[English] 日本語
Yorodumi
- PDB-2x2v: Structural basis of a novel proton-coordination type in an F1Fo-A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2x2v
TitleStructural basis of a novel proton-coordination type in an F1Fo-ATP synthase rotor ring
ComponentsATP SYNTHASE SUBUNIT C
KeywordsMEMBRANE PROTEIN / ION TRANSPORT / ATP SYNTHESIS / TRANSMEMBRANE / CF(0) / MEMBRANE / TRANSPORT / C-RING ROTOR / HYDRONIUM ION / ION BINDING POCKET / HYDROGEN ION TRANSPORT
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / lipid binding / plasma membrane
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
dodecyl 2-(trimethylammonio)ethyl phosphate / ATP synthase subunit c
Similarity search - Component
Biological speciesBACILLUS PSEUDOFIRMUS OF4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPreiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
CitationJournal: Plos Biol. / Year: 2010
Title: A New Type of Proton Coordination in an F(1)F(O)- ATP Synthase Rotor Ring.
Authors: Preiss, L. / Yildiz, O. / Hicks, D.B. / Krulwich, T.A. / Meier, T.
History
DepositionJan 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 SUBUNIT C
B: ATP SYNTHASE SUBUNIT C
C: ATP SYNTHASE SUBUNIT C
D: ATP SYNTHASE SUBUNIT C
E: ATP SYNTHASE SUBUNIT C
F: ATP SYNTHASE SUBUNIT C
G: ATP SYNTHASE SUBUNIT C
H: ATP SYNTHASE SUBUNIT C
I: ATP SYNTHASE SUBUNIT C
J: ATP SYNTHASE SUBUNIT C
K: ATP SYNTHASE SUBUNIT C
L: ATP SYNTHASE SUBUNIT C
M: ATP SYNTHASE SUBUNIT C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,63636
Polymers90,83713
Non-polymers4,79923
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49870 Å2
ΔGint-577.1 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.180, 97.340, 121.240
Angle α, β, γ (deg.)90.00, 104.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ATP SYNTHASE SUBUNIT C / / ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING ...ATP SYNTHASE F(0) SECTOR SUBUNIT C / F-TYPE ATPASE SUBUNIT C / F-ATPASE SUBUNIT C / LIPID-BINDING PROTEIN / OF4 C RING


Mass: 6987.461 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) BACILLUS PSEUDOFIRMUS OF4 (bacteria) / References: UniProt: P22483
#2: Chemical
ChemComp-DPV / dodecyl 2-(trimethylammonio)ethyl phosphate / dodecylphosphocholine


Mass: 351.462 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C17H38NO4P
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 4.47 Å3/Da / Density % sol: 72.27 % / Description: NONE
Crystal growpH: 4.3 / Details: pH 4.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→44.951 Å / Num. obs: 57111 / % possible obs: 98.8 % / Observed criterion σ(I): 1.6 / Redundancy: 3.6 % / Biso Wilson estimate: 46.04 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.62 / % possible all: 92.8

-
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: 2.5→44.951 Å / SU ML: 0.33 / σ(F): 1.99 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2345 2854 5 %
Rwork0.1876 --
obs0.1899 57052 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.456 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4674 Å2-0 Å21.7453 Å2
2--0.0696 Å2-0 Å2
3---6.3978 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.951 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6372 0 309 84 6765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076721
X-RAY DIFFRACTIONf_angle_d0.9329126
X-RAY DIFFRACTIONf_dihedral_angle_d19.5772444
X-RAY DIFFRACTIONf_chiral_restr0.0531235
X-RAY DIFFRACTIONf_plane_restr0.0061053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.33471220.30232333X-RAY DIFFRACTION87
2.5431-2.58930.25621390.25042649X-RAY DIFFRACTION97
2.5893-2.63910.28561450.23152755X-RAY DIFFRACTION99
2.6391-2.6930.30371410.22552672X-RAY DIFFRACTION99
2.693-2.75160.27161430.2122724X-RAY DIFFRACTION99
2.7516-2.81560.22551430.18492712X-RAY DIFFRACTION99
2.8156-2.8860.23741430.1672704X-RAY DIFFRACTION99
2.886-2.9640.24671450.1562759X-RAY DIFFRACTION99
2.964-3.05120.19331440.16212727X-RAY DIFFRACTION100
3.0512-3.14960.22531420.15862713X-RAY DIFFRACTION100
3.1496-3.26220.24421430.16362715X-RAY DIFFRACTION99
3.2622-3.39270.21721450.15292747X-RAY DIFFRACTION100
3.3927-3.54710.21051430.15562728X-RAY DIFFRACTION100
3.5471-3.7340.19911440.16212735X-RAY DIFFRACTION100
3.734-3.96780.23371440.16012736X-RAY DIFFRACTION100
3.9678-4.2740.19331450.16252744X-RAY DIFFRACTION100
4.274-4.70370.16641450.1452757X-RAY DIFFRACTION100
4.7037-5.38330.22631450.19112753X-RAY DIFFRACTION100
5.3833-6.77870.26961460.23532777X-RAY DIFFRACTION100
6.7787-44.95870.28171470.23242758X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 27.9329 Å / Origin y: -17.0887 Å / Origin z: 32.3585 Å
111213212223313233
T0.1582 Å2-0.0047 Å20.1521 Å2-0.1676 Å2-0.0244 Å2--0.1299 Å2
L1.3673 °20.0315 °20.0439 °2-1.1481 °2-0.1096 °2--0.7771 °2
S-0.0372 Å °0.2185 Å °-0.0904 Å °-0.0834 Å °0.021 Å °-0.0937 Å °-0.0112 Å °-0.0098 Å °0.0115 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