[English] 日本語
Yorodumi
- PDB-2ch0: Solution structure of the human MAN1 C-terminal domain (residues ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ch0
TitleSolution structure of the human MAN1 C-terminal domain (residues 655- 775)
ComponentsINNER NUCLEAR MEMBRANE PROTEIN MAN1
KeywordsNUCLEAR PROTEIN / MAN1 / WINGED HELIX MOTIF / DNA
Function / homology
Function and homology information


Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / negative regulation of activin receptor signaling pathway / Initiation of Nuclear Envelope (NE) Reformation / U1 snRNP binding / RHOD GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / nuclear inner membrane ...Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / negative regulation of activin receptor signaling pathway / Initiation of Nuclear Envelope (NE) Reformation / U1 snRNP binding / RHOD GTPase cycle / RND1 GTPase cycle / RND2 GTPase cycle / nuclear inner membrane / RND3 GTPase cycle / negative regulation of BMP signaling pathway / RHOG GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / RAC1 GTPase cycle / negative regulation of transforming growth factor beta receptor signaling pathway / chromatin DNA binding / nuclear membrane / membrane
Similarity search - Function
MAN1, winged-helix domain / MAN1, RNA recognition motif / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily ...MAN1, winged-helix domain / MAN1, RNA recognition motif / MAN1, winged-helix domain / Man1/Src1, C-terminal / Man1-Src1p-C-terminal domain / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / RNA-binding domain superfamily / Arc Repressor Mutant, subunit A / Nucleotide-binding alpha-beta plait domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Inner nuclear membrane protein Man1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsCaputo, S. / Couprie, J. / Duband-Goulet, I. / Lin, F. / Braud, S. / Gondry, M. / Worman, H.J. / Gilquin, B. / Zinn-Justin, S.
CitationJournal: J. Biol. Chem. / Year: 2006
Title: The carboxyl-terminal nucleoplasmic region of MAN1 exhibits a DNA binding winged helix domain.
Authors: Caputo, S. / Couprie, J. / Duband-Goulet, I. / Konde, E. / Lin, F. / Braud, S. / Gondry, M. / Gilquin, B. / Worman, H.J. / Zinn-Justin, S.
History
DepositionMar 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Database references
Category: citation / citation_author / pdbx_nmr_spectrometer
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_nmr_spectrometer.model
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: INNER NUCLEAR MEMBRANE PROTEIN MAN1


Theoretical massNumber of molelcules
Total (without water)15,9211
Polymers15,9211
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 / 1000BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Representative

-
Components

#1: Protein INNER NUCLEAR MEMBRANE PROTEIN MAN1 / LEM DOMAIN CONTAINING PROTEIN 3


Mass: 15921.214 Da / Num. of mol.: 1 / Fragment: 655-775
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-4T-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y2U8
Sequence detailsBECAUSE OF THE CLONING STRATEGY, THE PEPTIDE RESULTING FROM THE CLEAVAGE COMPRISES ADDITIONAL ...BECAUSE OF THE CLONING STRATEGY, THE PEPTIDE RESULTING FROM THE CLEAVAGE COMPRISES ADDITIONAL RESIDUES FROM 1 TO 5, MAN1 RESIDUES FROM 6 TO 126 AND AGAIN ADDITIONAL RESIDUES FROM 127 TO 133.

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N HSQC-NOESY
22115N HSQC- NOESY
33113C HSQC-NOESY
44113C HSQC-NOESY
55113C HSQC- NOESY IN THE 13C AROMATIC REGION
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

-
Sample preparation

DetailsContents: 90% H2O, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHTemperature (K)
150 MM PHOSPHATE, 150MM NACL 6.0 303.0 K
250 MM PHOSPHATE, 150MM NACL 6.0 303.0 K
350 MM PHOSPHATE, 150MM NACL 6.0 303.0 K
450 MM PHOSPHATE, 150MM NACL 6.0 303.0 K
550 MM PHOSPHATE, 150MM NACL 6.0 303.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX9002
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX9004
Bruker DRXBrukerDRX6005

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
XwinNMR2.5structure solution
NMRPipe2structure solution
Felix2000.1structure solution
CNS1structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURE ARE BASED ON A TOTAL OF 1811 NOE-DERIVED CONSTRAINTS, 169 DIHEDRAL ANGLE RESTRAINTS.
NMR ensembleConformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE ...Conformer selection criteria: BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM, STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY, STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS, STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 1000 / 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