[English] 日本語
Yorodumi
- PDB-4rpd: Crystal Structure of P Domain of 485 Norovirus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rpd
TitleCrystal Structure of P Domain of 485 Norovirus
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Virus Binding / HBGA / Virus surface / Protruding domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.51 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: mSphere / Year: 2016
Title: Structural Constraints on Human Norovirus Binding to Histo-Blood Group Antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)67,3512
Polymers67,3512
Non-polymers00
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-12 kcal/mol
Surface area23260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.410, 73.500, 81.810
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Capsid protein


Mass: 33675.602 Da / Num. of mol.: 2 / Fragment: P DOMAIN RESIDUES 225-525
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus / Gene: ORF2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q20K66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 291 K
Details: Potassium Formate 0.2 M, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 3, 2014
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→48.84 Å / Num. obs: 92638 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.95 Å2 / Rmerge(I) obs: 0.065 / Χ2: 0.984 / Net I/σ(I): 14.24

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.51→48.84 Å / SU ML: 0.16 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 4560 5 %
Rwork0.146 --
obs-91190 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.82 Å2
Refinement stepCycle: LAST / Resolution: 1.51→48.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 0 652 5318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094948
X-RAY DIFFRACTIONf_angle_d1.2866807
X-RAY DIFFRACTIONf_dihedral_angle_d12.3211793
X-RAY DIFFRACTIONf_chiral_restr0.05750
X-RAY DIFFRACTIONf_plane_restr0.007911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.52720.27831500.22142860301099
1.5272-1.54510.2941530.23022890304399
1.5451-1.5640.32831480.24452811295998
1.564-1.58380.29781540.211729323086100
1.5838-1.60460.27681520.197128853037100
1.6046-1.62660.23551530.193729003053100
1.6266-1.64980.26221510.173828673018100
1.6498-1.67450.25871540.16629383092100
1.6745-1.70060.22871520.157728783030100
1.7006-1.72850.23311520.151728873039100
1.7285-1.75830.20891520.14972896304899
1.7583-1.79030.23761510.148728883039100
1.7903-1.82470.20251530.15292896304999
1.8247-1.8620.20211500.15262846299698
1.862-1.90250.1941520.154428943046100
1.9025-1.94670.24031540.15529293083100
1.9467-1.99540.22221530.145629083061100
1.9954-2.04940.20851510.13752865301699
2.0494-2.10970.19241530.141729083061100
2.1097-2.17780.18951510.13792863301499
2.1778-2.25560.19431520.14172902305499
2.2556-2.34590.18261500.13192846299698
2.3459-2.45270.16171530.13642898305199
2.4527-2.5820.16811530.14112914306799
2.582-2.74370.19651520.14192882303499
2.7437-2.95550.18911530.14332913306699
2.9555-3.25290.13531510.14292858300998
3.2529-3.72350.16671490.14412847299697
3.7235-4.69060.14491540.12562909306398
4.6906-48.86230.15411540.13872920307497

+
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