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- PDB-1fft: The structure of ubiquinol oxidase from Escherichia coli -

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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


oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / 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 / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity ...oxidoreduction-driven active transmembrane transporter activity / cytochrome o ubiquinol oxidase complex / 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 / cytochrome-c oxidase activity / ubiquinone binding / electron transport coupled proton transport / proton transmembrane transporter activity / ATP synthesis coupled electron transport / 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 II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / 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/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 / Cupredoxin / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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.

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Components

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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

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Non-polymers , 3 types, 6 molecules

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


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


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


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

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Experimental details

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Experiment

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

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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

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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

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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

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