[English] 日本語
Yorodumi
- PDB-8vrv: GII.4c H2-tri HBGA norovirus protruding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vrv
TitleGII.4c H2-tri HBGA norovirus protruding domain
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / norovirus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / FORMIC ACID / Capsid protein
Function and homology information
Biological speciesNorovirus GII.4
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKher, G. / Prewitt, A. / Pancera, M. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: To Be Published
Title: Advancement of norovirus therapies
Authors: Hansman, G. / Kher, G.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,17212
Polymers67,3352
Non-polymers83710
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint6 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.666, 90.470, 91.339
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Capsid protein


Mass: 33667.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A168DBN0
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
LFucpa1-2DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a1221m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(2+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: SG1 1-24 0.2 M Magnesium formate dihydrate 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.61→49.26 Å / Num. obs: 82708 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.083 / Χ2: 0.56 / Net I/σ(I): 11.7 / Num. measured all: 562066
Reflection shellResolution: 1.61→1.64 Å / % possible obs: 98.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.797 / Num. measured all: 26494 / Num. unique obs: 3989 / CC1/2: 0.769 / Rpim(I) all: 0.326 / Rrim(I) all: 0.862 / Χ2: 0.51 / Net I/σ(I) obs: 1.7

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→45.67 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1849 4133 5 %
Rwork0.1565 --
obs0.1579 82627 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4726 0 55 669 5450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084916
X-RAY DIFFRACTIONf_angle_d0.9756717
X-RAY DIFFRACTIONf_dihedral_angle_d8.101672
X-RAY DIFFRACTIONf_chiral_restr0.059751
X-RAY DIFFRACTIONf_plane_restr0.009887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.31491360.25532539X-RAY DIFFRACTION98
1.63-1.650.25021410.20352589X-RAY DIFFRACTION100
1.65-1.670.23341250.1912595X-RAY DIFFRACTION100
1.67-1.690.22361410.192556X-RAY DIFFRACTION100
1.69-1.710.20351360.18162587X-RAY DIFFRACTION100
1.71-1.730.23241340.17932593X-RAY DIFFRACTION100
1.73-1.760.21221450.17112586X-RAY DIFFRACTION100
1.76-1.790.20711300.17152625X-RAY DIFFRACTION100
1.79-1.810.21091400.17132561X-RAY DIFFRACTION100
1.81-1.840.19791360.17022578X-RAY DIFFRACTION100
1.84-1.880.2141380.17392611X-RAY DIFFRACTION100
1.88-1.910.20891410.1652602X-RAY DIFFRACTION100
1.91-1.950.20231280.16282615X-RAY DIFFRACTION100
1.95-1.990.19611390.15992582X-RAY DIFFRACTION100
1.99-2.030.20131400.15162603X-RAY DIFFRACTION100
2.03-2.080.19271390.15552618X-RAY DIFFRACTION100
2.08-2.130.17911330.15512589X-RAY DIFFRACTION100
2.13-2.190.19321390.15192598X-RAY DIFFRACTION100
2.19-2.250.1781360.15442626X-RAY DIFFRACTION100
2.25-2.320.18971370.14822605X-RAY DIFFRACTION100
2.32-2.410.17691400.1472617X-RAY DIFFRACTION100
2.41-2.50.20131370.14862613X-RAY DIFFRACTION100
2.5-2.620.17141410.15272622X-RAY DIFFRACTION100
2.62-2.750.18551400.15742641X-RAY DIFFRACTION100
2.75-2.930.1721410.15982645X-RAY DIFFRACTION100
2.93-3.150.19781360.16242634X-RAY DIFFRACTION100
3.15-3.470.19171390.15082659X-RAY DIFFRACTION100
3.47-3.970.17041380.15262676X-RAY DIFFRACTION100
3.97-50.13821430.12222696X-RAY DIFFRACTION100
5-45.670.15831440.16222833X-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://pdbjlvh1.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