[English] 日本語
Yorodumi
- PDB-4bem: Crystal structure of the F-type ATP synthase c-ring from Acetobac... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bem
TitleCrystal structure of the F-type ATP synthase c-ring from Acetobacterium woodii.
Components
  • F1FO ATPASE C1 SUBUNIT
  • F1FO ATPASE C2 SUBUNIT
KeywordsHYDROLASE
Function / homology
Function and homology information


proton-transporting ATP synthase complex, coupling factor F(o) / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / hydrolase activity / lipid binding / plasma membrane
Similarity search - Function
lithium bound rotor ring of v- atpase / 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 ...lithium bound rotor ring of v- atpase / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / ATP synthase subunit c / ATP synthase subunit c / ATP synthase subunit c / ATP synthase subunit c
Similarity search - Component
Biological speciesACETOBACTERIUM WOODII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMatthies, D. / Meier, T. / Yildiz, O.
CitationJournal: Nat.Commun. / Year: 2014
Title: High-Resolution Structure and Mechanism of an F/V-Hybrid Rotor Ring in a Na+-Coupled ATP Synthase
Authors: Matthies, D. / Zhou, W. / Klyszejko, A.L. / Anselmi, C. / Yildiz, O. / Brandt, K. / Muller, V. / Faraldo-Gomez, J.D. / Meier, T.
History
DepositionMar 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F1FO ATPASE C2 SUBUNIT
B: F1FO ATPASE C2 SUBUNIT
C: F1FO ATPASE C2 SUBUNIT
D: F1FO ATPASE C2 SUBUNIT
E: F1FO ATPASE C2 SUBUNIT
F: F1FO ATPASE C2 SUBUNIT
G: F1FO ATPASE C2 SUBUNIT
H: F1FO ATPASE C2 SUBUNIT
I: F1FO ATPASE C2 SUBUNIT
J: F1FO ATPASE C1 SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,89646
Polymers92,33610
Non-polymers6,56036
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46220 Å2
ΔGint-493.4 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.170, 121.170, 150.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 2 types, 10 molecules ABCDEFGHIJ

#1: Protein
F1FO ATPASE C2 SUBUNIT / F1FO ATPASE C3 SUBUNIT


Mass: 8213.572 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) ACETOBACTERIUM WOODII (bacteria) / Strain: DSM 1030 / References: UniProt: Q59166, UniProt: H6LFT2*PLUS
#2: Protein F1FO ATPASE C1 SUBUNIT


Mass: 18413.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACETOBACTERIUM WOODII (bacteria) / Strain: DSM 1030 / References: UniProt: Q9RMB5, UniProt: H6LFT0*PLUS

-
Sugars , 1 types, 19 molecules

#4: Sugar
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM

-
Non-polymers , 6 types, 181 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#8: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.99 Å3/Da / Density % sol: 0.6 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 65395 / % possible obs: 99.3 % / Observed criterion σ(I): 1.6 / Redundancy: 16.6 % / Biso Wilson estimate: 37.21 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.08
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 16.5 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 1.58 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCE

1yce


Resolution: 2.1→47.2 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 20.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 3270 5 %
Rwork0.1818 --
obs0.1837 65363 99.22 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 415 164 7053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076964
X-RAY DIFFRACTIONf_angle_d0.9369361
X-RAY DIFFRACTIONf_dihedral_angle_d16.4222578
X-RAY DIFFRACTIONf_chiral_restr0.0591140
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0999-2.13130.3251390.27762643X-RAY DIFFRACTION99
2.1313-2.16460.31151390.25772652X-RAY DIFFRACTION99
2.1646-2.20010.29291390.23762640X-RAY DIFFRACTION99
2.2001-2.2380.27971400.2212651X-RAY DIFFRACTION99
2.238-2.27870.23381400.21142660X-RAY DIFFRACTION99
2.2787-2.32250.24731390.22633X-RAY DIFFRACTION99
2.3225-2.36990.26771400.19472665X-RAY DIFFRACTION99
2.3699-2.42150.22941410.18732679X-RAY DIFFRACTION99
2.4215-2.47780.22431400.16572673X-RAY DIFFRACTION99
2.4778-2.53980.22771400.16472647X-RAY DIFFRACTION99
2.5398-2.60840.1921400.14812671X-RAY DIFFRACTION99
2.6084-2.68520.22381430.16592708X-RAY DIFFRACTION99
2.6852-2.77180.18611400.15252668X-RAY DIFFRACTION99
2.7718-2.87090.17941420.13892686X-RAY DIFFRACTION99
2.8709-2.98580.17531420.14562695X-RAY DIFFRACTION99
2.9858-3.12170.19141430.16052721X-RAY DIFFRACTION100
3.1217-3.28620.20261420.15952701X-RAY DIFFRACTION99
3.2862-3.49210.20331430.15992724X-RAY DIFFRACTION100
3.4921-3.76160.21491440.16292729X-RAY DIFFRACTION100
3.7616-4.13990.19921450.15562751X-RAY DIFFRACTION100
4.1399-4.73850.22451460.16982773X-RAY DIFFRACTION100
4.7385-5.96810.2081480.21532803X-RAY DIFFRACTION100
5.9681-47.21150.24941550.22772920X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.4461 Å / Origin y: 23.5329 Å / Origin z: 36.7719 Å
111213212223313233
T0.2967 Å2-0.0406 Å20.0169 Å2-0.3221 Å20.0268 Å2--0.2933 Å2
L2.3368 °21.1926 °2-0.3656 °2-2.1647 °2-0.4106 °2--1.2201 °2
S0.1477 Å °-0.0972 Å °0.3247 Å °0.2862 Å °-0.1489 Å °0.0644 Å °-0.153 Å °0.2203 Å °0.0029 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