[English] 日本語
Yorodumi
- PDB-2pcb: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pcb
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN ELECTRON TRANSFER PARTNERS, CYTOCHROME C PEROXIDASE AND CYTOCHROME C
Components
  • CYTOCHROME C PEROXIDASE (CCP)
  • CYTOCHROME C
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / response to reactive oxygen species ...cytochrome c-heme linkage / cytochrome complex / cytochrome-c peroxidase / positive regulation of cysteine-type endopeptidase activity / cytochrome-c peroxidase activity / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / respirasome / response to reactive oxygen species / hydrogen peroxide catabolic process / peroxidase activity / mitochondrial intermembrane space / cellular response to oxidative stress / electron transfer activity / mitochondrial matrix / positive regulation of apoptotic process / apoptotic process / lipid binding / heme binding / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 ...Cytochrome c, class IA/ IB / Class I peroxidase / Heme-binding peroxidase Ccp1-like / Cytochrome c / Peroxidase; domain 2 / Peroxidase, domain 2 / Peroxidase; domain 1 - #10 / Cytochrome c-like domain / Peroxidase; domain 1 / Cytochrome Bc1 Complex; Chain D, domain 2 / Peroxidases heam-ligand binding site / Peroxidase, active site / Peroxidases active site signature. / Plant heme peroxidase family profile. / Haem peroxidase / Peroxidase / Peroxidases proximal heme-ligand signature. / Haem peroxidase superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c / Cytochrome c peroxidase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Equus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsPelletier, H. / Kraut, J.
Citation
Journal: Science / Year: 1992
Title: Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c.
Authors: Pelletier, H. / Kraut, J.
#1: Journal: Biochemistry / Year: 1990
Title: X-Ray Structures of Recombinant Yeast Cytochrome C Peroxidase and Three Heme-Cleft Mutants Prepared by Site-Directed Mutagenesis
Authors: Wang, J. / Mauro, J.M. / Edwards, S.L. / Oatley, S.J. / Fishel, L.A. / Ashford, V.A. / Xuong, N.-H. / Kraut, J.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: High-Resolution Three Dimensional Structure of Horse Heart Cytochrome C
Authors: Bushnell, G.W. / Louie, G.V. / Brayer, G.D.
#3: Journal: J.Biol.Chem. / Year: 1987
Title: Co-Crystals of Yeast Cytochrome C Peroxidase and Horse Heart Cytochrome C
Authors: Poulos, T.L. / Sheriff, S. / Howard, A.J.
History
DepositionApr 14, 1993Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / 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_database_status.process_site / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME C PEROXIDASE (CCP)
B: CYTOCHROME C
C: CYTOCHROME C PEROXIDASE (CCP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,1146
Polymers79,2653
Non-polymers1,8493
Water6,071337
1
A: CYTOCHROME C PEROXIDASE (CCP)
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7284
Polymers45,4952
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: CYTOCHROME C PEROXIDASE (CCP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3862
Polymers33,7701
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.300, 105.300, 186.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein CYTOCHROME C PEROXIDASE (CCP)


Mass: 33769.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Organ: HEART / References: UniProt: P00431
#2: Protein CYTOCHROME C /


Mass: 11725.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / References: UniProt: P00004
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.25 Å3/Da / Density % sol: 62.2 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mM1dropKH2PO4
21.5 mMprotein1drop
318-22 %MPD1reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 24671 / % possible obs: 93 % / Rmerge(I) obs: 0.055

-
Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→6 Å / Rfactor Rwork: 0.178
Details: THE YEAST CCP USED HERE IS A RECOMBINANT (CALLED CCP(MI) AND EXPRESSED IN E. COLI) WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS ...Details: THE YEAST CCP USED HERE IS A RECOMBINANT (CALLED CCP(MI) AND EXPRESSED IN E. COLI) WHICH HAS A MET-ILE DIPEPTIDE FUSED TO THE N-TERMINUS. THIS MET-ILE DIPEPTIDE WAS NOT INCLUDED IN THIS STRUCTURE DUE TO DISORDER. AFTER FINAL REFINEMENT THERE WAS ADDITIONAL ELECTRON DENSITY FOUND IN THE ASYMMETRIC UNIT WHICH HAS BEEN ATTRIBUTED TO A PARTIALLY OCCUPIED SECOND CYTOCHROME C MOLECULE. THE COORDINATES FOR A POSSIBLE SECOND CYTOCHROME C SITE HAVE NOT BEEN INCLUDED IN THIS ENTRY. SEE REFERENCE 1 FOR DETAILS.
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 129 337 6031
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_d2.7

+
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