[English] 日本語
Yorodumi
- PDB-2rq1: Solution structure of the 4.1R FERM alpha lobe domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rq1
TitleSolution structure of the 4.1R FERM alpha lobe domain
ComponentsProtein 4.1
KeywordsMEMBRANE PROTEIN / PROTEIN / Actin-binding / Alternative splicing / Cytoplasm / Cytoskeleton / Elliptocytosis / Glycoprotein / Hereditary hemolytic anemia / Nucleus / Phosphoprotein / Polymorphism / Pyropoikilocytosis
Function / homology
Function and homology information


1-phosphatidylinositol binding / regulation of intestinal absorption / spectrin-associated cytoskeleton / actomyosin structure organization / Neurexins and neuroligins / cortical actin cytoskeleton organization / spectrin binding / cortical cytoskeleton / intercellular bridge / regulation of calcium ion transport ...1-phosphatidylinositol binding / regulation of intestinal absorption / spectrin-associated cytoskeleton / actomyosin structure organization / Neurexins and neuroligins / cortical actin cytoskeleton organization / spectrin binding / cortical cytoskeleton / intercellular bridge / regulation of calcium ion transport / positive regulation of protein localization to cell cortex / phosphoprotein binding / structural constituent of cytoskeleton / cytoplasmic side of plasma membrane / mitotic spindle / cell junction / actin binding / cell cortex / positive regulation of protein binding / actin cytoskeleton organization / basolateral plasma membrane / protein-containing complex assembly / nuclear body / cytoskeleton / calmodulin binding / cell cycle / cell division / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
Band 4.1 protein, chordates / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Band 4.1 protein, chordates / SAB domain / Band 4.1, C-terminal / SAB domain / 4.1 protein C-terminal domain (CTD) / FERM adjacent (FA) / FERM adjacent (FA) / FERM adjacent (FA) / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-like domain superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsKusunoki, H. / Kohno, T.
CitationJournal: Proteins / Year: 2009
Title: Solution structure and glycophorin C binding studies of the protein 4.1R FERM alpha-lobe domain
Authors: Kusunoki, H. / Kohno, T.
History
DepositionJan 9, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein 4.1


Theoretical massNumber of molelcules
Total (without water)12,4201
Polymers12,4201
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)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein 4.1 / Band 4.1 / P4.1 / EPB4.1 / 4.1R


Mass: 12420.041 Da / Num. of mol.: 1 / Fragment: 4.1R_FERM_alpha-lobe_domain, UNP residues 292-396
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPB41, E41P / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P11171

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1213D 1H-15N NOESY
1313D 1H-13C NOESY
1412D 1H-15N HSQC
1512D 1H-13C HSQC
1612D 1H-1H TOCSY
1713D CBCA(CO)NH
1813D C(CO)NH
1913D HNCO
11013D HNCA
11113D HN(CA)CB
11213D H(CCO)NH
11313D (H)CCH-TOCSY
11413D HNHA
11513D HNHB
11613D HN(CO)CA
11713D HN(CA)CO

-
Sample preparation

DetailsContents: 0.12-0.8mM 4.1R FERM alpha-lobe domain-1, 0.12-0.8mM [U-98% 15N] 4.1R FERM alpha-lobe domain-2, 0.12-0.8mM [U-98% 13C; U-98% 15N] 4.1R FERM alpha-lobe domain-3, 90% H2O/10% D2O or 100% D2O
Solvent system: 90% H2O/10% D2O or 100% D2O
Sample
UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mM4.1R FERM alpha-lobe domain-10.121
mM4.1R FERM alpha-lobe domain-2[U-98% 15N]0.121
mM4.1R FERM alpha-lobe domain-3[U-98% 13C; U-98% 15N]0.121
Sample conditionsIonic strength: 45 / pH: 6.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1Brunger, Adams, Clore, Gros, Nilges, Readrefinement
CYANA2.1Guntert, Mumenthaler, Wuthrichnoe collection
TopSpinBruker Biospinprocessing
SparkyGoddarddata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 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