[English] 日本語
Yorodumi
- PDB-2jqr: Solution model of crosslinked complex of cytochrome c and adrenodoxin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jqr
TitleSolution model of crosslinked complex of cytochrome c and adrenodoxin
Components
  • Adrenodoxin, mitochondrial
  • Cytochrome c iso-1
KeywordsELECTRON TRANSPORT / Cytochrome c / Adrenodoxin / Crosslinked complex / 2Fe2S Ferredoxin / Pseudocontact shift / Paramagnetic relaxation enhancement / encounter complex
Function / homology
Function and homology information


Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species ...Mitochondrial iron-sulfur cluster biogenesis / Pregnenolone biosynthesis / Electron transport from NADPH to Ferredoxin / Endogenous sterols / Protein lipoylation / hormone biosynthetic process / P450-containing electron transport chain / Release of apoptotic factors from the mitochondria / Pyroptosis / Detoxification of Reactive Oxygen Species / Respiratory electron transport / steroid biosynthetic process / cardiolipin binding / mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / cholesterol metabolic process / cellular response to forskolin / cellular response to cAMP / respiratory electron transport chain / electron transport chain / mitochondrial intermembrane space / 2 iron, 2 sulfur cluster binding / electron transfer activity / mitochondrial matrix / heme binding / protein homodimerization activity / mitochondrion / metal ion binding
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome c, class IA/ IB / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Beta-grasp domain superfamily ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Cytochrome c, class IA/ IB / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Beta-grasp domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / HEME C / Cytochrome c isoform 1 / Adrenodoxin, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Bos taurus (domestic cattle)
MethodSOLUTION NMR / molecular dynamics
AuthorsXu, X. / Reinle, W. / Hannemann, F. / Konarev, P.V. / Svergun, D.I. / Bernhardt, R. / Ubbink, M.
Citation
Journal: J Am Chem Soc / Year: 2008
Title: Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy.
Authors: Xingfu Xu / Wolfgang Reinle / Frank Hannemann / Peter V Konarev / Dmitri I Svergun / Rita Bernhardt / Marcellus Ubbink /
Abstract: In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the ...In the general view of protein-complex formation, a transient and dynamic encounter complex proceeds to form a more stable, well-defined, and active form. In weak protein complexes, however, the encounter state can represent a significant population of the complex. The redox proteins adrenodoxin (Adx) and cytochrome c (C c) associate to form such a weak and short-lived complex, which is nevertheless active in electron transfer. To study the conformational freedom within the protein complex, the native complex has been compared to a cross-linked counterpart by using solution scattering and NMR spectroscopy. Oligomerization behavior of the native complex in solution revealed by small-angle X-ray scattering indicates a stochastic nature of complex formation. For the cross-linked complex, interprotein paramagnetic effects are observed, whereas for the native complex, extensive averaging occurs, consistent with multiple orientations of the proteins within the complex. Simulations show that C c samples about half of the surface area of adrenodoxin. It is concluded that the complex of Adx/C c is entirely dynamic and can be considered as a pure encounter complex.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: High-resolution refinement of yeast iso-1-cytochrome C and comparisons with other eukaryotic cytochromes C
Authors: Louie, G.V. / Brayer, G.D.
#2: Journal: Structure / Year: 1998
Title: New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, Adx(4-108)
Authors: Muller, A. / Muller, J.J. / Muller, Y.A. / Uhlmann, H. / Bernhardt, R. / Heinemann, U.
History
DepositionJun 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytochrome c iso-1
B: Adrenodoxin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5054
Polymers23,7112
Non-polymers7942
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Cytochrome c iso-1


Mass: 12075.808 Da / Num. of mol.: 1 / Mutation: V28C, C102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CYC1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00044
#2: Protein Adrenodoxin, mitochondrial / Adrenal ferredoxin / Ferredoxin- 1 / Hepato-ferredoxin


Mass: 11635.125 Da / Num. of mol.: 1 / Fragment: 2Fe-2S ferredoxin-type domain, residues 62-166 / Mutation: L80C, C95S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: FDX1, ADX / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00257
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1332D 1H-15N HSQC
1442D 1H-15N HSQC
2513D 1H-15N NOESY
2623D 1H-15N NOESY
2743D 1H-15N NOESY
2843D 1H-15N TOCSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-98% 15N] CcV28C, 0.2-0.6 mM AdxL80C, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
20.4 mM [U-98% 15N] AdxL80C, 0.2-0.6 mM CcV28C, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
31.0 mM [U-98% 15N] CcV28C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
40.6 mM [U-98% 15N] AdxL80C, 5 mM DTT, 20 mM potassium phosphate, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMCcV28C[U-98% 15N]1
0.2 mMAdxL80C1
20 mMpotassium phosphate1
0.2 mMAdxL80C[U-98% 15N]2
0.2 mMCcV28C2
20 mMpotassium phosphate2
1.0 mMCcV28C[U-98% 15N]3
5 mMDTT3
20 mMpotassium phosphate3
0.5 mMAdxL80C[U-98% 15N]4
5 mMDTT4
20 mMpotassium phosphate4
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)Ionic strength
17.4ambient 285 K
27.4ambient 301 K0.4

-
NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
AzaraBoucherprocessing
ANSIGKraulisdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: All structure models are from rigid body modeling. The coordinate of Cytochrome C (Chain A) is from PDB entry 1YCC. All complex structure models are superimposed with Chain A.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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