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- PDB-8ua5: Crystal Structure of infected cell protein 0 (ICP0) from herpes s... -

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Basic information

Entry
Database: PDB / ID: 8ua5
TitleCrystal Structure of infected cell protein 0 (ICP0) from herpes simplex virus 1 (A636-Q776)
ComponentsRL2
KeywordsPROTEIN BINDING / infected cell protein 0 (ICP0) / herpes simplex virus 1 / beta barrel / dimization
Function / homology
Function and homology information


ligase activity / ubiquitin protein ligase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / protein ubiquitination / zinc ion binding
Similarity search - Function
Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Biological speciesHuman alphaherpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLovell, S. / Kashipathy, M. / Battaile, K.P. / Cooper, A. / Davido, D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM1110761 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113117 United States
CitationJournal: Proteins / Year: 2024
Title: HSV-1 ICP0 dimer domain adopts a novel beta-barrel fold.
Authors: McCloskey, E. / Kashipathy, M. / Cooper, A. / Gao, P. / Johnson, D.K. / Battaile, K.P. / Lovell, S. / Davido, D.J.
History
DepositionSep 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RL2
B: RL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1947
Polymers35,6862
Non-polymers5085
Water75742
1
A: RL2
B: RL2
hetero molecules

A: RL2
B: RL2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,38814
Polymers71,3724
Non-polymers1,01710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area17650 Å2
ΔGint-143 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.150, 97.150, 76.721
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RL2 / Ubiquitin E3 ligase ICP0


Mass: 17842.926 Da / Num. of mol.: 2 / Fragment: A636-Q776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human alphaherpesvirus 1 (Herpes simplex virus type 1)
Gene: RL2, RL2_1, HHV1gp002, HHV1gp082 / Plasmid: pTBSG / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H9E965
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PACT G3: 20% (w/v) PEG 3350, 100 mM Bis-Tris Propane pH 7.5, 200 mM NaI, 80% crystallization solution and 20% (v/v) PEG 200.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2019
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→43.45 Å / Num. obs: 14026 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.048 / Rrim(I) all: 0.124 / Χ2: 0.72 / Net I/σ(I): 13.1 / Num. measured all: 89786
Reflection shellResolution: 2.45→2.55 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.926 / Num. measured all: 9814 / Num. unique obs: 1562 / CC1/2: 0.714 / Rpim(I) all: 0.402 / Rrim(I) all: 1.012 / Χ2: 0.48 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_4336: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.45 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 667 4.77 %
Rwork0.1915 --
obs0.1943 13990 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→43.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 10 42 1795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091792
X-RAY DIFFRACTIONf_angle_d0.9912459
X-RAY DIFFRACTIONf_dihedral_angle_d12.569620
X-RAY DIFFRACTIONf_chiral_restr0.053293
X-RAY DIFFRACTIONf_plane_restr0.009309
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.640.34921390.25232603X-RAY DIFFRACTION100
2.64-2.90.28371260.21912612X-RAY DIFFRACTION100
2.9-3.320.26461390.21592637X-RAY DIFFRACTION100
3.33-4.190.21941340.17592662X-RAY DIFFRACTION100
4.19-43.450.24171290.17232809X-RAY DIFFRACTION99

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