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- PDB-6ci0: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -

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Basic information

Entry
Database: PDB / ID: 6ci0
TitleCatalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with E101A (II) mutation
Components(Cytochrome c oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Oxidase / electron transfer / proton pumping
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; Chain A / Cytochrome c oxidase-like, subunit I domain / 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 ...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 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 / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, J. / Hiser, C. / Ferguson-Miller, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM26916 United States
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain.
Authors: Hiser, C. / Liu, J. / Ferguson-Miller, S.
History
DepositionFeb 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 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 / 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)187,62948
Polymers176,3744
Non-polymers11,25544
Water4,360242
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,64932
Polymers88,1872
Non-polymers7,46230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21660 Å2
ΔGint-143 kcal/mol
Surface area26900 Å2
MethodPISA
2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98016
Polymers88,1872
Non-polymers3,79314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14080 Å2
ΔGint-142 kcal/mol
Surface area26100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.916, 130.969, 177.788
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 30 through 85 or (resid 86...
21(chain D and (resid 30 through 97 or resid 99 through 285))
12(chain A and (resid 20 through 21 or (resid 22...
22(chain C and (resid 20 through 222 or (resid 223...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUGLUGLU(chain B and (resid 30 through 85 or (resid 86...BB30 - 852 - 57
121LYSLYSARGARG(chain B and (resid 30 through 85 or (resid 86...BB86 - 8758 - 59
131LEULEUHISHIS(chain B and (resid 30 through 85 or (resid 86...BB30 - 2852 - 257
141LEULEUHISHIS(chain B and (resid 30 through 85 or (resid 86...BB30 - 2852 - 257
151LEULEUHISHIS(chain B and (resid 30 through 85 or (resid 86...BB30 - 2852 - 257
161LEULEUHISHIS(chain B and (resid 30 through 85 or (resid 86...BB30 - 2852 - 257
211LEULEUASNASN(chain D and (resid 30 through 97 or resid 99 through 285))DD30 - 972 - 69
221PROPROHISHIS(chain D and (resid 30 through 97 or resid 99 through 285))DD99 - 28571 - 257
112TRPTRPPHEPHE(chain A and (resid 20 through 21 or (resid 22...AA20 - 214 - 5
122METMETMETMET(chain A and (resid 20 through 21 or (resid 22...AA226
132PHEPHEPHEPHE(chain A and (resid 20 through 21 or (resid 22...AA17 - 5511 - 535
142PHEPHEPHEPHE(chain A and (resid 20 through 21 or (resid 22...AA17 - 5511 - 535
152PHEPHEPHEPHE(chain A and (resid 20 through 21 or (resid 22...AA17 - 5511 - 535
162PHEPHEPHEPHE(chain A and (resid 20 through 21 or (resid 22...AA17 - 5511 - 535
212TRPTRPMETMET(chain C and (resid 20 through 222 or (resid 223...CC20 - 2224 - 206
222HISHISLYSLYS(chain C and (resid 20 through 222 or (resid 223...CC223 - 224207 - 208
232TRPTRPTHRTHR(chain C and (resid 20 through 222 or (resid 223...CC20 - 5504 - 534
242TRPTRPTHRTHR(chain C and (resid 20 through 222 or (resid 223...CC20 - 5504 - 534
252TRPTRPTHRTHR(chain C and (resid 20 through 222 or (resid 223...CC20 - 5504 - 534
262TRPTRPTHRTHR(chain C and (resid 20 through 222 or (resid 223...CC20 - 5504 - 534

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 / / Cytochrome aa3 subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 59540.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaD / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: P33517, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome aa3 subunit 2 / Cytochrome c oxidase polypeptide II / Oxidase aa(3) subunit 2


Mass: 28646.676 Da / Num. of mol.: 2 / Mutation: E101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaC, coxII, ctaB / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q03736, cytochrome-c oxidase

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Sugars , 2 types, 9 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.: 3
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
#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 10 types, 277 molecules

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


Mass: 184.361 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C13H28
#6: Chemical
ChemComp-CU / COPPER (II) ION / Copper


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C49H56FeN4O6
#10: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#11: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H16O3
#12: 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
#13: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 24% PEG400, MES 100mM, pH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.21 Å / Num. obs: 129037 / % possible obs: 99.6 % / Redundancy: 7.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.076 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 7.5 % / Rmerge(I) obs: 1.277 / Num. unique obs: 12726 / CC1/2: 0.707 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSM

2gsm


Resolution: 2.4→42.089 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 3458 3.04 %
Rwork0.1987 110440 -
obs0.1998 113898 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 142.16 Å2 / Biso mean: 66.4561 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.4→42.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12262 0 726 242 13230
Biso mean--74.06 55.55 -
Num. residues----1580
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B3196X-RAY DIFFRACTION3.1TORSIONAL
12D3196X-RAY DIFFRACTION3.1TORSIONAL
21A1534X-RAY DIFFRACTION3.1TORSIONAL
22C1534X-RAY DIFFRACTION3.1TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.43290.3031410.275743624503100
2.4329-2.46760.27881190.268344254544100
2.4676-2.50450.28391340.25843624496100
2.5045-2.54360.31451460.255543904536100
2.5436-2.58530.30351300.247943934523100
2.5853-2.62990.33481330.236443674500100
2.6299-2.67770.26871400.230644104550100
2.6777-2.72920.29981590.223343744533100
2.7292-2.78490.26531520.224644004552100
2.7849-2.84540.28081500.219443624512100
2.8454-2.91160.28491450.212144044549100
2.9116-2.98440.26441100.20744364546100
2.9844-3.0650.23521260.210144314557100
3.065-3.15520.22941300.197443684498100
3.1552-3.2570.25451470.200744124559100
3.257-3.37340.25021320.200244494581100
3.3734-3.50840.24191370.202644184555100
3.5084-3.66790.23521340.199944304564100
3.6679-3.86120.22081380.193444454583100
3.8612-4.10290.20511290.186444624591100
4.1029-4.41940.21281370.176944504587100
4.4194-4.86360.20041570.16744604617100
4.8636-5.5660.21221540.184744864640100
5.566-7.00730.20841320.193345644696100
7.0073-42.09570.23011460.24380452693

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