[English] 日本語
Yorodumi
- PDB-6pw1: Cytochrome c Oxidase delta 16 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pw1
TitleCytochrome c Oxidase delta 16
Components(Cytochrome c oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Oxidase / proton pumping / electron transfer / MEMBRANE PROTEIN
Function / homology
Function and homology information


respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / Cytochrome C oxidase subunit II, transmembrane domain / 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 / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / : / COPPER (II) ION / HEME-A / (2S,3R)-heptane-1,2,3-triol / TRIDECANE / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, J. / Ferguson-Miller, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry.
Authors: Berg, J. / Liu, J. / Svahn, E. / Ferguson-Miller, S. / Brzezinski, P.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_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.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / pdbx_entry_details ...chem_comp_atom / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _chem_comp_atom.pdbx_stereo_config / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,11447
Polymers176,1644
Non-polymers10,95143
Water8,971498
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46931
Polymers88,0822
Non-polymers7,38729
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20920 Å2
ΔGint-152 kcal/mol
Surface area26670 Å2
MethodPISA
2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,64516
Polymers88,0822
Non-polymers3,56314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14660 Å2
ΔGint-153 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.315, 130.000, 177.539
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain 'A' and (resid 18 through 68 or (resid 69...AA18 - 5502 - 534
21THRTHRTHRTHR(chain 'C' and (resid 18 through 19 or (resid 20...CC18 - 5502 - 534
12LEULEUHISHIS(chain 'B' and (resid 30 through 86 or (resid 87...BB30 - 2852 - 257
22LEULEUHISHISchain 'D'DD30 - 2852 - 257

NCS ensembles :
ID
1
2

-
Components

-
Cytochrome c oxidase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Cytochrome c oxidase subunit 1


Mass: 59393.180 Da / Num. of mol.: 2 / Mutation: Last 16 residues of C-terminus were deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxI, RSP_1877 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J5A7, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2


Mass: 28688.711 Da / Num. of mol.: 2 / Mutation: 6 histidine tag were added at the C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxII, RSP_1826 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J5G0, cytochrome-c oxidase

-
Sugars , 2 types, 8 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#5: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

-
Non-polymers , 9 types, 533 molecules

#4: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C13H28
#6: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Mg
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#11: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#12: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.98 Å3/Da / Density % sol: 69.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM MES, pH 6.3, 26-30 % PEG-400 and 2.5 % heptanetriol, 16mM MgCl2, 0.65 mM CdCl2 and 0.013 % Dodecyl maltoside

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 165884 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.024 / Net I/σ(I): 12.2 / Num. measured all: 1213258
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.185.50.599158811.034196.5
2.18-2.2670.473164521.067199.9
2.26-2.377.50.343165591.0591100
2.37-2.497.60.254165321.0451100
2.49-2.657.60.185165471.0311100
2.65-2.857.60.129165831.0441100
2.85-3.147.60.086166261.0321100
3.14-3.597.60.056166961.0131100
3.59-4.527.60.049168020.9691100
4.52-507.30.031172060.958199.5

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSM

2gsm


Resolution: 2.1→34.96 Å / SU ML: 0.1648 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9642
RfactorNum. reflection% reflection
Rfree0.2036 5009 3.03 %
Rwork0.1797 --
obs0.1804 165482 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 40.06 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12343 0 685 498 13526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007613463
X-RAY DIFFRACTIONf_angle_d1.308218379
X-RAY DIFFRACTIONf_chiral_restr0.07692010
X-RAY DIFFRACTIONf_plane_restr0.00692214
X-RAY DIFFRACTIONf_dihedral_angle_d8.56297476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.26861560.26284925X-RAY DIFFRACTION93.06
2.12-2.150.29191910.24435141X-RAY DIFFRACTION97.28
2.15-2.170.27371660.24255312X-RAY DIFFRACTION98.97
2.17-2.20.25631640.22385311X-RAY DIFFRACTION99.73
2.2-2.230.25621780.21895297X-RAY DIFFRACTION99.93
2.23-2.260.25881720.2085261X-RAY DIFFRACTION99.78
2.26-2.290.21351640.19975357X-RAY DIFFRACTION99.95
2.29-2.330.2181770.1885321X-RAY DIFFRACTION99.95
2.33-2.370.20011800.18475337X-RAY DIFFRACTION99.89
2.37-2.40.2021640.18015310X-RAY DIFFRACTION99.95
2.4-2.450.20691450.18035322X-RAY DIFFRACTION99.93
2.45-2.490.20861660.17675348X-RAY DIFFRACTION99.87
2.49-2.540.21571580.17995342X-RAY DIFFRACTION99.91
2.54-2.590.19651720.17775314X-RAY DIFFRACTION99.91
2.59-2.650.21281750.17625367X-RAY DIFFRACTION99.95
2.65-2.710.18151580.17455356X-RAY DIFFRACTION99.93
2.71-2.770.21031580.17145352X-RAY DIFFRACTION99.87
2.77-2.850.19011580.17475345X-RAY DIFFRACTION99.91
2.85-2.930.2121560.16895397X-RAY DIFFRACTION99.95
2.93-3.030.1941620.17565353X-RAY DIFFRACTION99.91
3.03-3.140.20761770.17885337X-RAY DIFFRACTION99.98
3.14-3.260.20421800.1725365X-RAY DIFFRACTION99.96
3.26-3.410.20291540.17545412X-RAY DIFFRACTION99.96
3.41-3.590.20561630.1795374X-RAY DIFFRACTION99.93
3.59-3.810.20491730.18145403X-RAY DIFFRACTION99.98
3.81-4.110.17811620.17075426X-RAY DIFFRACTION100
4.11-4.520.19841660.15965446X-RAY DIFFRACTION99.98
4.52-5.170.17311840.16265448X-RAY DIFFRACTION100
5.17-6.510.19811760.17815526X-RAY DIFFRACTION100
6.51-34.960.20741540.19175668X-RAY DIFFRACTION98.8

+
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