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- PDB-6pw1: Cytochrome c Oxidase delta 16 -

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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 / respirasome / 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 subunit I domain / Cytochrome c oxidase, subunit II / 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 / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / 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 / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Helix Hairpins / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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

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Non-polymers , 9 types, 533 molecules

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


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


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 / Tris


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 / Water


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

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Details

Has ligand of interestY

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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: 3.98 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

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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

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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

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