[English] 日本語
Yorodumi
- PDB-1fft: The structure of ubiquinol oxidase from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fft
TitleThe structure of ubiquinol oxidase from Escherichia coli
Components(UBIQUINOL OXIDASE) x 4
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / CYTOCHROME OXIDASE / MEMBRANE PROTEIN
Function / homology
Function and homology information


cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / ubiquinone binding / electron transport coupled proton transport / cytochrome-c oxidase activity / proton transmembrane transporter activity ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / ubiquinone binding / electron transport coupled proton transport / cytochrome-c oxidase activity / proton transmembrane transporter activity / ATP synthesis coupled electron transport / respirasome / aerobic respiration / respiratory electron transport chain / electron transfer activity / copper ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / COX aromatic rich motif / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A ...Cytochrome o ubiquinol oxidase, subunit III / Cytochrome o ubiquinol oxidase, subunit I / Ubiquinol oxidase subunit III domain / COX aromatic rich motif / COX Aromatic Rich Motif / Cytochrome o ubiquinol oxidase subunit II / Ubiquinol oxidase subunit 2, cupredoxin domain / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase subunit III / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / HEME O / Cytochrome bo(3) ubiquinol oxidase subunit 1 / Cytochrome bo(3) ubiquinol oxidase subunit 2 / Cytochrome bo(3) ubiquinol oxidase subunit 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsAbramson, J. / Riistama, S. / Larsson, G. / Jasaitis, A. / Svensson-Ek, M. / Puustinen, A. / Iwata, S. / Wikstrom, M.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The structure of the ubiquinol oxidase from Escherichia coli and its ubiquinone binding site.
Authors: Abramson, J. / Riistama, S. / Larsson, G. / Jasaitis, A. / Svensson-Ek, M. / Laakkonen, L. / Puustinen, A. / Iwata, S. / Wikstrom, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Purification, crystallization and preliminary crystallographic studies on an integral membrane protein, cytochrome bo3 ubiquinol oxidase from Escherichia coli.
Authors: Abramson, J. / Larsson, G. / Byrne, B. / Puustinen, A. / Garcia-Horsman, A. / Iwata, S.
History
DepositionJul 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Jun 17, 2020Group: Data collection / Database references / Category: pdbx_validate_chiral / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.pdbx_dist_value / _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: UBIQUINOL OXIDASE
B: UBIQUINOL OXIDASE
C: UBIQUINOL OXIDASE
D: UBIQUINOL OXIDASE
F: UBIQUINOL OXIDASE
G: UBIQUINOL OXIDASE
H: UBIQUINOL OXIDASE
I: UBIQUINOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,65514
Polymers282,6178
Non-polymers3,0386
Water0
1
A: UBIQUINOL OXIDASE
B: UBIQUINOL OXIDASE
C: UBIQUINOL OXIDASE
D: UBIQUINOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8287
Polymers141,3094
Non-polymers1,5193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15290 Å2
ΔGint-197 kcal/mol
Surface area43470 Å2
MethodPISA
2
F: UBIQUINOL OXIDASE
G: UBIQUINOL OXIDASE
H: UBIQUINOL OXIDASE
I: UBIQUINOL OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8287
Polymers141,3094
Non-polymers1,5193
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-203 kcal/mol
Surface area42930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.100, 372.500, 232.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a monomer composed of chains A, B, C, D, and E.

-
Components

-
Protein , 4 types, 8 molecules AFBGCHDI

#1: Protein UBIQUINOL OXIDASE /


Mass: 74424.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABI8, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#2: Protein UBIQUINOL OXIDASE /


Mass: 34947.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABJ1, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#3: Protein UBIQUINOL OXIDASE /


Mass: 22642.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ABJ3, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor
#4: Protein UBIQUINOL OXIDASE /


Mass: 9294.448 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PBR322 / Production host: Escherichia coli (E. coli)
References: Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor

-
Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical ChemComp-HEO / HEME O / Heme O


Mass: 838.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H58FeN4O5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 9-10% PEG 1500, 100 mM NaCl, 100 mM MgCl2, 5% ethanol & 100 mM HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
21 %OG1drop
320 mg/mlprotein1drop
49-10 %(w/v)PEG15001reservoir
5100 mM1reservoirNaCl
6100 mM1reservoirMgCl2
75 %(v/v)ethanol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.95
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 11, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 44359 / % possible obs: 87 % / Observed criterion σ(I): -0.2 / Redundancy: 3.2 % / Biso Wilson estimate: 37.1 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.86
Reflection shellResolution: 3.5→3.63 Å / Rmerge(I) obs: 0.399 / Num. unique all: 3956 / % possible all: 78.5
Reflection shell
*PLUS
% possible obs: 78.5 % / Num. unique obs: 3956 / Mean I/σ(I) obs: 1.47

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementResolution: 3.5→40 Å / Details: This is a non-refined structure.
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15930 0 206 0 16136
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 40 Å / Rfactor obs: 0.446
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.482

+
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