[English] 日本語
Yorodumi
- PDB-1wy3: Chicken villin subdomain HP-35, K65(NLE), N68H, pH7.0 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wy3
TitleChicken villin subdomain HP-35, K65(NLE), N68H, pH7.0
ComponentsVillin
KeywordsSTRUCTURAL PROTEIN / villin headgroup subdomain
Function / homology
Function and homology information


regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / microvillus / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / ruffle / cellular response to epidermal growth factor stimulus / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Villin headpiece / Villin headpiece domain superfamily / Villin headpiece domain / Headpiece (HP) domain profile. / Villin headpiece domain / Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsChiu, T.K. / Kubelka, J. / Herbst-Irmer, R. / Eaton, W.A. / Hofrichter, J. / Davies, D.R.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein.
Authors: Chiu, T.K. / Kubelka, J. / Herbst-Irmer, R. / Eaton, W.A. / Hofrichter, J. / Davies, D.R.
History
DepositionFeb 4, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Villin


Theoretical massNumber of molelcules
Total (without water)4,0731
Polymers4,0731
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)19.689, 40.022, 75.148
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1037-

HOH

-
Components

#1: Protein/peptide Villin


Mass: 4072.729 Da / Num. of mol.: 1 / Fragment: VHP / Mutation: K65(NLE), N68H / Source method: obtained synthetically
Details: synthetic peptide, sequence corresponds to Chicken Villin residues 792-826, residue 65 is norleucine (lysine without terminal NH3 group)
References: UniProt: P02640
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 293 K / pH: 7
Details: 1ul 50mg/ml peptide plus 1ul (200mM KFormate, 20% PEG3350), pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 7.00

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.95→30 Å / Num. obs: 17326 / % possible obs: 90.1 % / Observed criterion σ(I): -3 / Redundancy: 16.3 % / Rsym value: 0.064 / Net I/σ(I): 20.5
Reflection shellResolution: 0.95→0.98 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.213 / % possible all: 57.6

-
Processing

Software
NameClassification
MAR345data collection
HKL-2000data reduction
EPMRphasing
SHELXL-97refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRF

1yrf


Resolution: 0.95→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC B-VALUE FOR ALL ATOMS RIDING HYDROGENS; RESIDUE 65 IS NORLEUCINE (LYSINE WITHOUT TERMINAL NH3 GROUP) SHELX: DEFS 0.02 0.02 0.01, SIMU 0.05, ISOR 0.05, WGHT 0.25, SWAT.
RfactorNum. reflectionSelection details
Rfree0.171 666 RANDOM
obs0.145 --
all-17315 -
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 0.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms605 0 0 51 656
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0.02
X-RAY DIFFRACTIONs_from_restr_planes0.02
X-RAY DIFFRACTIONs_zero_chiral_vol0.02
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

+
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