[English] 日本語
Yorodumi
- PDB-2xqs: Microscopic rotary mechanism of ion translocation in the Fo compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xqs
TitleMicroscopic rotary mechanism of ion translocation in the Fo complex of ATP synthases
ComponentsATP SYNTHASE C CHAIN
KeywordsMEMBRANE PROTEIN / F1FO-ATP SYNTHASE ROTOR / C-RING / ION (PROTON / H+)-TRANSLOCATION / N / N'- DICYCLOHEXYLCARBODIIMIDE (DCCD) INHIBITOR
Function / homology
Function and homology information


plasma membrane-derived thylakoid membrane / proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / lipid binding
Similarity search - Function
F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C ...F1F0 ATP synthase subunit C / F1FO ATP Synthase / ATP synthase, F0 complex, subunit C, bacterial/chloroplast / 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. / V-ATPase proteolipid subunit C-like domain / F/V-ATP synthase subunit C superfamily / ATP synthase subunit C / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CYMAL-4 / ATP synthase subunit c
Similarity search - Component
Biological speciesARTHROSPIRA PLATENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Microscopic Rotary Mechanism of Ion Translocation in the Fo Complex of ATP Synthases
Authors: Pogoryelov, D. / Krah, A. / Langer, J. / Yildiz, O. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionSep 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,27945
Polymers41,0585
Non-polymers19,22240
Water905
1
A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules

A: ATP SYNTHASE C CHAIN
B: ATP SYNTHASE C CHAIN
C: ATP SYNTHASE C CHAIN
D: ATP SYNTHASE C CHAIN
E: ATP SYNTHASE C CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,838135
Polymers123,17315
Non-polymers57,666120
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area64140 Å2
ΔGint-584.3 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.930, 92.930, 258.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein
ATP SYNTHASE C CHAIN / C15_RING


Mass: 8211.530 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ARTHROSPIRA PLATENSIS (bacteria) / References: UniProt: D5A0Q7
#2: Chemical...
ChemComp-CVM / CYMAL-4 / 4-CYCLOHEXYLBUTYL 4-O-ALPHA-D-GLUCOPYRANOSYL-BETA-D-GLUCOPYRANOSIDE


Mass: 480.546 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C22H40O11
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.66 % / Description: NONE
Crystal growpH: 10.2 / Details: pH 10.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 13974 / % possible obs: 99.6 % / Observed criterion σ(I): 1.8 / Redundancy: 4.1 % / Biso Wilson estimate: 57.08 Å2 / Rmerge(I) obs: 0.3 / Net I/σ(I): 7.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 4 % / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.8 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WIE

2wie


Resolution: 3→45.732 Å / SU ML: 0.38 / σ(F): 2 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 696 5 %
Rwork0.1927 --
obs0.1955 13929 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.306 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 49.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.4478 Å20 Å20 Å2
2--10.4478 Å20 Å2
3----20.8957 Å2
Refinement stepCycle: LAST / Resolution: 3→45.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 375 5 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073303
X-RAY DIFFRACTIONf_angle_d1.0874416
X-RAY DIFFRACTIONf_dihedral_angle_d19.3971302
X-RAY DIFFRACTIONf_chiral_restr0.061556
X-RAY DIFFRACTIONf_plane_restr0.003511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.23170.31911340.2442549X-RAY DIFFRACTION99
3.2317-3.55680.28281360.18892585X-RAY DIFFRACTION100
3.5568-4.07120.22491380.15662616X-RAY DIFFRACTION100
4.0712-5.12820.18971400.14482661X-RAY DIFFRACTION100
5.1282-45.73760.27091480.24672822X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -45.0872 Å / Origin y: 7.097 Å / Origin z: 30.2318 Å
111213212223313233
T0.1522 Å2-0.0043 Å20.0137 Å2-0.0132 Å2-0.0291 Å2--0.0769 Å2
L0.1831 °2-0.0678 °2-0.0077 °2-0.2751 °2-0.0187 °2--0.0946 °2
S-0.0393 Å °-0.0549 Å °-0.069 Å °-0.0769 Å °-0.0124 Å °0.0068 Å °0.174 Å °0.0522 Å °-0.0292 Å °
Refinement TLS groupSelection details: ALL

+
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