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- PDB-5weh: Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state -

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Basic information

Entry
Database: PDB / ID: 5weh
TitleCytochrome c oxidase from Rhodobacter sphaeroides in the reduced state
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Aa3-type cytochrome c oxidase subunit IV
  • Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
KeywordsOXIDOREDUCTASE / oxidase / Complex IV / reduced
Function / homology
Function and homology information


aerobic electron transport chain / 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 ...aerobic electron transport chain / 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
Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / 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 domain ...Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit IV, bacterial aa3 type / Bacterial aa3 type cytochrome c oxidase subunit IV superfamily / Bacterial aa3 type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / 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 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 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 / 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. / Helix Hairpins - #70 / Cupredoxins - blue copper proteins / Cupredoxin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1,2-Distearoyl-sn-glycerophosphoethanolamine / COPPER (I) ION / HEME-A / Cytochrome c oxidase subunit 1 / cytochrome-c oxidase / Cytochrome c oxidase subunit 2 / Aa3-type cytochrome c oxidase subunit IV
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsLiu, J. / Ferguson-Miller, F. / Ling, Q. / Hiser, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM57323 United States
CitationJournal: Biochem. Soc. Trans. / Year: 2017
Title: Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity.
Authors: Liu, J. / Hiser, C. / Ferguson-Miller, S.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 30, 2021Group: Advisory / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 2.0Jul 7, 2021Group: 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 / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _atom_site.label_comp_id / _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.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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
G: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
D: Aa3-type cytochrome c oxidase subunit IV
H: Cytochrome c oxidase subunit 2
I: Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
J: Aa3-type cytochrome c oxidase subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,75436
Polymers256,0728
Non-polymers13,68228
Water181
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
D: Aa3-type cytochrome c oxidase subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,24817
Polymers128,0364
Non-polymers6,21213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27810 Å2
ΔGint-289 kcal/mol
Surface area36710 Å2
MethodPISA
2
G: Cytochrome c oxidase subunit 1
H: Cytochrome c oxidase subunit 2
I: Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)
J: Aa3-type cytochrome c oxidase subunit IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,50619
Polymers128,0364
Non-polymers7,47015
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27330 Å2
ΔGint-301 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)339.221, 339.221, 89.199
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 3 through 41 or (resid 42...
21(chain I and ((resid 3 through 5 and (name N...
12(chain B and (resid 30 through 125 or (resid 126...
22(chain H and ((resid 30 through 31 and (name N...
13(chain A and (resid 14 through 77 or (resid 78...
23(chain G and (resid 14 through 15 or (resid 16...
14(chain D and (resid 12 through 47 or (resid 48...
24(chain J and (resid 12 through 15 or (resid 16...

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
111HISHISPROPRO(chain C and (resid 3 through 41 or (resid 42...CD3 - 413 - 41
121TRPTRPTRPTRP(chain C and (resid 3 through 41 or (resid 42...CD4242
131HISHISGLNGLN(chain C and (resid 3 through 41 or (resid 42...CD3 - 2663 - 266
141HISHISGLNGLN(chain C and (resid 3 through 41 or (resid 42...CD3 - 2663 - 266
151HISHISGLNGLN(chain C and (resid 3 through 41 or (resid 42...CD3 - 2663 - 266
161HISHISGLNGLN(chain C and (resid 3 through 41 or (resid 42...CD3 - 2663 - 266
211HISHISLYSLYS(chain I and ((resid 3 through 5 and (name N...IG3 - 53 - 5
221HISHISGLNGLN(chain I and ((resid 3 through 5 and (name N...IG3 - 2663 - 266
231HISHISGLNGLN(chain I and ((resid 3 through 5 and (name N...IG3 - 2663 - 266
241HISHISGLNGLN(chain I and ((resid 3 through 5 and (name N...IG3 - 2663 - 266
251HISHISGLNGLN(chain I and ((resid 3 through 5 and (name N...IG3 - 2663 - 266
112LEULEUASNASN(chain B and (resid 30 through 125 or (resid 126...BC30 - 1255 - 100
122GLNGLNGLNGLN(chain B and (resid 30 through 125 or (resid 126...BC126101
132LEULEUHISHIS(chain B and (resid 30 through 125 or (resid 126...BC30 - 2835 - 258
142LEULEUHISHIS(chain B and (resid 30 through 125 or (resid 126...BC30 - 2835 - 258
152LEULEUHISHIS(chain B and (resid 30 through 125 or (resid 126...BC30 - 2835 - 258
162LEULEUHISHIS(chain B and (resid 30 through 125 or (resid 126...BC30 - 2835 - 258
212LEULEUGLUGLU(chain H and ((resid 30 through 31 and (name N...HF30 - 315 - 6
222LEULEUHISHIS(chain H and ((resid 30 through 31 and (name N...HF30 - 2825 - 257
232LEULEUHISHIS(chain H and ((resid 30 through 31 and (name N...HF30 - 2825 - 257
242LEULEUHISHIS(chain H and ((resid 30 through 31 and (name N...HF30 - 2825 - 257
252LEULEUHISHIS(chain H and ((resid 30 through 31 and (name N...HF30 - 2825 - 257
113ARGARGPHEPHE(chain A and (resid 14 through 77 or (resid 78...AA14 - 7714 - 77
123GLNGLNGLNGLN(chain A and (resid 14 through 77 or (resid 78...AA7878
133ARGARGTRPTRP(chain A and (resid 14 through 77 or (resid 78...AA14 - 56014 - 560
143ARGARGTRPTRP(chain A and (resid 14 through 77 or (resid 78...AA14 - 56014 - 560
153ARGARGTRPTRP(chain A and (resid 14 through 77 or (resid 78...AA14 - 56014 - 560
163ARGARGTRPTRP(chain A and (resid 14 through 77 or (resid 78...AA14 - 56014 - 560
213ARGARGGLYGLY(chain G and (resid 14 through 15 or (resid 16...GB14 - 1514 - 15
223PHEPHEPHEPHE(chain G and (resid 14 through 15 or (resid 16...GB1616
233ARGARGTRPTRP(chain G and (resid 14 through 15 or (resid 16...GB14 - 56014 - 560
243ARGARGTRPTRP(chain G and (resid 14 through 15 or (resid 16...GB14 - 56014 - 560
253ARGARGTRPTRP(chain G and (resid 14 through 15 or (resid 16...GB14 - 56014 - 560
263ARGARGTRPTRP(chain G and (resid 14 through 15 or (resid 16...GB14 - 56014 - 560
114VALVALALAALA(chain D and (resid 12 through 47 or (resid 48...DE12 - 4711 - 46
124LEULEUALAALA(chain D and (resid 12 through 47 or (resid 48...DE48 - 4947 - 48
134VALVALALAALA(chain D and (resid 12 through 47 or (resid 48...DE12 - 5111 - 50
144VALVALALAALA(chain D and (resid 12 through 47 or (resid 48...DE12 - 5111 - 50
154VALVALALAALA(chain D and (resid 12 through 47 or (resid 48...DE12 - 5111 - 50
164VALVALALAALA(chain D and (resid 12 through 47 or (resid 48...DE12 - 5111 - 50
214VALVALSERSER(chain J and (resid 12 through 15 or (resid 16...JH12 - 1511 - 14
224METMETMETMET(chain J and (resid 12 through 15 or (resid 16...JH1615
234GLYGLYALAALA(chain J and (resid 12 through 15 or (resid 16...JH10 - 519 - 50
244GLYGLYALAALA(chain J and (resid 12 through 15 or (resid 16...JH10 - 519 - 50
254GLYGLYALAALA(chain J and (resid 12 through 15 or (resid 16...JH10 - 519 - 50
264GLYGLYALAALA(chain J and (resid 12 through 15 or (resid 16...JH10 - 519 - 50

