[English] 日本語
Yorodumi
- PDB-8v9a: GII.NA1 Loreto 1257 norovirus protruding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v9a
TitleGII.NA1 Loreto 1257 norovirus protruding domain
ComponentsCapsid protein VP1
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 / VP1
Function and homology information
Biological speciesNorovirus GII
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKher, G. / Kim, I. / Pancera, M. / Hansman, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)FOR2327 Germany
CitationJournal: J.Virol. / Year: 2024
Title: Development of a broad-spectrum therapeutic Fc-nanobody for human noroviruses.
Authors: Hansman, G.S. / Kher, G. / Svirina, A.D. / Tame, J.R.H. / Hartley-Tassell, L. / Irie, H. / Haselhorst, T. / von Itzstein, M. / Rudd, P.A. / Pancera, M.
History
DepositionDec 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,11921
Polymers118,9392
Non-polymers1,17919
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.704, 71.156, 78.386
Angle α, β, γ (deg.)90.00, 110.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Capsid protein VP1


Mass: 59469.730 Da / Num. of mol.: 2 / Fragment: NA1-Loreto1257 P Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2H4Y915
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M Tris (Ph 7.0) 10% w/v PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.67→45.38 Å / Num. obs: 75438 / % possible obs: 99.5 % / Redundancy: 4.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.071 / Rrim(I) all: 0.153 / Χ2: 0.51 / Net I/σ(I): 6.3 / Num. measured all: 344784
Reflection shellResolution: 1.67→1.69 Å / % possible obs: 92.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.309 / Num. measured all: 15533 / Num. unique obs: 3505 / CC1/2: 0.453 / Rpim(I) all: 0.683 / Rrim(I) all: 1.481 / Χ2: 0.42 / Net I/σ(I) obs: 0.8

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→45.38 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 3763 4.99 %
Rwork0.1851 --
obs0.1865 75383 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→45.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4806 0 76 456 5338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115007
X-RAY DIFFRACTIONf_angle_d1.0356820
X-RAY DIFFRACTIONf_dihedral_angle_d13.5141815
X-RAY DIFFRACTIONf_chiral_restr0.06748
X-RAY DIFFRACTIONf_plane_restr0.01900
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.36961290.32242377X-RAY DIFFRACTION89
1.69-1.710.30741290.29382680X-RAY DIFFRACTION100
1.71-1.730.31061630.2862629X-RAY DIFFRACTION100
1.73-1.760.32821320.26512649X-RAY DIFFRACTION100
1.76-1.780.26981270.24932691X-RAY DIFFRACTION100
1.78-1.810.2591400.23892597X-RAY DIFFRACTION100
1.81-1.840.26221430.2322681X-RAY DIFFRACTION100
1.84-1.870.251520.22792643X-RAY DIFFRACTION100
1.87-1.910.25091270.21682656X-RAY DIFFRACTION100
1.91-1.940.2431490.21742623X-RAY DIFFRACTION100
1.94-1.980.22631300.21492651X-RAY DIFFRACTION99
1.98-2.030.24381330.19832682X-RAY DIFFRACTION100
2.03-2.070.21911420.18122631X-RAY DIFFRACTION100
2.07-2.120.19621410.17222655X-RAY DIFFRACTION100
2.12-2.180.22941440.172652X-RAY DIFFRACTION100
2.18-2.250.21111410.16952682X-RAY DIFFRACTION100
2.25-2.320.1981290.16862663X-RAY DIFFRACTION100
2.32-2.40.20311480.17642628X-RAY DIFFRACTION100
2.4-2.50.22481400.17122670X-RAY DIFFRACTION100
2.5-2.610.23771450.17382676X-RAY DIFFRACTION100
2.61-2.750.21771310.17422658X-RAY DIFFRACTION100
2.75-2.920.21341470.18062660X-RAY DIFFRACTION100
2.92-3.150.19751380.17762687X-RAY DIFFRACTION100
3.15-3.460.19771400.17762678X-RAY DIFFRACTION100
3.46-3.960.1781420.16562682X-RAY DIFFRACTION100
3.96-4.990.14941350.14042689X-RAY DIFFRACTION100
5-45.380.19331460.18682750X-RAY DIFFRACTION99

+
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