[English] 日本語
Yorodumi
- PDB-2d2c: Crystal Structure Of Cytochrome B6F Complex with DBMIB From M. La... -

+
Open data


ID or keywords:

Loading...

-
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-f complex iron-sulfur subunit
  • Cytochrome b6Cytochrome b
KeywordsPHOTOSYNTHESIS
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 / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain ...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 / 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 / intracellular membrane-bounded organelle / 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 / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rieske iron-sulphur protein / Rudiment single hybrid motif / 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 / 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-OPC / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f ...BETA-CAROTENE / 2,5-DIBROMO-3-ISOPROPYL-6-METHYLBENZO-1,4-QUINONE / CHLOROPHYLL A / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)227,25436
Polymers215,25716
Non-polymers11,99720
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

-
Components

-
Protein , 3 types, 6 molecules ANCPDQ

#1: Protein Cytochrome b6 / Cytochrome b


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, EC: 1.10.99.1

-
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

-
Non-polymers , 8 types, 22 molecules

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


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: 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 / Phosphatidylcholine


Mass: 801.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H87NO8P / Comment: phospholipid*YM
#12: 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
#13: Chemical ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


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


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


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


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more