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- PDB-3fye: Catalytic core subunits (I and II) of cytochrome c oxidase from R... -

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Basic information

Entry
Database: PDB / ID: 3fye
TitleCatalytic core subunits (I and II) of cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state
Components(Cytochrome C oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / conformational changes / Cell membrane / Copper / Electron transport / Heme / Hydrogen ion transport / Ion transport / Iron / Membrane / Metal-binding / Respiratory chain / Transmembrane / Transport
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
: / COPPER (I) ION / HEME-A / 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: 2.15 Å
AuthorsQin, L. / Mills, D.A. / Proshlyakov, D.A. / Hiser, C. / Ferguson-Miller, S.
CitationJournal: Biochemistry / Year: 2009
Title: Redox dependent conformational changes in cytochrome c oxidase suggest a gating mechanism for proton uptake.
Authors: Qin, L. / Liu, J. / Mills, D. / Proshlyakov, D.A. / Hiser, C. / Ferguson-Miller, S.
History
DepositionJan 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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

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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)196,67947
Polymers185,1224
Non-polymers11,55743
Water8,647480
1
A: Cytochrome C oxidase subunit 1
B: Cytochrome C oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,89625
Polymers92,5612
Non-polymers6,33523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-185 kcal/mol
Surface area26680 Å2
MethodPISA
2
C: Cytochrome C oxidase subunit 1
D: Cytochrome C oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,78322
Polymers92,5612
Non-polymers5,22220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17170 Å2
ΔGint-168 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.613, 131.472, 176.192
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 c oxidase polypeptide I / Cytochrome aa3 subunit 1


Mass: 63195.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaD / Plasmid: PRK415 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): deltaIdeltaIV / References: UniProt: P33517, cytochrome-c oxidase
#2: Protein Cytochrome C oxidase subunit 2 / Cytochrome c oxidase polypeptide II / Cytochrome aa3 subunit 2 / Oxidase aa(3) subunit 2


Mass: 29365.385 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: ctaC, coxII, ctaB / Plasmid: PRK415 / Production host: Rhodobacter sphaeroides (bacteria) / Strain (production host): deltaIdeltaIV / References: UniProt: Q03736, cytochrome-c oxidase

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Sugars , 1 types, 10 molecules

#8: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 9 types, 513 molecules

#3: Chemical
ChemComp-HEA / HEME-A


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


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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#9: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C13H28
#10: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#11: Chemical
ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 480 / 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: 3.9 Å3/Da / Density % sol: 68.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 23-24% PEG-400, crystal reduced by dithionite, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 162159 / % possible obs: 98.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.066 / Χ2: 1.006
Reflection shellResolution: 2.15→2.206 Å / Redundancy: 4 % / Rmerge(I) obs: 0.606 / Num. unique all: 10331 / Χ2: 0.963 / % possible all: 92.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSM

2gsm


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.069 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.16 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: (1) THERE IS A COVALENT LINKAGE BETWEEN NE2 OF HIS284 OF SUBUNIT I AND CE2 OF TYR288 OF SUBUNIT I. (2) THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN ...Details: (1) THERE IS A COVALENT LINKAGE BETWEEN NE2 OF HIS284 OF SUBUNIT I AND CE2 OF TYR288 OF SUBUNIT I. (2) THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN BOTH MOLECULES AND THE B -FACTOR FOR EACH MAGNESIUM ION IS UNUSUALLY LOW. THESE OBSERVATIONS SUGGEST THAT THIS MAGNESIUM SITE MAY BE PARTIALLY OCCUPIED BY A HEAVIER METAL ION IN THE PROTEIN CRYSTAL. (3) THE SIDE CHAINS OF THE FOLLOWING RESIDUES ARE NOT FULLY RESOLVED. THE UNRESOLVED SIDE CHAIN ATOMS ARE ASSIGNED AN OCCUPANCY OF 0.00 AND AN ARBITORY B-FACTOR OF 100.00: PHE-A-17 THR-A-18 ARG-A-19 LYS-A-74 LYS-A-224 GLU-A-548 LYS-B-86 GLU-B-131 LYS-C-74 ARG-C-137 LYS-C-224 GLU-C-548 HIS-C-549 LYS-D-86 HIS-D-284 (4) LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS (WITH DIFFERENT LENGTHS) OF EITHER DMU OR NATIVE MEMBRANE LIPIDS SUCH AS PHOSPHATIDYL ETHANOLAMINE OR CARDIOLIPIN. SOME OF THE DETERGENTS LABELLED AS DMU DO NOT CONTAIN THE CARBON CHAIN, OR THE DISTAL GLUCOSE MOIETY. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES YET. (5) THERE IS AN UNKOWN ATOM OR ION NEAR HIS26 AND THR550 OF SUBUNIT I.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4375 2.8 %RANDOM
Rwork0.196 ---
all0.196 151414 --
obs0.196 151414 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 45.8 Å2 / Biso min: 9.91 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2---0.22 Å20 Å2
3---2.26 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12452 0 679 480 13611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02213586
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.98218531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66751580
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0722.803528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.707151880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7291541
X-RAY DIFFRACTIONr_chiral_restr0.0880.22025
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210201
X-RAY DIFFRACTIONr_nbd_refined0.1960.27100
X-RAY DIFFRACTIONr_nbtor_refined0.310.29372
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2684
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.225
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.23
X-RAY DIFFRACTIONr_mcbond_it0.6251.58078
X-RAY DIFFRACTIONr_mcangle_it1.025212673
X-RAY DIFFRACTIONr_scbond_it1.43236508
X-RAY DIFFRACTIONr_scangle_it2.0424.55850
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 314 -
Rwork0.274 10311 -
all-10625 -
obs--92.73 %

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