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

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Basic information

Entry
Database: PDB / ID: 3fyi
TitleCatalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides in the reduced state bound with cyanide
Components(Cytochrome c oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / conformational changes / cyanide binding / Cell membrane / 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 / 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
: / COPPER (I) ION / CYANIDE 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: 2.2 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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

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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)196,73147
Polymers185,1224
Non-polymers11,60943
Water8,467470
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,92225
Polymers92,5612
Non-polymers6,36123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19430 Å2
ΔGint-189 kcal/mol
Surface area26780 Å2
MethodPISA
2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,80922
Polymers92,5612
Non-polymers5,24820
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17320 Å2
ΔGint-167 kcal/mol
Surface area26800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.344, 131.877, 176.160
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: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 9 types, 503 molecules

#3: Chemical
ChemComp-HEA / HEME-A / Heme A


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


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-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#9: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT / Tridecane


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 / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 23%-24% PEG-400, crystals reduced with dithionite and soaked with cyanide, 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: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 22, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 145489 / % possible obs: 95.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.2→2.257 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.52 / % possible all: 73.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSM

2gsm


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.002 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.155 / 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 GLU-A-548 GLU-B-131 LYS-C-74 ARG-C- 137 LYS-C-224 ARG-C-521 ARG-C-524 GLU-C-548 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 CHAINS, OR THE DISTAL GLUCOSE MOIETY. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES YET.
RfactorNum. reflection% reflectionSelection details
Rfree0.21906 3933 2.8 %RANDOM
Rwork0.1943 ---
obs0.195 137425 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.024 Å2
Baniso -1Baniso -2Baniso -3
1--1.73 Å20 Å20 Å2
2---0.18 Å20 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12434 0 685 470 13589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213587
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.98218524
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53351578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90422.789527
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.646151878
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0061541
X-RAY DIFFRACTIONr_chiral_restr0.0820.22024
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210193
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.26987
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.29369
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2661
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1230.217
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5081.57842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.964212667
X-RAY DIFFRACTIONr_scbond_it1.34235745
X-RAY DIFFRACTIONr_scangle_it2.1614.55853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 218 -
Rwork0.255 7652 -
obs--73.51 %

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