[English] 日本語
Yorodumi
- PDB-8ufo: Crystal Structure of Gastrointestinal HAstV VA1 capsid spike doma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ufo
TitleCrystal Structure of Gastrointestinal HAstV VA1 capsid spike domain at 1.46 A resolution
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / Human Astrovirus / Capsid spike domain / Antigenicity
Function / homologyCapsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / Capsid polyprotein VP86
Function and homology information
Biological speciesAstrovirus VA1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsGhosh, A. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI144090 United States
CitationJournal: Plos Pathog. / Year: 2024
Title: Structure and antigenicity of the divergent human astrovirus VA1 capsid spike.
Authors: Ghosh, A. / Delgado-Cunningham, K. / Lopez, T. / Green, K. / Arias, C.F. / DuBois, R.M.
History
DepositionOct 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid polyprotein VP90
C: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)64,4672
Polymers64,4672
Non-polymers00
Water10,070559
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-36 kcal/mol
Surface area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.616, 82.559, 61.120
Angle α, β, γ (deg.)90.000, 102.710, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-920-

HOH

21A-982-

HOH

-
Components

#1: Protein Capsid polyprotein VP90


Mass: 32233.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Astrovirus VA1 / Production host: Escherichia coli (E. coli) / References: UniProt: C7BG48
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 559 / 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: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris-HCl pH 8.5, and 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.46→65.35 Å / Num. obs: 91234 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 10.82 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.7
Reflection shellResolution: 1.46→1.49 Å / Rmerge(I) obs: 0.15 / Num. unique obs: 9043 / CC1/2: 0.981

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→41.28 Å / SU ML: 0.1169 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.389
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1771 2000 2.19 %
Rwork0.1528 89234 -
obs0.1533 91234 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.83 Å2
Refinement stepCycle: LAST / Resolution: 1.46→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 0 559 4817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00674454
X-RAY DIFFRACTIONf_angle_d1.03686089
X-RAY DIFFRACTIONf_chiral_restr0.0907662
X-RAY DIFFRACTIONf_plane_restr0.0101781
X-RAY DIFFRACTIONf_dihedral_angle_d13.22991589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.19981410.18126318X-RAY DIFFRACTION99.92
1.5-1.540.18891420.16496323X-RAY DIFFRACTION99.98
1.54-1.590.19721440.15796376X-RAY DIFFRACTION99.98
1.59-1.640.15941430.1536381X-RAY DIFFRACTION100
1.64-1.70.19411410.15756342X-RAY DIFFRACTION100
1.7-1.760.18221430.15876354X-RAY DIFFRACTION100
1.76-1.840.20031420.15956364X-RAY DIFFRACTION100
1.84-1.940.20621430.15526367X-RAY DIFFRACTION100
1.94-2.060.16371420.15066355X-RAY DIFFRACTION100
2.06-2.220.16431430.14846375X-RAY DIFFRACTION100
2.22-2.450.1951440.1536407X-RAY DIFFRACTION100
2.45-2.80.17971430.1616359X-RAY DIFFRACTION100
2.8-3.530.15751430.15216411X-RAY DIFFRACTION100
3.53-41.280.16811460.146502X-RAY DIFFRACTION99.97

+
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