[English] 日本語
Yorodumi
- PDB-2lm4: Solution NMR Structure of mitochondrial succinate dehydrogenase a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lm4
TitleSolution NMR Structure of mitochondrial succinate dehydrogenase assembly factor 2 from Saccharomyces cerevisiae, Northeast Structural Genomics Consortium Target YT682A
ComponentsSuccinate dehydrogenase assembly factor 2, mitochondrial
KeywordsPROTEIN BINDING / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-Biology / Protein Structure Initiative / Mitochondrial Protein Partnership / MPP
Function / homology
Function and homology information


protein-FAD linkage / protein flavinylation / mitochondrial respiratory chain complex II assembly / Maturation of TCA enzymes and regulation of TCA cycle / ascospore formation / mitochondrial electron transport, succinate to ubiquinone / tricarboxylic acid cycle / mitochondrial matrix / mitochondrion
Similarity search - Function
Succinate dehydrogenase assembly factor 2, mitochondrial / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase / Flavinator of succinate dehydrogenase superfamily / Flavinator of succinate dehydrogenase / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Succinate dehydrogenase assembly factor 2, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Winge, D.R. / Lee, H. / Lee, D. / Kohan, E. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. ...Eletsky, A. / Winge, D.R. / Lee, H. / Lee, D. / Kohan, E. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP)
CitationJournal: Biochemistry / Year: 2012
Title: Solution NMR structure of yeast succinate dehydrogenase flavinylation factor sdh5 reveals a putative sdh1 binding site.
Authors: Eletsky, A. / Jeong, M.Y. / Kim, H. / Lee, H.W. / Xiao, R. / Pagliarini, D.J. / Prestegard, J.H. / Winge, D.R. / Montelione, G.T. / Szyperski, T.
History
DepositionNov 22, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 30, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Succinate dehydrogenase assembly factor 2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)13,1931
Polymers13,1931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Succinate dehydrogenase assembly factor 2, mitochondrial / SDH assembly factor 2 / Early meiotic induction protein 5 / Succinate dehydrogenase subunit 5 / mitochondrial


Mass: 13193.031 Da / Num. of mol.: 1 / Fragment: UNP residues 55-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: EMI5, SDH5, YOL071W / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q08230

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C CT-HSQC aliphatic
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1813D HN(CA)CO
1912D 1H-13C CT-HSQC aromatic
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY aliphatic
11213D (H)CCH-COSY aromatic
11311D 15N T1
11411D 15N T2
11522D 1H-13C CT-HSQC methyl
11622D J-resolved 1H-15N HSQC
11732D J-resolved 1H-15N HSQC
11842D J-resolved 1H-15N HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] YT682A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [5% 13C; U-100% 15N] YT682A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 95% H2O/5% D2O95% H2O/5% D2O
30.7 mM [5% 13C; U-100% 15N] YT682A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 4 % C12E5 PEG, 4 % hexanol, 90% H2O/10% D2O90% H2O/10% D2O
41.1 mM [5% 13C; U-100% 15N] YT682A, 20 mM MES, 100 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMYT682A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
50 uMDSS-71
1.1 mMYT682A-8[5% 13C; U-100% 15N]2
20 mMMES-92
100 mMsodium chloride-102
5 mMcalcium chloride-112
10 mMDTT-122
0.02 %sodium azide-132
50 uMDSS-142
0.7 mMYT682A-15[5% 13C; U-100% 15N]3
20 mMMES-163
100 mMsodium chloride-173
5 mMcalcium chloride-183
10 mMDTT-193
0.02 %sodium azide-203
50 uMDSS-213
4 %C12E5 PEG-223
4 %hexanol-233
1.1 mMYT682A-24[5% 13C; U-100% 15N]4
20 mMMES-254
100 mMsodium chloride-264
5 mMcalcium chloride-274
10 mMDTT-284
0.02 %sodium azide-294
50 uMDSS-304
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement, structure solution, geometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement, geometry optimization, structure solution
ASDP1Huang, Tejero, Powers and Montelionedata analysis, refinement
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionedata analysis, chemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3.13Bartels et al.data analysis
PROSA6.4Guntertprocessing
VnmrJ2.2DVariancollection
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
CARA1.8.4Keller and Wuthrichdata analysis,peak picking,chemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments ...Details: Structure determination was performed by running CYANA and ASDP in parallel using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. Consensus peak assignments were selected and used in iterative refinement with CYANA, with RDC constraints added at later stages. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field
NMR constraintsNOE constraints total: 1723 / NOE intraresidue total count: 525 / NOE long range total count: 390 / NOE medium range total count: 406 / NOE sequential total count: 402 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 59 / Protein psi angle constraints total count: 59
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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