[English] 日本語
Yorodumi
- PDB-5ewo: Crystal structure of the human astrovirus 1 capsid protein spike ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ewo
TitleCrystal structure of the human astrovirus 1 capsid protein spike domain at 0.95-A resolution
ComponentsStructural protein
KeywordsVIRAL PROTEIN / capsid protein / icosahedral virus / beta barrel
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / host extracellular space / Capsid polyprotein VP90
Function and homology information
Biological speciesHuman astrovirus-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsBogdanoff, W. / York, R.L. / Yousefi, P.A. / Haile, S. / Tripathi, S. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095369 United States
CitationJournal: J.Virol. / Year: 2015
Title: Structural, Mechanistic, and Antigenic Characterization of the Human Astrovirus Capsid.
Authors: York, R.L. / Yousefi, P.A. / Bogdanoff, W. / Haile, S. / Tripathi, S. / DuBois, R.M.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6165
Polymers25,2321
Non-polymers3844
Water2,918162
1
A: Structural protein
hetero molecules

A: Structural protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,23210
Polymers50,4632
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4970 Å2
ΔGint-110 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.230, 103.230, 41.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-933-

HOH

-
Components

#1: Protein Structural protein


Mass: 25231.674 Da / Num. of mol.: 1 / Fragment: spike domain (UNP residues 429-645)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus-1 / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q82452
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: PEG 400, Ammonium sulfate , MES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 0.95→16.21 Å / Num. obs: 141071 / % possible obs: 90.5 % / Redundancy: 6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Net I/σ(I): 13.7 / Num. measured all: 756406
Reflection shell

Rpim(I) all: 0.022 / Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rsym value% possible all
0.95-14.50.4553.160237134630.8420.05167.4
3-16.216.20.05127.12275136510.9960.05676.2

-
Processing

Software
NameVersionClassification
MOSFLM3.3.21data reduction
SCALA3.3.21data scaling
PHASERphasing
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QSQ

3qsq


Resolution: 0.95→16.122 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / Phase error: 11.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1425 6354 5.01 %
Rwork0.1313 --
obs0.1319 126817 89.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.04 Å2 / Biso mean: 11.7822 Å2 / Biso min: 4.15 Å2
Refinement stepCycle: final / Resolution: 0.95→16.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 20 162 1860
Biso mean--17.48 18.23 -
Num. residues----214

+
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