[English] 日本語
Yorodumi
- PDB-1gg3: CRYSTAL STRUCTURE OF THE PROTEIN 4.1R MEMBRANE BINDING DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gg3
TitleCRYSTAL STRUCTURE OF THE PROTEIN 4.1R MEMBRANE BINDING DOMAIN
ComponentsERYTHROID MEMBRANE PROTEIN 4.1R
KeywordsMEMBRANE PROTEIN / BLOOD / 4.1R / MEMBRANE / 30kD / N-terminal domain / calmodulin
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 / intercellular bridge / cortical cytoskeleton / 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 / intercellular bridge / cortical cytoskeleton / regulation of calcium ion transport / positive regulation of protein localization to cell cortex / phosphoprotein binding / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
Model detailsPROTEIN 4.1R 30KD N-TERMINAL DOMAIN PROVIDES MULTIPLE BINDING SITES FOR TRANSMEMBRANE PROTEINS AND ...PROTEIN 4.1R 30KD N-TERMINAL DOMAIN PROVIDES MULTIPLE BINDING SITES FOR TRANSMEMBRANE PROTEINS AND IS REGULATED BY CALMODULIN
AuthorsHan, B.G.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Protein 4.1R core domain structure and insights into regulation of cytoskeletal organization.
Authors: Han, B.G. / Nunomura, W. / Takakuwa, Y. / Mohandas, N. / Jap, B.K.
History
DepositionJul 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ERYTHROID MEMBRANE PROTEIN 4.1R
B: ERYTHROID MEMBRANE PROTEIN 4.1R
C: ERYTHROID MEMBRANE PROTEIN 4.1R


Theoretical massNumber of molelcules
Total (without water)97,0873
Polymers97,0873
Non-polymers00
Water0
1
A: ERYTHROID MEMBRANE PROTEIN 4.1R


Theoretical massNumber of molelcules
Total (without water)32,3621
Polymers32,3621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ERYTHROID MEMBRANE PROTEIN 4.1R


Theoretical massNumber of molelcules
Total (without water)32,3621
Polymers32,3621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ERYTHROID MEMBRANE PROTEIN 4.1R


Theoretical massNumber of molelcules
Total (without water)32,3621
Polymers32,3621
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)163.900, 106.500, 93.500
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein ERYTHROID MEMBRANE PROTEIN 4.1R / 4.1R


Mass: 32362.322 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Plasmid: PGEX-6P / Production host: Escherichia coli (E. coli) / References: UniProt: P11171

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.59 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.8
Details: PEG 1000, SODIUM CITRATE, SODIUM CHLORIDE, pH 5.8, EVAPORATION, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Han, B.G., (2000) Acta Crystallogr., D56, 187.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 M1dropNaCl
23 %PEG30001drop
30.1 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 39521 / Num. obs: 39441 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 75.5 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.36 / Num. unique all: 1905 / % possible all: 94.6
Reflection shell
*PLUS
% possible obs: 98 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1263789.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1949 5 %RANDOM
Rwork0.226 ---
obs0.226 38874 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.26 Å2 / ksol: 0.283 e/Å3
Displacement parametersBiso mean: 59.5 Å2
Baniso -1Baniso -2Baniso -3
1--10.34 Å20 Å29.23 Å2
2--17.98 Å20 Å2
3----7.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6837 0 0 0 6837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 318 5.2 %
Rwork0.328 5849 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 59.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.397 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.328

+
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