941).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2WPD

2wpd

RefinementHighest resolution: 37 Å
Refinement stepCycle: LAST / Highest resolution: 37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms68216 0 304 0 68520

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
Yorodumi

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

Read more