NCS ensembles :
ID
1
2
3
4

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Components

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules AGBH

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome aa3 subunit 1 / Cytochrome c oxidase polypeptide I


Mass: 63195.383 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 (bacteria) / Strain (production host): 169 / 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: 29365.385 Da / Num. of mol.: 2 / Fragment: UNP residues 26-281
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaC, coxII, ctaB / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 169 / References: UniProt: Q03736, cytochrome-c oxidase

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Protein / Protein/peptide / Sugars , 3 types, 7 molecules CIDJ

#10: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Protein Cytochrome c oxidase polypeptide III (Cytochrome AA3 subunit 3)


Mass: 30197.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 169 / References: UniProt: P84153, cytochrome-c oxidase
#4: Protein/peptide Aa3-type cytochrome c oxidase subunit IV


Mass: 5278.071 Da / Num. of mol.: 2 / Fragment: UNP residues 12-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: coxIV / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): 169 / References: UniProt: Q8KRK5

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Non-polymers , 6 types, 26 molecules

#5: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#6: Chemical
ChemComp-CU1 / COPPER (I) ION


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-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.99 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: PEG400 23%, MES pH 5.9, Sodium Chloride 50 mM,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.45→30 Å / Num. obs: 48530 / % possible obs: 94.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 106.5 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.8
Reflection shellResolution: 3.45→3.57 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.37 / Num. unique obs: 3998 / % possible all: 77.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Blu-Icedata collection
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M56

1m56


Resolution: 3.45→28.45 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 33.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1371 2.96 %RANDOM
Rwork0.2232 44957 --
obs0.2244 46328 92.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.06 Å2 / Biso mean: 116.6919 Å2 / Biso min: 58.33 Å2
Refinement stepCycle: final / Resolution: 3.45→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17163 0 745 1 17909
Biso mean--115.59 96.01 -
Num. residues----2211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00618543
X-RAY DIFFRACTIONf_angle_d1.68325339
X-RAY DIFFRACTIONf_chiral_restr0.0762717
X-RAY DIFFRACTIONf_plane_restr0.0063086
X-RAY DIFFRACTIONf_dihedral_angle_d8.95810262
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C2292X-RAY DIFFRACTION8.32TORSIONAL
12I2292X-RAY DIFFRACTION8.32TORSIONAL
21B2228X-RAY DIFFRACTION8.32TORSIONAL
22H2228X-RAY DIFFRACTION8.32TORSIONAL
31A4920X-RAY DIFFRACTION8.32TORSIONAL
32G4920X-RAY DIFFRACTION8.32TORSIONAL
41D308X-RAY DIFFRACTION8.32TORSIONAL
42J308X-RAY DIFFRACTION8.32TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.4501-3.57320.38881220.32653746386876
3.5732-3.7160.38011150.31124021413683
3.716-3.88470.40351430.31614354449789
3.8847-4.08890.30911270.27554612473995
4.0889-4.34430.30571270.25494601472895
4.3443-4.67830.26661490.22654704485396
4.6783-5.14660.23931520.21174702485497
5.1466-5.88560.26751570.20914801495899
5.8856-7.39370.24211240.196248995023100
7.3937-28.45140.19951550.17884517467293

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