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- PDB-1vf5: Crystal Structure of Cytochrome b6f Complex from M.laminosus -

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Basic information

Entry
Database: PDB / ID: 1vf5
TitleCrystal Structure of Cytochrome b6f Complex from M.laminosus
Components
  • CYTOCHROME B6
  • CYTOCHROME F
  • PROTEIN PET G
  • PROTEIN PET L
  • PROTEIN PET M
  • PROTEIN PET N
  • RIESKE IRON-SULFUR PROTEIN
  • SUBUNIT IV
KeywordsPHOTOSYNTHESIS / membrane protein complex / electron transfer complex
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / ubiquinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / ubiquinol-cytochrome-c reductase activity / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rudiment single hybrid motif / Rieske iron-sulphur protein / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / Chem-PL9 / Chem-TDS / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f ...BETA-CAROTENE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / Chem-PL9 / Chem-TDS / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3 Å
AuthorsKurisu, G. / Zhang, H. / Smith, J.L. / Cramer, W.A.
Citation
Journal: Science / Year: 2003
Title: Structure of the Cytochrome B6F Complex of Oxygenic Photosynthesis: Tuning the Cavity
Authors: Kurisu, G. / Zhang, H. / Smith, J.L. / Cramer, W.A.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A Defined Protein-Detergent-Lipid Complex for Crystallization of Integral Membrane Proteins: The Cytochrome B6F Complex of Oxygenic Photosynthesis
Authors: Zhang, H. / Kurisu, G. / Smith, J.L. / Cramer, W.A.
History
DepositionApr 8, 2004Deposition site: PDBJ / Processing site: PDBJ
SupersessionApr 20, 2004ID: 1UM3
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _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_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 B6
B: SUBUNIT IV
C: CYTOCHROME F
D: RIESKE IRON-SULFUR PROTEIN
E: PROTEIN PET L
F: PROTEIN PET M
G: PROTEIN PET G
H: PROTEIN PET N
N: CYTOCHROME B6
O: SUBUNIT IV
P: CYTOCHROME F
Q: RIESKE IRON-SULFUR PROTEIN
R: PROTEIN PET L
S: PROTEIN PET M
T: PROTEIN PET G
U: PROTEIN PET N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,94138
Polymers215,25716
Non-polymers13,68422
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67560 Å2
ΔGint-794 kcal/mol
Surface area82140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.536, 157.536, 360.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 4 types, 8 molecules ANBOCPDQ

#1: Protein CYTOCHROME B6


Mass: 24245.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#2: Protein SUBUNIT IV


Mass: 17636.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#3: Protein CYTOCHROME F


Mass: 31655.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein RIESKE IRON-SULFUR PROTEIN


Mass: 19450.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794

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Protein/peptide , 4 types, 8 molecules ERFSGTHU

#5: Protein/peptide PROTEIN PET L


Mass: 3504.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide PROTEIN PET M


Mass: 3843.595 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide PROTEIN PET G


Mass: 4016.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide PROTEIN PET N


Mass: 3276.932 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: THERMOPHILIC CYANOBACTERIUM / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798

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Non-polymers , 8 types, 24 molecules

#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-TDS / 8-HYDROXY-5,7-DIMETHOXY-3-METHYL-2-TRIDECYL-4H-CHROMEN-4-ONE / TRIDECYL-STIGMATELLIN


Mass: 418.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H38O5
#11: Chemical ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#12: Chemical
ChemComp-OPC / (7R,17E)-4-HYDROXY-N,N,N,7-TETRAMETHYL-7-[(8E)-OCTADEC-8-ENOYLOXY]-10-OXO-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-17-EN-1-AMINIUM 4-OXIDE / DIOLEOYL-PHOSPHATIDYLCHOLINE


Mass: 801.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#13: Chemical ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#14: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#15: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 5.8 Å3/Da / Density % sol: 78.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: PEG400, pH 7.50, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332
DetectorType: SBC-3 / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3→150 Å / Num. obs: 100622 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 17.9
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
MLPHAREphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MIR / Resolution: 3→48.16 Å / Data cutoff high absF: 2928724.46 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: Twinning was treated during refinement and the twinning fraction set to 0.50.
RfactorNum. reflection% reflectionSelection details
Rfree0.346 2788 3 %RANDOM
Rwork0.258 ---
obs0.258 100530 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.1547 Å2 / ksol: 0.31323 e/Å3
Displacement parametersBiso mean: 87.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.71 Å2-9.44 Å20 Å2
2---5.39 Å20 Å2
3---11.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.79 Å0.63 Å
Luzzati d res low-5 Å
Luzzati sigma a0.8 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3→48.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14141 0 948 2 15091
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
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→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.422 358 3 %
Rwork0.398 12188 -
obs--100 %

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