[English] 日本語
Yorodumi
- PDB-1h9e: LEM-LIKE DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN LAP2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1h9e
TitleLEM-LIKE DOMAIN OF HUMAN INNER NUCLEAR MEMBRANE PROTEIN LAP2
ComponentsLAMINA-ASSOCIATED POLYPEPTIDE 2
KeywordsMEMBRANE PROTEIN / INNER NUCLEAR MEMBRANE PROTEIN / LAMINA-ASSOCIATED POLYPEPTIDE / EMERIN / LEM DOMAIN
Function / homology
Function and homology information


Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / lamin binding / Initiation of Nuclear Envelope (NE) Reformation / nuclear inner membrane / nuclear envelope / nuclear membrane / membrane => GO:0016020 / cadherin binding / chromatin ...Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / lamin binding / Initiation of Nuclear Envelope (NE) Reformation / nuclear inner membrane / nuclear envelope / nuclear membrane / membrane => GO:0016020 / cadherin binding / chromatin / DNA binding / membrane / nucleus / cytoplasm
Similarity search - Function
Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / LEM domain / LEM domain / LEM domain profile. ...Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 - #40 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lamina-associated polypeptide 2, isoform alpha / Lamina-associated polypeptide 2, isoforms beta/gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLaguri, C. / Gilquin, B. / Wolff, N. / Romi-Lebrun, R. / Courchay, K. / Callebaut, I. / Worman, H.J. / Zinn-Justin, S.
CitationJournal: Structure / Year: 2001
Title: Structural Characterization of the Lem Motif Common to Three Human Inner Nuclear Membrane Proteins
Authors: Laguri, C. / Gilquin, B. / Wolff, N. / Romi-Lebrun, R. / Courchay, K. / Callebaut, I. / Worman, H.J. / Zinn-Justin, S.
History
DepositionMar 8, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 14, 2017Group: Structure summary / Category: pdbx_nmr_representative / Item: _pdbx_nmr_representative.conformer_id
Remark 650 HELIX DETERMINATION METHOD: RAMACHANDRAN

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LAMINA-ASSOCIATED POLYPEPTIDE 2


Theoretical massNumber of molelcules
Total (without water)6,2801
Polymers6,2801
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200LOWER ENERGY
RepresentativeModel #2

-
Components

#1: Protein LAMINA-ASSOCIATED POLYPEPTIDE 2 / THYMOPOIETIN / TP BETA/GAMMA / THYMOPOIETIN-RELATED PEPTIDE ISOFORMS BETA/GAMMA / TPRP ISOFORMS BETA/GAMMA


Mass: 6280.145 Da / Num. of mol.: 1 / Fragment: LEM-LIKE DOMAIN, RESIDUES 2-57 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P42167, UniProt: P42166*PLUS
Compound detailsPLAYS IMPORTANT ROLES IN T-CELL DEVELOPMENT AND FUNCTION.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131NOESY
141ROESY

-
Sample preparation

Sample conditionsIonic strength: 20 mM / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR ensembleConformer selection criteria: LOWER ENERGY / Conformers calculated total number: 200 / 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