[English] 日本語
Yorodumi
- PDB-9dr0: Hare calicivirus protruding domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dr0
TitleHare calicivirus protruding domain
ComponentsHare calicivirus protruding domain
KeywordsVIRAL PROTEIN / lagovirus / hare calicivirus
Function / homologyACETIC ACID
Function and homology information
Biological speciesHare calicivirus Australia-1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsReese, T. / Pancera, M. / Hansman, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2024
Title: Structural analysis of a non-pathogenic hare calicivirus capsid bound to a histo-blood group antigen co-factor.
Authors: Hansman, G.S. / Reese, T. / Pancera, M. / Rudd, P.A. / Masic, V. / Haselhorst, T. / von Itzstein, M.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hare calicivirus protruding domain
B: Hare calicivirus protruding domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,56210
Polymers70,0692
Non-polymers4938
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint3 kcal/mol
Surface area22860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.475, 82.972, 74.566
Angle α, β, γ (deg.)90.000, 90.890, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Hare calicivirus protruding domain


Mass: 35034.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hare calicivirus Australia-1 / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.4 Å3/Da / Density % sol: 48.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium acetate tetrahydrate, 0.1 M MES, pH 6.5, 20% w/v PEG8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.55→44.31 Å / Num. obs: 94671 / % possible obs: 99.45 % / Redundancy: 4 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.997 / Net I/σ(I): 7.6
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.335 / Num. unique obs: 9173

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→44.31 Å / SU ML: 0.2072 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3275
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1803 1990 2.1 %
Rwork0.1613 92681 -
obs0.1617 94671 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.33 Å2
Refinement stepCycle: LAST / Resolution: 1.55→44.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4842 0 32 502 5376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00995060
X-RAY DIFFRACTIONf_angle_d1.06376953
X-RAY DIFFRACTIONf_chiral_restr0.0709788
X-RAY DIFFRACTIONf_plane_restr0.01927
X-RAY DIFFRACTIONf_dihedral_angle_d12.71821725
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.33951330.3126353X-RAY DIFFRACTION96.27
1.59-1.640.29651400.28126605X-RAY DIFFRACTION99.75
1.64-1.680.28251510.26126599X-RAY DIFFRACTION99.79
1.68-1.740.27231380.23426621X-RAY DIFFRACTION99.66
1.74-1.80.22831470.20966634X-RAY DIFFRACTION99.79
1.8-1.870.23631390.18896655X-RAY DIFFRACTION99.9
1.87-1.960.20871410.17726622X-RAY DIFFRACTION99.9
1.96-2.060.17141430.15396623X-RAY DIFFRACTION99.79
2.06-2.190.16831500.14966649X-RAY DIFFRACTION99.82
2.19-2.360.20531390.15356644X-RAY DIFFRACTION99.79
2.36-2.60.17981430.15816648X-RAY DIFFRACTION99.82
2.6-2.970.1741400.15456652X-RAY DIFFRACTION99.74
2.97-3.750.17971420.14086657X-RAY DIFFRACTION99.5
3.75-44.310.12151440.13456719X-RAY DIFFRACTION98.82

+
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