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- PDB-8hw5: Crystal structure of African swine fever virus CP312R -

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Basic information

Entry
Database: PDB / ID: 8hw5
TitleCrystal structure of African swine fever virus CP312R
ComponentsCP312R
KeywordsVIRAL PROTEIN / CP312R / African swine fever virus
Function / homologyACETIC ACID / CP312R
Function and homology information
Biological speciesAfrican swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, W.M. / Wang, Z.Y. / Fu, D. / Guo, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31941011 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: African swine fever virus pCP312R interacts with host RPS27A to shut off host protein translation and promotes viral replication.
Authors: Hagoss, Y.T. / Shen, D. / Wang, W. / Zhang, Z. / Li, F. / Sun, E. / Zhu, Y. / Ge, J. / Guo, Y. / Bu, Z. / Zhao, D.
History
DepositionDec 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CP312R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7795
Polymers31,5381
Non-polymers2404
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.993, 79.799, 47.545
Angle α, β, γ (deg.)90.00, 118.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CP312R / CP312R CDS protein / CP312R protein


Mass: 31538.459 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) African swine fever virus / Gene: CP312R CDS, CP312R, ASFV-Georgia_4-120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2X0RVH4
#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride BIS-TRIS PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 13790 / % possible obs: 98.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.992 / Χ2: 0.053 / Net I/σ(I): 12.8 / Num. measured all: 85579
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.3-2.342.80.2513290.944198.2
2.34-2.383.10.24313781.098198.5
2.38-2.433.30.22513071.079199.4
2.43-2.483.40.20213331.15199.2
2.48-2.533.40.19913451.147199.6
2.53-2.593.40.17813201.356198.8
2.59-2.663.40.16213491.428199.3
2.66-2.733.40.14413131.651199
2.73-2.813.30.12913631.892199.1
2.81-2.93.30.11613192.036199
2.9-33.30.10613572.251199.2
3-3.123.30.09413052.68198.4
3.12-3.263.20.08213323.042199
3.26-3.4430.07313503.211198.5
3.44-3.653.10.06813173.4198.9
3.65-3.9330.06213453.501199.1
3.93-4.333.10.05813053.743198.3
4.33-4.9530.05413303.769198
4.95-6.243.10.05213473.201199.6
6.24-503.10.04713133.025197.1

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.3→24.07 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 1372 10.01 %
Rwork0.1863 --
obs0.1914 13709 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→24.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2067 0 16 155 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042133
X-RAY DIFFRACTIONf_angle_d0.5872874
X-RAY DIFFRACTIONf_dihedral_angle_d5.122270
X-RAY DIFFRACTIONf_chiral_restr0.047327
X-RAY DIFFRACTIONf_plane_restr0.005375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.380.27491390.21821217X-RAY DIFFRACTION97
2.38-2.470.25731400.20351211X-RAY DIFFRACTION100
2.47-2.590.24351300.211246X-RAY DIFFRACTION100
2.59-2.720.31771360.20751233X-RAY DIFFRACTION100
2.72-2.890.26951550.21561215X-RAY DIFFRACTION100
2.89-3.120.26091260.20231248X-RAY DIFFRACTION100
3.12-3.430.24771430.20171242X-RAY DIFFRACTION100
3.43-3.920.21781420.18161230X-RAY DIFFRACTION100
3.92-4.940.20941310.14881239X-RAY DIFFRACTION99
4.94-24.070.20281300.17211256X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 0.4168 Å / Origin y: -0.9292 Å / Origin z: 12.7149 Å
111213212223313233
T0.153 Å20.0053 Å20.0009 Å2-0.1873 Å2-0.033 Å2--0.1751 Å2
L1.1083 °20.093 °2-0.1676 °2-1.8658 °2-0.4643 °2--1.2154 °2
S0.0148 Å °-0.1172 Å °0.0118 Å °0.0264 Å °-0.0468 Å °-0.0228 Å °-0.0944 Å °0.105 Å °0.04 Å °
Refinement TLS groupSelection details: all

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