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- PDB-9gdf: Chloride bound structure of oxidized ba3-type cytochrome c oxidas... -

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Basic information

Entry
Database: PDB / ID: 9gdf
TitleChloride bound structure of oxidized ba3-type cytochrome c oxidase confirmed by single-wavelength anomalous diffraction
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsOXIDOREDUCTASE / Anomalous diffraction / cytochrome c oxidase / high salt / low pH
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / copper ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. ...Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / 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 II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsKabbinale, A. / Johannesson, J. / Finke, D.
Funding supportEuropean Union, Sweden, 4items
OrganizationGrant numberCountry
European Research Council (ERC)789030European Union
European Research Council (ERC)963936European Union
Swedish Research Council2021-05662 Sweden
Swedish Research Council2015-00560 Sweden
CitationJournal: To Be Published
Title: Structural changes in cytochrome c oxidase following the reduction of dioxygen to water
Authors: Zoric, D. / Johannesson, J. / Kabbinale, A. / Sandelin, E. / Vallejos, A. / Ghosh, S. / Dahl, P. / Ronnholm, J. / Bjelcic, M. / Finke, A. / Bostedt, C. / Bacellar Cases da Silveira, C. / ...Authors: Zoric, D. / Johannesson, J. / Kabbinale, A. / Sandelin, E. / Vallejos, A. / Ghosh, S. / Dahl, P. / Ronnholm, J. / Bjelcic, M. / Finke, A. / Bostedt, C. / Bacellar Cases da Silveira, C. / Beale, E. / Cirelli, C. / Johnson, P. / Ozerov, D. / Boutet, S. / Batyuk, A. / Kupitz, C. / Peck, A. / Poitevin, F. / Sierra, R. / Lisova, S. / Wallentin, C. / Branden, G. / Ostojic, L. / Glerup, J. / Neutze, R.
History
DepositionAug 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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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 polypeptide 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,03824
Polymers85,8913
Non-polymers7,14721
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.688, 98.340, 94.085
Angle α, β, γ (deg.)90.00, 127.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c ba(3) subunit I / Cytochrome c oxidase polypeptide I / Cytochrome cba3 subunit 1


Mass: 63540.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaA, TTHA1135 / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): DSM 579 / HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 18581.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaB, ctaC, TTHA1134 / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): DSM 579 / HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cytochrome c oxidase polypeptide 2A / Cytochrome c ba(3) subunit IIA / Cytochrome c oxidase polypeptide IIA / Cytochrome cba3 subunit 2A


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaD, TTHA1133 / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): DSM 579 / HB8 / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 7 types, 127 molecules

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


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C21H40O4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 5.3 / Details: 1.4 M NaCl, 100 mM MES. 40-43 % (v/v) PEG 400 / Temp details: Cryogenic

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryogenic / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.9997 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2023 / Details: Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9997 Å / Relative weight: 1
ReflectionResolution: 2.28→74.54 Å / Num. obs: 44643 / % possible obs: 94.4 % / Redundancy: 9.2 % / CC1/2: 0.998 / Net I/σ(I): 18
Reflection shellResolution: 2.28→2.36 Å / Num. unique obs: 2943 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→74.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.902 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19652 2187 4.9 %RANDOM
Rwork0.15308 ---
obs0.15527 42456 94.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.693 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å2-0 Å21.59 Å2
2---2.11 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 2.28→74.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 386 106 6402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126506
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166404
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.6738845
X-RAY DIFFRACTIONr_angle_other_deg0.5371.58214648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.65749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.6377.29248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81410890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0810.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027368
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021539
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.944.5153005
X-RAY DIFFRACTIONr_mcbond_other3.9394.5153004
X-RAY DIFFRACTIONr_mcangle_it5.1348.1123751
X-RAY DIFFRACTIONr_mcangle_other5.1358.1113752
X-RAY DIFFRACTIONr_scbond_it5.2885.1973501
X-RAY DIFFRACTIONr_scbond_other5.2875.1993502
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.529.2435095
X-RAY DIFFRACTIONr_long_range_B_refined8.51244.557299
X-RAY DIFFRACTIONr_long_range_B_other8.51244.557299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.281→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 92 -
Rwork0.179 2119 -
obs--64.03 %

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