[English] 日本語
Yorodumi
- PDB-6h9w: Unraveling the role of the secretor antigen in human rotavirus at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h9w
TitleUnraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / histo-blood group antigen rotavirus
Function / homology
Function and homology information


host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / ISOPROPYL ALCOHOL / Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsCiges-Tomas, J.R. / Gozalbo-Rovira, R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Rodriguez-Diaz, J. / Marina, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2016-78571-P Spain
CitationJournal: Plos Pathog. / Year: 2019
Title: Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens.
Authors: Gozalbo-Rovira, R. / Ciges-Tomas, J.R. / Vila-Vicent, S. / Buesa, J. / Santiso-Bellon, C. / Monedero, V. / Yebra, M.J. / Marina, A. / Rodriguez-Diaz, J.
History
DepositionAug 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2478
Polymers18,5501
Non-polymers6977
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-27 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.148, 76.148, 70.084
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-205-

CIT

-
Components

#1: Protein Outer capsid protein VP4


Mass: 18550.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G1 and S2 are residuals from tag digestion / Source: (gene. exp.) Rotavirus A / Gene: VP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S0VKY7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop
Details: 1.2M (NH 4 ) 2 SO 4 3% iso-propanol and 0.1M sodium citrate pH4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.35→65.95 Å / Num. obs: 52302 / % possible obs: 99.9 % / Redundancy: 10 % / CC1/2: 0.999 / Rpim(I) all: 0.021 / Net I/σ(I): 15.9
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7527 / CC1/2: 0.932 / Rpim(I) all: 0.266 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
Aimless5.8.0158data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I2S

2i2s


Resolution: 1.35→65.95 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.201 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2273 2612 5 %RANDOM
Rwork0.2058 ---
obs0.2069 49656 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.2 Å2 / Biso mean: 27.175 Å2 / Biso min: 14.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20.37 Å20 Å2
2--0.74 Å2-0 Å2
3----2.39 Å2
Refinement stepCycle: final / Resolution: 1.35→65.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 41 211 1544
Biso mean--38.74 39.09 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.021385
X-RAY DIFFRACTIONr_bond_other_d0.0030.021164
X-RAY DIFFRACTIONr_angle_refined_deg2.7031.9351894
X-RAY DIFFRACTIONr_angle_other_deg1.2532711
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.055166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93924.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84815209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.539159
X-RAY DIFFRACTIONr_chiral_restr0.1640.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021548
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02297
LS refinement shellResolution: 1.347→1.382 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 193 -
Rwork0.34 3608 -
all-3801 -
obs--99.14 %

+
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