[English] 日本語
Yorodumi
- PDB-1g4m: CRYSTAL STRUCTURE OF BOVINE BETA-ARRESTIN 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1g4m
TitleCRYSTAL STRUCTURE OF BOVINE BETA-ARRESTIN 1
ComponentsBETA-ARRESTIN1
KeywordsSIGNALING PROTEIN / Sensory transduction / alternative splicing
Function / homology
Function and homology information


TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis ...TGFBR3 regulates TGF-beta signaling / MAP2K and MAPK activation / Activation of SMO / Golgi Associated Vesicle Biogenesis / Lysosome Vesicle Biogenesis / AP-2 adaptor complex binding / Ub-specific processing proteases / clathrin coat of coated pit / clathrin heavy chain binding / Cargo recognition for clathrin-mediated endocytosis / desensitization of G protein-coupled receptor signaling pathway / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / acetylcholine receptor binding / G protein-coupled receptor internalization / inositol hexakisphosphate binding / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (s) signalling events / clathrin binding / small molecule binding / pseudopodium / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of receptor internalization / negative regulation of Notch signaling pathway / G protein-coupled receptor binding / receptor internalization / positive regulation of protein phosphorylation / protein transport / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / signal transduction / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain ...Immunoglobulin-like - #840 / Immunoglobulin-like - #640 / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SIRAS / Resolution: 1.9 Å
AuthorsSchubert, C. / Han, M.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of beta-arrestin at 1.9 A: possible mechanism of receptor binding and membrane Translocation.
Authors: Han, M. / Gurevich, V.V. / Vishnivetskiy, S.A. / Sigler, P.B. / Schubert, C.
History
DepositionOct 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-ARRESTIN1
B: BETA-ARRESTIN1


Theoretical massNumber of molelcules
Total (without water)88,6192
Polymers88,6192
Non-polymers00
Water4,846269
1
A: BETA-ARRESTIN1


Theoretical massNumber of molelcules
Total (without water)44,3101
Polymers44,3101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-ARRESTIN1


Theoretical massNumber of molelcules
Total (without water)44,3101
Polymers44,3101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.400, 73.717, 115.760
Angle α, β, γ (deg.)90.00, 98.73, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein BETA-ARRESTIN1


Mass: 44309.578 Da / Num. of mol.: 2 / Fragment: TRUNCATION MUTANT: 1-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Plasmid: PTRC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17870
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.33 %
Crystal grow
*PLUS
Temperature: 19-20 ℃ / pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein11or 7mg/ml
20.1 M11NaCl
320 mMTris-HCl11
41 mMEDTA11
510 mMdithiothreitol11
65 %glycerol11
712-14.5 %PEG400012
80.4 M12BaCl2
90.1 MTris-HCl12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979, 1.10
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Apr 30, 2000 / Details: mirrors and Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionBiso Wilson estimate: 22.3 Å2
Reflection
*PLUS
Highest resolution: 1.96 Å / Lowest resolution: 35 Å / Num. obs: 49309 / % possible obs: 65.8 % / Redundancy: 3.2 % / Num. measured all: 158905 / Rmerge(I) obs: 0.047
Reflection shell
*PLUS
Redundancy: 1.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 1.1

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SIRAS
Starting model: PDB ENTRY 1CF1

1cf1


Resolution: 1.9→34.54 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2567021.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 5401 7.6 %RANDOM
Rwork0.235 ---
all0.249 81909 --
obs0.235 70650 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.45 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso mean: 55.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.21 Å20 Å2-7.14 Å2
2--17.93 Å20 Å2
3----9.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 1.9→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5657 0 0 269 5926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it3.531.5
X-RAY DIFFRACTIONc_mcangle_it4.922
X-RAY DIFFRACTIONc_scbond_it4.732
X-RAY DIFFRACTIONc_scangle_it6.382.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.402 237 8 %
Rwork0.379 2709 -
obs--36.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 7.6 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 55.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.11
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.402 / % reflection Rfree: 8 % / Rfactor Rwork: 0.379

+
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