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- PDB-1qle: CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOC... -

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Basic information

Entry
Database: PDB / ID: 1qle
TitleCRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT
Components
  • (CYTOCHROME C OXIDASE POLYPEPTIDE ...) x 3
  • CCYTOCHROME C OXIDASE
  • HEAVY CHAIN ANTIBODY FV FRAGMENT
  • LIGHT CHAIN ANTIBODY FV FRAGMENT
KeywordsOXIDOREDUCTASE/IMMUNE SYSTEM / COMPLEX (OXIDOREDUCTASE-ANTIBODY) / ELECTRON TRANSPORT / TRANSMEMBRANE / CYTOCHROME OXIDASE / ANTIBODY COMPLEX / OXIDOREDUCTASE-IMMUNE SYSTEM complex
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 / 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. / 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 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-A / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c oxidase subunit 3 / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 4 / Cytochrome c oxidase subunit 1-beta
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
PARACOCCUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsHarrenga, A. / Michel, H.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: The Cytochrome C Oxidase from Paracoccus Denitrificans Does not Change the Metal Center Ligation Upon Reduction
Authors: Harrenga, A. / Michel, H.
History
DepositionAug 30, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.0May 4, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
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.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _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
Revision 2.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_chiral
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA
B: CYTOCHROME C OXIDASE POLYPEPTIDE II
C: CYTOCHROME C OXIDASE POLYPEPTIDE III
D: CCYTOCHROME C OXIDASE
H: HEAVY CHAIN ANTIBODY FV FRAGMENT
L: LIGHT CHAIN ANTIBODY FV FRAGMENT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,42014
Polymers148,8486
Non-polymers3,5728
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24580 Å2
ΔGint-229.6 kcal/mol
Surface area61150 Å2
MethodPQS
Unit cell
Length a, b, c (Å)205.200, 205.200, 81.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
DetailsTHE CRYSTAL STRUCTURE SHOWS A CRYSTAL PACKING ARRANGEMENT WHERETHERE IS CONTACT BETWEEN CHAINS C AND H GIVING A CYCLICPACKING WITHCHAIN- H ... (CHAIN-C...CHAIN-H) ... CHAIN-C(Y,-X,Z ) ASU: X,Y,Z (-Y,X,Z)

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Components

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CYTOCHROME C OXIDASE POLYPEPTIDE ... , 3 types, 3 molecules ABC

#1: Protein CYTOCHROME C OXIDASE POLYPEPTIDE I-BETA / CYTOCHROME AA3 SUBUNIT 1-BETA


Mass: 60354.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P98002, cytochrome-c oxidase
#2: Protein CYTOCHROME C OXIDASE POLYPEPTIDE II / CYTOCHROME AA3 SUBUNIT 2 / OXIDASE AA(3) SUBUNIT 2


Mass: 27972.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P08306, cytochrome-c oxidase
#3: Protein CYTOCHROME C OXIDASE POLYPEPTIDE III / CYTOCHROME AA3SUBUNIT 3 / OXIDASE AA(3) SUBUNIT 3


Mass: 30676.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P06030, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules D

#4: Protein/peptide CCYTOCHROME C OXIDASE / CYTOCHROME AA3


Mass: 4701.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: CYTOPLASMIC MEMBRANE / References: UniProt: P77921, cytochrome-c oxidase

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Antibody , 2 types, 2 molecules HL

#5: Antibody HEAVY CHAIN ANTIBODY FV FRAGMENT


Mass: 13356.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)
#6: Antibody LIGHT CHAIN ANTIBODY FV FRAGMENT


Mass: 11786.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 6 types, 8 molecules

#7: Chemical ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#8: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#11: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#12: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM

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Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF VH AND VL IS DESCRIBED IN THE FOLLOWING REFERENCE, OSTERMEIER C. ET AL. (1995) ...THE SEQUENCE OF VH AND VL IS DESCRIBED IN THE FOLLOWING REFERENCE, OSTERMEIER C. ET AL. (1995) PROTEINS 21: 74-77. THE NCBI REFERENCE LOCUS FOR CHAIN H IS 2914143 THE NCBI REFERENCE LOCUS FOR CHAIN L IS 2914144

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.74 Å3/Da / Density % sol: 75 %
Crystal growpH: 8 / Details: pH 8.00
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1400 mMammonium acetate1reservoir
27 %1reservoirMe2SO
310-14 %mPEG20001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9875
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 64653 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.6
Reflection
*PLUS
Num. measured all: 165650

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: OTHER / Resolution: 3→6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5840810 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1975 5 %RANDOM
Rwork0.235 ---
obs0.235 39276 66.2 %-
Displacement parametersBiso mean: 31.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å20 Å2
2---0.39 Å20 Å2
3---0.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.55 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10529 0 233 0 10762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.5
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.16 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 203 5.4 %
Rwork0.282 3561 -
obs--38.5 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.5

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