[English] 日本語
Yorodumi
- PDB-5i1p: Villin headpiece subdomain with a Lys30 to beta-3-homolysine subs... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i1p
TitleVillin headpiece subdomain with a Lys30 to beta-3-homolysine substitution
Components
  • D-Villin headpiece subdomain
  • Villin-1
KeywordsDE NOVO PROTEIN / quasiracemic
Function / homology
Function and homology information


regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping ...regulation of actin nucleation / lysophosphatidic acid binding / cytoplasmic actin-based contraction involved in cell motility / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to hepatocyte growth factor stimulus / actin filament bundle / microvillus / positive regulation of epithelial cell migration / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / cellular response to epidermal growth factor stimulus / response to bacterium / filopodium / epidermal growth factor receptor signaling pathway / actin filament binding / regulation of cell shape / lamellipodium / actin cytoskeleton / 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
ETHANOL / polypeptide(D) / polypeptide(D) (> 10) / Villin-1
Similarity search - Component
Biological speciesGallus gallus (chicken)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsKreitler, D.F. / Mortenson, D.E. / Gellman, S.H. / Forest, K.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 1518160 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM00839 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM061238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08293 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2016
Title: Effects of Single alpha-to-beta Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization.
Authors: Kreitler, D.F. / Mortenson, D.E. / Forest, K.T. / Gellman, S.H.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Refinement description
Revision 1.3Jul 13, 2016Group: Refinement description
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Villin-1
B: Villin-1
C: Villin-1
D: Villin-1
E: D-Villin headpiece subdomain
F: D-Villin headpiece subdomain
G: D-Villin headpiece subdomain
H: D-Villin headpiece subdomain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,88011
Polymers32,7428
Non-polymers1383
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-14 kcal/mol
Surface area16230 Å2
Unit cell
Length a, b, c (Å)24.570, 40.600, 59.020
Angle α, β, γ (deg.)96.450, 90.660, 95.370
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein/peptide
Villin-1


Mass: 4101.770 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P02640
#2: Polypeptide(D)
D-Villin headpiece subdomain


Mass: 4083.716 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.78 Å3/Da / Density % sol: 31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl pH 8.5, 20% (v/v) ethanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→40.16 Å / Num. obs: 42605 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9.76
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.441.371.07193.3
1.44-1.481.1741.3193.6
1.48-1.520.8451.76193.9
1.52-1.570.6352.3194.4
1.57-1.620.5532.62194.8
1.62-1.670.4413.21195
1.67-1.740.3274.1195.4
1.74-1.810.2455.27195.6
1.81-1.890.1876.69196
1.89-1.980.1368.76196.5
1.98-2.090.09711.44196.6
2.09-2.210.07414.4197.3
2.21-2.370.06117.11197.5
2.37-2.560.05319.68197.7
2.56-2.80.04821.6197.9
2.8-3.130.04324.47198.3
3.13-3.610.03528.26198.6
3.61-4.430.03231.73199.1
4.43-6.260.0330.9199.3
6.260.03231.52196.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TRY

3try


Resolution: 1.4→40.16 Å / Rfactor Rfree: 0.235 / Rfactor Rwork: 0.21 / Cross valid method: FREE R-VALUE
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 29.6654 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 9 151 2438

+
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