[English] 日本語
Yorodumi
- PDB-2mrb: THREE-DIMENSIONAL STRUCTURE OF RABBIT LIVER CD-7 METALLOTHIONEIN-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mrb
TitleTHREE-DIMENSIONAL STRUCTURE OF RABBIT LIVER CD-7 METALLOTHIONEIN-2A IN AQUEOUS SOLUTION DETERMINED BY NUCLEAR MAGNETIC RESONANCE
ComponentsCD7 METALLOTHIONEIN-2A
KeywordsMETALLOTHIONEIN
Function / homology
Function and homology information


negative regulation of growth / cellular response to zinc ion / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Metallothionein, vertebrate / Metallothionein, vertebrate, metal binding site / Metallothionein domain superfamily, vertebrate / Metallothionein / Vertebrate metallothioneins signature. / Metallothionein domain superfamily
Similarity search - Domain/homology
: / Metallothionein-2A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodSOLUTION NMR
AuthorsBraun, W. / Arseniev, A. / Schultze, P. / Woergoetter, E. / Wagner, G. / Vasak, M. / Kaegi, J.H.R. / Wuthrich, K.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Three-dimensional structure of rabbit liver [Cd7]metallothionein-2a in aqueous solution determined by nuclear magnetic resonance.
Authors: Arseniev, A. / Schultze, P. / Worgotter, E. / Braun, W. / Wagner, G. / Vasak, M. / Kagi, J.H. / Wuthrich, K.
#1: Journal: J.Mol.Biol. / Year: 1986
Title: Nuclear Magnetic Resonance Identification of "Half-Turn" and 310-Helix Secondary Structure in Rabbit Liver Metallothionein-2
Authors: Wagner, G. / Neuhaus, D. / Woergoetter, E. / Vasak, M. / Kaegi, J.H.R. / Wuthrich, K.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Polypeptide Fold in the Two Metal Clusters of Metallothionein-2 by Nuclear Magnetic Resonance in Solution
Authors: Braun, W. / Wagner, G. / Woergoetter, E. / Vasak, M. / Kaegi, J.H.R. / Wuthrich, K.
#3: Journal: Eur.J.Biochem. / Year: 1986
Title: Sequence-Specific 1H-NMR Assignments in Rabbit-Liver Metallothionein-2
Authors: Wagner, G. / Neuhaus, D. / Woergoetter, E. / Vasak, M. / Kaegi, J.H.R. / Wuthrich, K.
#4: Journal: Eur.J.Biochem. / Year: 1985
Title: Systematic Application of High-Resolution,Phase-Sensitive Two-Dimensional 1H-NMR Techniques for the Identification of the Amino-Acid-Proton Spin Systems in Proteins
Authors: Neuhaus, D. / Wagner, G. / Vasak, M. / Kaegi, J.H.R. / Wuthrich, K.
#5: Journal: J.Am.Chem.Soc. / Year: 1985
Title: Polypeptide-Metal Cluster Connectivies in Metallo Thionein 2 by Novel 1H-113Cd Heteronuclear Two-Dimensional NMR Experiments
Authors: Frey, M.H. / Wagner, G. / Vasak, M. / Sorensen, O.W. / Neuhaus, D. / Woergoetter, E. / Kaegi, J.H.R. / Ernst, R.R. / Wuthrich, K.
History
DepositionMay 14, 1990Processing site: BNL
Revision 1.0Apr 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD7 METALLOTHIONEIN-2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4224
Polymers3,0851
Non-polymers3373
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: THE THREE CADMIUM ATOMS AND THE NINE SULPHUR ATOMS TO WHICH THEY ARE BONDED FORM A CD3 S9 METAL CLUSTER.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein/peptide CD7 METALLOTHIONEIN-2A


Mass: 3084.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / References: UniProt: P18055
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Processing

NMR softwareName: DISMAN / Developer: BRAUN,GO / Classification: refinement
NMR ensembleConformers submitted total number: 1

+
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