[English] 日本語
Yorodumi
- PDB-9nsm: Crystal structure of the bat rotavirus apo P[10] VP8* receptor bi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nsm
TitleCrystal structure of the bat rotavirus apo P[10] VP8* receptor binding domain at 1.85 angstrom resolution
ComponentsOuter capsid protein VP8*
KeywordsVIRAL PROTEIN / Rotavirus / receptor binding domain
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsKennedy, M.A. / Ni, S. / Li, F. / Wang, D. / Soni, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the bat rotavirus apo P[10] VP8* receptor binding domain at 1.85 angstrom resolution
Authors: Kennedy, M.A. / Ni, S. / Li, F. / Wang, D. / Soni, S.
History
DepositionMar 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer capsid protein VP8*
B: Outer capsid protein VP8*
C: Outer capsid protein VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,06219
Polymers59,4183
Non-polymers64416
Water3,945219
1
A: Outer capsid protein VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1058
Polymers19,8061
Non-polymers2997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0137
Polymers19,8061
Non-polymers2076
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer capsid protein VP8*
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9444
Polymers19,8061
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)158.345, 92.996, 42.534
Angle α, β, γ (deg.)90.00, 93.48, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Outer capsid protein VP8*


Mass: 19805.980 Da / Num. of mol.: 3
Fragment: The protein contains an N-terminal 6x-His tag that includes a thrombin cut site.
Source method: isolated from a genetically manipulated source
Details: Receptor binding domain / Source: (gene. exp.) Rotavirus / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7R7E052
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Crystallization buffer 0.2 mM lithium sulfate, 0.1 M Tris, pH 8.5 25% PEG 4000, 10 % glycerol Protein buffer 250 mM NaCl, 20 mM Tris, pH 8.0, 10 % glycerol, 300 mM imidazole

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.85→46.5 Å / Num. obs: 59422 / % possible obs: 97.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.834 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.191 / Rpim(I) all: 0.089 / Rrim(I) all: 0.221 / Net I/σ(I): 7.4
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 7.44 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 14416 / CC1/2: 0.747 / Rpim(I) all: 0.361 / Rrim(I) all: 0.998 / % possible all: 96.75

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
DIALSdata scaling
xia2data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45.84 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 1749 3.42 %
Rwork0.1945 --
obs0.1951 51170 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 36 219 4207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064078
X-RAY DIFFRACTIONf_angle_d0.8385574
X-RAY DIFFRACTIONf_dihedral_angle_d14.3911450
X-RAY DIFFRACTIONf_chiral_restr0.054624
X-RAY DIFFRACTIONf_plane_restr0.008712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.34711310.33034032X-RAY DIFFRACTION96
1.9-1.970.30341290.29064042X-RAY DIFFRACTION96
1.97-2.040.30051060.26613975X-RAY DIFFRACTION93
2.04-2.120.25941230.24254137X-RAY DIFFRACTION98
2.12-2.210.25771480.22194140X-RAY DIFFRACTION98
2.21-2.330.26841670.21784116X-RAY DIFFRACTION98
2.33-2.480.23841610.2044162X-RAY DIFFRACTION99
2.48-2.670.23981430.20764157X-RAY DIFFRACTION99
2.67-2.940.21531660.2094145X-RAY DIFFRACTION99
2.94-3.360.22141650.19324145X-RAY DIFFRACTION99
3.36-4.230.18241460.16144103X-RAY DIFFRACTION96
4.23-45.840.15321640.14994267X-RAY DIFFRACTION100

+
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