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- PDB-2d2c: Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. La... -

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Basic information

Entry
Database: PDB / ID: 2d2c
TitleCrystal Structure Of Cytochrome B6F Complex with DBMIB From M. Laminosus
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6
  • Cytochrome b6-f complex iron-sulfur subunit
KeywordsPHOTOSYNTHESIS
Function / homology
Function and homology information


cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / : / plasma membrane-derived thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen ...cytochrome b6f complex / plastoquinol-plastocyanin reductase / plastoquinol--plastocyanin reductase activity / : / cytochrome complex assembly / photosynthetic electron transport chain / quinol-cytochrome-c reductase activity / : / plasma membrane-derived thylakoid membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / photosynthesis / respiratory electron transport chain / monooxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / electron transfer activity / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome f large domain / 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 ...Single helix bin / plastocyanin oxidoreductase / Cytochrome f large domain / 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 / Iron-sulfur subunit PetC transmembrane anchor / 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 / : / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / 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 / 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 / Rieske iron-sulphur protein / Rudiment single hybrid motif / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur 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 / Beta Barrel / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / Chem-OPC / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit ...BETA-CAROTENE / 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / Chem-OPC / 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 / Resolution: 3.8 Å
AuthorsYan, J. / Kurisu, G. / Cramer, W.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Intraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex
Authors: Yan, J. / Kurisu, G. / Cramer, W.A.
History
DepositionSep 7, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2014Group: Database references / Other
Revision 2.0Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.pdbx_synonyms ..._chem_comp.formula / _chem_comp.pdbx_synonyms / _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 3.0Dec 24, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.ref_comp_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit VI
F: Cytochrome b6-f complex subunit VII
G: Cytochrome b6-f complex subunit V
H: Cytochrome b6-f complex subunit VIII
N: Cytochrome b6
O: Cytochrome b6-f complex subunit 4
P: Apocytochrome f
Q: Cytochrome b6-f complex iron-sulfur subunit
R: Cytochrome b6-f complex subunit VI
S: Cytochrome b6-f complex subunit VII
T: Cytochrome b6-f complex subunit V
U: Cytochrome b6-f complex subunit VIII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,26636
Polymers215,25716
Non-polymers12,00920
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58880 Å2
ΔGint-688 kcal/mol
Surface area92020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.587, 156.587, 361.786
Angle α, β, γ (deg.)90.00, 90.00, 120
Int Tables number169
Space group name H-MP61

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Components

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Protein , 3 types, 6 molecules ANCPDQ

#1: Protein Cytochrome b6


Mass: 24245.529 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#3: Protein Apocytochrome f


Mass: 31655.088 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein Cytochrome b6-f complex iron-sulfur subunit / Rieske iron-sulfur protein / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP


Mass: 19450.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria)
References: UniProt: P83794, plastoquinol-plastocyanin reductase

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Cytochrome b6-f complex subunit ... , 5 types, 10 molecules BOERFSGTHU

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17636.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#5: Protein/peptide Cytochrome b6-f complex subunit VI / Cytochrome b6f complex subunit petL


Mass: 3504.444 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide Cytochrome b6-f complex subunit VII / Cytochrome b6f complex subunit petM


Mass: 3843.595 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide Cytochrome b6-f complex subunit V / Cytochrome b6f complex subunit petG


Mass: 4016.661 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide Cytochrome b6-f complex subunit VIII / Cytochrome b6f complex subunit petN


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

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Non-polymers , 7 types, 22 molecules

#9: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: 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
#11: Chemical ChemComp-BNT / 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE / 2,5-DIBROMO-3-METHYL-6-ISOPROPYLBENZOQUINONE / DBMIB


Mass: 321.993 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H10Br2O2
#12: Chemical ChemComp-CLA / CHLOROPHYLL A


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


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


Mass: 536.873 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56
#15: 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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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.94 Å3/Da / Density % sol: 79.31 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 3.8→24.76 Å / Data cutoff high absF: 6062657.43 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.378 1288 2.8 %RANDOM
Rwork0.276 ---
obs0.276 45748 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 92.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å210.29 Å20 Å2
2---0.24 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 3.8→24.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14176 0 806 2 14984
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_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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: 3.8→3.97 Å / Total num. of bins used: 8 /
Rfactor% reflection
Rfree0.47 2.8 %
Rwork0.365 -
obs-79.2 %

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