[English] 日本語
Yorodumi
- PDB-1i7a: EVH1 DOMAIN FROM MURINE HOMER 2B/VESL 2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i7a
TitleEVH1 DOMAIN FROM MURINE HOMER 2B/VESL 2
Components
  • HOMER 2B
  • PHE-ALA-PHE
KeywordsSIGNALING PROTEIN / EVH1 domain / Homer / Vesl / X-ray crystal structure / brain
Function / homology
Function and homology information


G protein-coupled glutamate receptor binding / Neurexins and neuroligins / intracellular organelle / synaptic receptor adaptor activity / stereocilium tip / G protein-coupled glutamate receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / behavioral response to cocaine ...G protein-coupled glutamate receptor binding / Neurexins and neuroligins / intracellular organelle / synaptic receptor adaptor activity / stereocilium tip / G protein-coupled glutamate receptor signaling pathway / regulation of G protein-coupled receptor signaling pathway / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / behavioral response to cocaine / calcium-mediated signaling / sensory perception of sound / apical part of cell / actin binding / postsynaptic density / glutamatergic synapse / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Homer, EVH1 domain / Homer family / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / PHENYLALANINE / Homer protein homolog 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsBarzik, M. / Carl, U.D. / Schubert, W.-D. / Wehland, J. / Heinz, D.W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The N-terminal domain of Homer/Vesl is a new class II EVH1 domain.
Authors: Barzik, M. / Carl, U.D. / Schubert, W.D. / Frank, R. / Wehland, J. / Heinz, D.W.
History
DepositionMar 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Aug 9, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: HOMER 2B
B: HOMER 2B
C: HOMER 2B
D: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,56210
Polymers50,6885
Non-polymers8745
Water1,910106
1
A: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3144
Polymers12,9602
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9303
Polymers12,5761
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HOMER 2B


Theoretical massNumber of molelcules
Total (without water)12,5761
Polymers12,5761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7412
Polymers12,5761
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: HOMER 2B
hetero molecules

B: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0556
Polymers25,5363
Non-polymers5193
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_556-x,y+1/2,-z+11
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-13 kcal/mol
Surface area10380 Å2
MethodPISA
6
A: HOMER 2B
hetero molecules

C: HOMER 2B


Theoretical massNumber of molelcules
Total (without water)25,5074
Polymers25,1522
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area2610 Å2
ΔGint-6 kcal/mol
Surface area10230 Å2
MethodPISA
7
C: HOMER 2B

A: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8905
Polymers25,5363
Non-polymers3542
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation2_646-x+1,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-11 kcal/mol
Surface area10290 Å2
MethodPISA
8
B: HOMER 2B
hetero molecules

D: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6725
Polymers25,1522
Non-polymers5193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y+1/2,-z+11
Buried area2650 Å2
ΔGint-7 kcal/mol
Surface area10320 Å2
MethodPISA
9
E: PHE-ALA-PHE


  • defined by software
  • 383 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)3831
Polymers3831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
B: HOMER 2B
E: PHE-ALA-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3144
Polymers12,9602
Non-polymers3542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-6 kcal/mol
Surface area6350 Å2
MethodPISA
11
A: HOMER 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9303
Polymers12,5761
Non-polymers3542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.716, 50.014, 73.098
Angle α, β, γ (deg.)90.00, 101.19, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
HOMER 2B / HOMER 2B/VESL 2


Mass: 12576.193 Da / Num. of mol.: 4 / Fragment: EVH1 DOMAIN (N-TERMINAL)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Plasmid: PGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CODON + / References: UniProt: Q9QWW1
#2: Protein/peptide PHE-ALA-PHE


Mass: 383.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M SODIUM CITRATE, O.1 M CHES, pH 9.8, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal
*PLUS
Density % sol: 55.3 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.6 Mammonium sulfate11
20.1 MHEPES11
310 mMNAD11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2000 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 59066 / Num. obs: 22446 / % possible obs: 95.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3 / Num. unique all: 2060 / % possible all: 88.2
Reflection shell
*PLUS
% possible obs: 88.2 % / Rmerge(I) obs: 0.28

-
Processing

Software
NameClassification
EPMRphasing
CNSrefinement
REFMACrefinement
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DDW (SAME MOLECULE IN DIFFERENT PACKING DERIVED FROM HOMER 1B FROM RAT

1ddw


Resolution: 2.24→15 Å / Isotropic thermal model: Isotropic / σ(F): 3 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: The crystal had a particularly high mosaicity.
RfactorNum. reflection% reflectionSelection details
Rfree0.296 961 4.9 %random
Rwork0.235 ---
all-23487 --
obs-19460 85.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.77 Å21.19 Å20.23 Å2
2--0 Å2-0.89 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.24→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 60 108 3515
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d1.186
X-RAY DIFFRACTIONp_bond_d0.068
LS refinement shellResolution: 2.2→2.24 Å
RfactorNum. reflection% reflection
Rfree0.35 26 -
Rwork0.25 --
obs-705 83.7 %
Software
*PLUS
Name: CNS/REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 3 / % reflection Rfree: 4.9 % / Rfactor obs: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_d

+
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