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- PDB-5ndc: Structure of ba3-type cytochrome c oxidase from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 5ndc
TitleStructure of ba3-type cytochrome c oxidase from Thermus thermophilus by serial femtosecond crystallography
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide IIA
KeywordsOXIDOREDUCTASE / Cytochrome c oxidase / SFX / Respiratory chain enzyme
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / membrane => GO:0016020 / copper ion binding / heme binding / metal ion 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 / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain ...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 / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cupredoxins - blue copper proteins / Cupredoxin / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
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 IIA / 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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAndersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. ...Andersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. / Bosman, E. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G.
Funding support Sweden, 3items
OrganizationGrant numberCountry
The Swedish Foundation of Strategic ResearchSRL10-0036 Sweden
The Swedish Foundation of Strategic Research2015-00560, 349-2011-6485 Sweden
The Knut and Alice Wallenberg FoundationKAW 2012.0284 Sweden
CitationJournal: Sci Rep / Year: 2017
Title: Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature.
Authors: Andersson, R. / Safari, C. / Dods, R. / Nango, E. / Tanaka, R. / Yamashita, A. / Nakane, T. / Tono, K. / Joti, Y. / Bath, P. / Dunevall, E. / Bosman, R. / Nureki, O. / Iwata, S. / Neutze, R. / Branden, G.
History
DepositionMar 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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 IIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,96722
Polymers85,8913
Non-polymers7,07619
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-153 kcal/mol
Surface area26420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.850, 100.320, 96.620
Angle α, β, γ (deg.)90.00, 126.76, 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) / 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) / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cytochrome c oxidase polypeptide IIA / Cytchrome c oxidase subunit 3


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HGMM_F04D06C07, TTMY_0198 / Production host: Thermus thermophilus HB8 (bacteria) / References: UniProt: A0A1J1EEV7, UniProt: P82543*PLUS

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Non-polymers , 6 types, 111 molecules

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


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


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


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#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-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.3
Details: 100mM sodium cacodylate trihydrate pH 5.3, 37% PEG400, 1.4M NaCl Room temperature for 2-3 days

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.6314 Å
DetectorType: MPCCD / Detector: CCD / Date: Feb 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6314 Å / Relative weight: 1
ReflectionResolution: 2.3→36.4 Å / Num. all: 1864107 / Num. obs: 50602 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.956 / R split: 0.1937 / Net I/σ(I): 3.74
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 14.7 % / CC1/2: 0.366 / R split: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
CrystFEL0.6.1data reduction
CrystFEL0.6.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S8F

3s8f


Resolution: 2.3→36.4 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 14.121 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.17 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19749 2511 5.1 %RANDOM
Rwork0.16174 ---
obs0.1635 47055 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.446 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20.74 Å2
2---1.19 Å20 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.3→36.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5910 0 384 92 6386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196506
X-RAY DIFFRACTIONr_bond_other_d0.0020.026318
X-RAY DIFFRACTIONr_angle_refined_deg1.6122.0078838
X-RAY DIFFRACTIONr_angle_other_deg0.988314527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8765749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71922.237228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32115890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8541526
X-RAY DIFFRACTIONr_chiral_restr0.0850.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216942
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021440
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_it1.5964.1323005
X-RAY DIFFRACTIONr_mcbond_other1.5954.1323004
X-RAY DIFFRACTIONr_mcangle_it2.5156.1913751
X-RAY DIFFRACTIONr_mcangle_other2.5156.1913752
X-RAY DIFFRACTIONr_scbond_it1.9324.6393499
X-RAY DIFFRACTIONr_scbond_other1.9324.643500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1386.7515088
X-RAY DIFFRACTIONr_long_range_B_refined4.53347.9227060
X-RAY DIFFRACTIONr_long_range_B_other4.53347.937061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 188 -
Rwork0.289 3439 -
obs--99.94 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9071-0.01080.00880.27710.00810.20770.05310.03750.08410.0023-0.0188-0.07780.01790.0182-0.03430.05580.00920.05160.00540.01210.08539.9473.11628.916
21.1935-0.2552-0.15940.11960.14280.34520.0630.19880.0607-0.0022-0.04580.0061-0.0083-0.0763-0.01720.07420.00260.04320.05120.0180.0383-16.224-0.74519.736
38.655-1.5001-1.15990.32030.21030.34170.09550.26-0.1938-0.046-0.0860.03550.0938-0.0284-0.00960.11060.01910.00930.0683-0.02710.05212.572-14.05212.555
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 562
2X-RAY DIFFRACTION2B2 - 168
3X-RAY DIFFRACTION3C4 - 34

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