[English] 日本語
Yorodumi
- PDB-2lon: Backbone structure of human membrane protein HIGD1B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lon
TitleBackbone structure of human membrane protein HIGD1B
ComponentsHIG1 domain family member 1B
KeywordsMEMBRANE PROTEIN / Helical bundle
Function / homology
Function and homology information


mitochondrial respirasome assembly / membrane => GO:0016020 / mitochondrion
Similarity search - Function
Helix Hairpins - #1320 / Hypoxia induced protein, domain / Hypoxia induced protein conserved region / HIG1 domain profile. / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
HIG1 domain family member 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsKlammt, C. / Maslennikov, I. / Kwiatkowski, W. / Choe, S.
CitationJournal: Nat.Methods / Year: 2012
Title: Facile backbone structure determination of human membrane proteins by NMR spectroscopy.
Authors: Klammt, C. / Maslennikov, I. / Bayrhuber, M. / Eichmann, C. / Vajpai, N. / Chiu, E.J. / Blain, K.Y. / Esquivies, L. / Kwon, J.H. / Balana, B. / Pieper, U. / Sali, A. / Slesinger, P.A. / ...Authors: Klammt, C. / Maslennikov, I. / Bayrhuber, M. / Eichmann, C. / Vajpai, N. / Chiu, E.J. / Blain, K.Y. / Esquivies, L. / Kwon, J.H. / Balana, B. / Pieper, U. / Sali, A. / Slesinger, P.A. / Kwiatkowski, W. / Riek, R. / Choe, S.
History
DepositionJan 26, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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
Revision 1.3May 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: HIG1 domain family member 1B


Theoretical massNumber of molelcules
Total (without water)11,0751
Polymers11,0751
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 / 200target function
RepresentativeModel #1fewest violations

-
Components

#1: Protein HIG1 domain family member 1B / Protein CLST 11240


Mass: 11074.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIGD1B / Production host: CELL-FREE SYNTHESIS (others) / References: UniProt: Q9P298

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-15N HSQC
1312D HNCO
1432D 1H-15N HSQC
1533D HNCO
1633D HNHA
1733D HN(CA)CB
1823D 1H-15N NOESY
1953D 1H-15N NOESY
11033D 13C-15N HSQC-NOESY-HSQC
11143D 1H-15N NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
113C(1),15N-Selectively labeled-HIGD1B, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
215N-HIGD1B, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
313C,15N-HIGD1B, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
415N,2H(C)-HIGD1B, 20 mM MES-Bis-TRIS, 2 % LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
513C,15N-HIGD1B, 20 mM MES-Bis-TRIS, 2 % 95%-2H in alkyl chain d27-LMPG, 0.5 mM DSS, 95% H2O/5% D2O95% H2O/5% D2O
6
7
8
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMMES-Bis-TRIS-11
2 %LMPG-21
0.5 mMDSS-31
20 mMMES-Bis-TRIS-42
2 %LMPG-52
0.5 mMDSS-62
20 mMMES-Bis-TRIS-73
2 %LMPG-83
0.5 mMDSS-93
20 mMMES-Bis-TRIS-104
2 %LMPG-114
0.5 mMDSS-124
20 mMMES-Bis-TRIS-135
2 %d27-LMPG-1495%-2H in alkyl chain5
0.5 mMDSS-155
20 mMMES-Bis-TRIS-166
2 %LMPG-176
0.5 mMDSS-186
20 mMMES-Bis-TRIS-197
2 %LMPG-207
0.5 mMDSS-217
20 mMMES-Bis-TRIS-228
2 %LMPG-238
0.5 mMDSS-248
Sample conditionsIonic strength: 40 / pH: 6.0 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX7001
Varian Uniform NMR SystemVarianUniform NMR System5002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
PROSAGuntertprocessing
MCCLKwiatkowski, Maslennikovchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
MOLMOLKoradi, Billeter and Wuthrichstructure visualization
MOLMOLKoradi, Billeter and Wuthrichstructure analysis
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / 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://pdbjlvh1.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