[English] 日本語
Yorodumi
- PDB-1mph: PLECKSTRIN HOMOLOGY DOMAIN FROM MOUSE BETA-SPECTRIN, NMR, 50 STRU... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mph
TitlePLECKSTRIN HOMOLOGY DOMAIN FROM MOUSE BETA-SPECTRIN, NMR, 50 STRUCTURES
ComponentsBETA SPECTRIN
KeywordsSIGNAL TRANSDUCTION / INOSITOL PHOSPHATES
Function / homology
Function and homology information


Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / membrane assembly / RHOV GTPase cycle / NCAM signaling for neurite out-growth / central nervous system formation / RHOU GTPase cycle / spectrin / COPI-mediated anterograde transport / cuticular plate ...Interaction between L1 and Ankyrins / regulation of SMAD protein signal transduction / membrane assembly / RHOV GTPase cycle / NCAM signaling for neurite out-growth / central nervous system formation / RHOU GTPase cycle / spectrin / COPI-mediated anterograde transport / cuticular plate / RAF/MAP kinase cascade / plasma membrane organization / Golgi to plasma membrane protein transport / actin filament capping / M band / ankyrin binding / cortical cytoskeleton / mitotic cytokinesis / axolemma / endomembrane system / positive regulation of interleukin-2 production / central nervous system development / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / phospholipid binding / structural constituent of cytoskeleton / actin binding / actin cytoskeleton organization / GTPase binding / calmodulin binding / postsynaptic density / protein-containing complex binding / nucleolus / glutamatergic synapse / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. ...Pleckstrin homology domain, spectrin-type / Pleckstrin homology domain 9 / Pleckstrin homology domain / Spectrin, beta subunit / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin beta chain, non-erythrocytic 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNilges, M. / Macias, M.J. / O'Donoghue, S.I. / Oschkinat, H.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Automated NOESY interpretation with ambiguous distance restraints: the refined NMR solution structure of the pleckstrin homology domain from beta-spectrin.
Authors: Nilges, M. / Macias, M.J. / O'Donoghue, S.I. / Oschkinat, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Molecular Replacement with NMR Models Using Distance-Derived Pseudo B Factors
Authors: Wilmanns, M. / Nilges, M.
#2: Journal: Embo J. / Year: 1995
Title: Structure of the Binding Site for Inositol Phosphates in a Ph Domain
Authors: Hyvonen, M. / Macias, M.J. / Nilges, M. / Oschkinat, H. / Saraste, M. / Wilmanns, M.
#3: Journal: Nature / Year: 1994
Title: Structure of the Pleckstrin Homology Domain from Beta-Spectrin
Authors: Macias, M.J. / Musacchio, A. / Ponstingl, H. / Nilges, M. / Saraste, M. / Oschkinat, H.
History
DepositionApr 23, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA SPECTRIN


Theoretical massNumber of molelcules
Total (without water)12,2881
Polymers12,2881
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)50 / 200LOWEST ENERGY
Representative

-
Components

#1: Protein BETA SPECTRIN / PH DOMAIN


Mass: 12287.853 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Organ: BRAIN / Plasmid: PET21D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q62261

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
1313D TOCSY-NOESY

-
Sample preparation

Sample conditionspH: 6.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
ARIAstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR (SEE JRNL REFERENCE FOR DETAILS) WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY ...Details: STRUCTURES WERE CALCULATED WITH A MODIFIED VERSION OF X-PLOR (SEE JRNL REFERENCE FOR DETAILS) WITH A SIMULATED ANNEALING PROTOCOL. AN AUTOMATED PROCEDURE (ARIA) WAS USED TO AUTOMATICALLY ASSIGN AND AUGMENT AN INITIAL LIST OF 568 MANUALLY SELECTED RESTRAINTS, FROM PEAK LISTS FROM TWO H2O NOESY SPECTRA (30 AND 80 MS). 20 STRUCTURES WERE ITERATIVELY REFINED, AND THE NOE DATA RE-ASSIGNED ON THE BASIS OF THE 7 LOWEST ENERGY STRUCTURES IN EACH ITERATION. EIGHT REFINEMENT/ASSIGNMENT CYCLES WERE RUN, PLUS TWO IN AN EXPLICIT SHELL OF WATER. THE FINAL LIST OF RESTRAINTS CONTAINED 1328 UNAMBIGUOUS RESTRAINTS AND 486 AMBIGUOUS RESTRAINTS WITH MAXIMALLY 5 ASSIGNMENT POSSIBILITIES.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 50

+
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