[English] 日本語
Yorodumi
- PDB-3miw: Crystal Structure of Rotavirus NSP4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3miw
TitleCrystal Structure of Rotavirus NSP4
ComponentsNon-structural glycoprotein 4
KeywordsVIRAL PROTEIN / ROTAVIRUS ENTEROTOXIN / NON STRUCTURAL PROTEIN / NSP4 / PENTAMERIC COILED COIL / VIRULENCE
Function / homology
Function and homology information


host caveola / host cell rough endoplasmic reticulum membrane / : / : / : / protein complex oligomerization / monoatomic ion channel activity / toxin activity / membrane => GO:0016020 / induction by virus of host autophagy ...host caveola / host cell rough endoplasmic reticulum membrane / : / : / : / protein complex oligomerization / monoatomic ion channel activity / toxin activity / membrane => GO:0016020 / induction by virus of host autophagy / extracellular region / metal ion binding
Similarity search - Function
Rotavirus non-structural protein 4 / Rotavirus non structural protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Non-structural glycoprotein 4
Similarity search - Component
Biological speciesHuman rotavirus G4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChacko, A.R. / Read, R.J. / Dodson, E.J. / Rao, D.C. / Suguna, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: A new pentameric structure of rotavirus NSP4 revealed by molecular replacement.
Authors: Chacko, A.R. / Jeyakanthan, J. / Ueno, G. / Sekar, K. / Rao, C.D. / Dodson, E.J. / Suguna, K. / Read, R.J.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Non-structural glycoprotein 4
C: Non-structural glycoprotein 4
E: Non-structural glycoprotein 4
G: Non-structural glycoprotein 4
I: Non-structural glycoprotein 4
A: Non-structural glycoprotein 4
D: Non-structural glycoprotein 4
F: Non-structural glycoprotein 4
H: Non-structural glycoprotein 4
J: Non-structural glycoprotein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,73337
Polymers65,05710
Non-polymers1,67627
Water2,918162
1
B: Non-structural glycoprotein 4
C: Non-structural glycoprotein 4
E: Non-structural glycoprotein 4
G: Non-structural glycoprotein 4
I: Non-structural glycoprotein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,39819
Polymers32,5295
Non-polymers86914
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11910 Å2
ΔGint-82 kcal/mol
Surface area13080 Å2
MethodPISA
2
A: Non-structural glycoprotein 4
D: Non-structural glycoprotein 4
F: Non-structural glycoprotein 4
H: Non-structural glycoprotein 4
J: Non-structural glycoprotein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,33618
Polymers32,5295
Non-polymers80713
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10950 Å2
ΔGint-93 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.463, 63.463, 123.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11B-286-

HOH

21G-237-

HOH

31A-83-

HOH

41J-264-

HOH

-
Components

#1: Protein
Non-structural glycoprotein 4 / NSP4 / NCVP5 / NS28


Mass: 6505.740 Da / Num. of mol.: 10 / Fragment: DIARRHEA-INDUCING DOMAIN (UNP RESIDUES 95-146)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus G4 / Strain: strain St. Thomas 3 / Gene: G10 / Plasmid: PET22B+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q82035
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / 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: 1.91 Å3/Da / Density % sol: 35.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% Dioxane v/v, 0.1 M MES, 1.6 M Ammonium Sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 5, 2006 / Details: RH COATED BENT SI (1 1 1) MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.499
ReflectionResolution: 2.5→28.382 Å / Num. all: 16272 / Num. obs: 16272 / % possible obs: 95.1 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.21
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 2.22 / % possible all: 74.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)refinement
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→28.382 Å / σ(F): 1.34 / Phase error: 58.02 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2969 833 5.12 %
Rwork0.2612 --
obs0.2638 16272 96.37 %
all-16272 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 88.164 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.2547 Å20 Å2-0 Å2
2--21.2547 Å20 Å2
3----42.5094 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 108 162 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133403
X-RAY DIFFRACTIONf_angle_d1.5084511
X-RAY DIFFRACTIONf_dihedral_angle_d19.9131310
X-RAY DIFFRACTIONf_chiral_restr0.105560
X-RAY DIFFRACTIONf_plane_restr0.004575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5461-2.70530.439260.38562341X-RAY DIFFRACTION90
2.7053-2.91350.3496980.34632557X-RAY DIFFRACTION96
2.9135-3.20560.33421660.33342499X-RAY DIFFRACTION94
3.2056-3.66690.36082060.31522427X-RAY DIFFRACTION92
3.6669-4.61030.21631640.20662443X-RAY DIFFRACTION91
4.6103-19.80830.29981730.21522508X-RAY DIFFRACTION93

+
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