[English] 日本語
Yorodumi
- PDB-1kri: NMR Solution Structures of the Rhesus Rotavirus VP4 Sialic Acid B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kri
TitleNMR Solution Structures of the Rhesus Rotavirus VP4 Sialic Acid Binding Domain without Ligand
ComponentsVP4
KeywordsVIRAL PROTEIN / rotavirus / VP4 / VP8* / spike protein / outer capsid / sialic acid / hemagglutinin / cell attachment / neutralization antigen / lectin / galectin fold
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / 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 ...Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / 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
Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodSOLUTION NMR / simulated annealing
AuthorsDormitzer, P.R. / Sun, Z.-Y.J. / Wagner, G. / Harrison, S.C.
Citation
Journal: Embo J. / Year: 2002
Title: The Rhesus Rotavirus VP4 Sialic Acid Binding Domain has a Galectin Fold with a Novel Carbohydrate Binding Site
Authors: Dormitzer, P.R. / Sun, Z.-Y.J. / Wagner, G. / Harrison, S.C.
#1: Journal: J.Virol. / Year: 2001
Title: Proteolysis of Monomeric Recombinant Rotavirus VP4 Yields an Oligomeric VP5* Core
Authors: Dormitzer, P.R. / Greenberg, H.B. / Harrison, S.C.
History
DepositionJan 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 27, 2016Group: Other
Revision 1.4Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model
Revision 1.5May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700sheet determination method: author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: VP4


Theoretical massNumber of molelcules
Total (without water)20,8171
Polymers20,8171
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 25structures with the least restraint violations
RepresentativeModel #1least restraint violations

-
Components

#1: Protein VP4


Mass: 20816.887 Da / Num. of mol.: 1 / Fragment: sialic acid binding domain (residues 46-231)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Gene: segment 4 / Plasmid: pGEX-VP8(46-231) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 & DL39 / References: UniProt: P12473

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HSQC
122HNCA
132HN(CO)CA
142HN(CA)CB
152HN(CO)CACB
162HNCO
172HN(CA)CO
182(H)CC(CO)NH
193HSQC
1101HNHA
1111HNHB
11213D-15N-separated TOCHSQC
1134(H)CCH-TOCSY
114513C-HSQC
11562D-D2O-TOCSY
11643D-13C-separated NOESY
11713D-15N-separated NOEHSQC
11862D-D2O-NOESY
NMR detailsText: The N-terminal 19 residues (A46 to V64 of VP4) and the C-terminal 7 residues (P225 to R231 of VP4) are disordered and are not included in the models.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM EcVP8(46-231) U-15N90% H2O/10% D2O
21 mM EcVP8(46-231) U-15N, 13C, 2D90% H2O/10% D2O
30.1 mM EcVP8(46-231) U-15N-ile or U-15N-leu or U-15N-phe or U-15N-tyr or U-15N-val90% H2O/10% D2O
41 mM EcVP8(46-231) U-15N, 13C90% H2O/10% D2O
51 mM EcVP8(46-231) U-10% 13C90% H2O/10% D2O
61 mM EcVP8(46-231)100% D2O
Sample conditionsIonic strength: 20 mM NaPO4, 10 mM NaCl, 0.02% Na azide / pH: 7 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY5001
Bruker AVANCEBrukerAVANCE6002
Varian INOVAVarianINOVA7503

-
Processing

NMR software
NameVersionDeveloperClassification
PROSA3.7Guntert, P., Dotsch, V., Wider, G., Wuthrich, K.processing
XEASY1.3.13Bartels, C., Xia, T.-H., Billeter, M., Guntert., P., Wuthrich, K.data analysis
DYANA1.5Guntert, P., Murmenthaler, C., Wuthrich, K.data analysis
TALOSCornilescu, G., Delaglio, F., Bax, A.data analysis
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.structure solution
CNS1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T., Warren, G.L.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The models are based on a total of 1993 constraints (12.5 constraints per residue): 1793 NOE-derived distance constraints; 116 TALOS-derived dihedral angle constraints; and 84 hydrogen bond ...Details: The models are based on a total of 1993 constraints (12.5 constraints per residue): 1793 NOE-derived distance constraints; 116 TALOS-derived dihedral angle constraints; and 84 hydrogen bond constraints, based on the identification of slow exchange amide protons in D2O NOESY and TOCSY experiments, on characteristic NOE patterns for alpha-helices and beta-sheets, and on the proximity and orientation of potential hydrogen bond partners in annealed structures. The final set of 20 structures contains no violations of NOE distance constraints greater than 0.15 angstroms and no violations of dihedral angle constraints greater than 5 degrees.
NMR representativeSelection criteria: least restraint violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 25 / Conformers submitted total number: 20

+
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