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- PDB-4p2t: Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSH... -

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Basic information

Entry
Database: PDB / ID: 4p2t
TitleCrystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with a dimer disruptor
ComponentsKSHV Protease
KeywordsHYDROLASE / protein-protein interaction inhibition / serine protease / inhibitor complex / beta barrel and alpha helices
Function / homology
Function and homology information


assemblin / nuclear capsid assembly / viral release from host cell / host cell cytoplasm / serine-type endopeptidase activity / host cell nucleus / proteolysis / identical protein binding
Similarity search - Function
Serine Protease, Human Cytomegalovirus Protease; Chain A / Herpesvirus/Caudovirus protease domain / Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21) / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-24Q / Capsid scaffolding protein / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.15 Å
AuthorsGable, J.E.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI090592 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50-GM08250 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM008284 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1 TR000004 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)UL1 RR024131 United States
NCI and the Helen Diller Family Comprehensive Cancer CenterP30 CA 82103-13 United States
National Science Foundation (NSF, United States)GRFP1144247 United States
CitationJournal: Biochemistry / Year: 2014
Title: Broad-spectrum allosteric inhibition of herpesvirus proteases.
Authors: Gable, J.E. / Lee, G.M. / Jaishankar, P. / Hearn, B.R. / Waddling, C.A. / Renslo, A.R. / Craik, C.S.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KSHV Protease
B: KSHV Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2376
Polymers42,6422
Non-polymers1,5954
Water3,441191
1
A: KSHV Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9053
Polymers21,3211
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KSHV Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3323
Polymers21,3211
Non-polymers1,0112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: KSHV Protease
hetero molecules

A: KSHV Protease
hetero molecules

B: KSHV Protease
hetero molecules

B: KSHV Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,47512
Polymers85,2854
Non-polymers3,1908
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
crystal symmetry operation8_444x-1/2,-y-1/2,-z-1/21
Buried area10440 Å2
ΔGint-37 kcal/mol
Surface area31620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.737, 95.947, 119.245
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit.

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Components

#1: Protein KSHV Protease


Mass: 21321.240 Da / Num. of mol.: 2 / Fragment: UNP residues 1-194
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Production host: Escherichia coli (E. coli) / References: UniProt: O36607, UniProt: Q2HRB6*PLUS
#2: Chemical ChemComp-24Q / 6-(cyclohexylmethyl)-N-[4-(methylsulfonylcarbamoyl)-2-(phenylmethyl)phenyl]pyridine-2-carboxamide


Mass: 505.628 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H31N3O4S
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M sodium acetate pH 7.8, 0.88 M NaH2PO4, 1.32 M K2HPO4, 0.2 M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→74.753 Å / Num. all: 150688 / Num. obs: 22809 / % possible obs: 94.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/av σ(I): 6.026 / Net I/σ(I): 18.1 / Num. measured all: 150688
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym valueNet I/σ(I) obs% possible all
2.09-2.24.70.7081.11177624910.7081.772.6
2.2-2.345.60.5911.31682729960.5912.391.4
2.34-2.57.20.4811.62214330820.4813.499.9
2.5-2.77.20.3342.32088228900.3345.399.9
2.7-2.967.20.2173.41916426590.2178.799.9
2.96-3.37.10.1285.71728024210.12816.8100
3.3-3.827.10.0759.51516821470.07532.3100
3.82-4.676.80.05811.71253118360.05849.7100
4.67-6.616.40.05212.8922814380.05253100
6.61-74.7536.70.03219.156898490.03287.9100

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Processing

Software
NameVersionClassification
SCALA3.2.5data scaling
PHASER2.1phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementStarting model: 3NJQ

3njq


Resolution: 2.15→74.753 Å / FOM work R set: 0.8 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 26.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1886 8.77 %
Rwork0.1852 19612 -
obs0.1911 21498 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 202.94 Å2 / Biso mean: 42.73 Å2 / Biso min: 6.66 Å2
Refinement stepCycle: final / Resolution: 2.15→74.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 208 191 3359
Biso mean--31.83 38.12 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033249
X-RAY DIFFRACTIONf_angle_d0.7884467
X-RAY DIFFRACTIONf_chiral_restr0.029507
X-RAY DIFFRACTIONf_plane_restr0.003568
X-RAY DIFFRACTIONf_dihedral_angle_d14.251210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.20820.37111150.26961188130378
2.2082-2.27310.32931300.25751352148288
2.2731-2.34650.31651410.23761464160596
2.3465-2.43040.28951460.222215181664100
2.4304-2.52770.27431480.208215411689100
2.5277-2.64280.29391480.216715431691100
2.6428-2.78210.31491470.211515331680100
2.7821-2.95640.27591500.204315541704100
2.9564-3.18470.27931480.190215421690100
3.1847-3.50520.231510.17215661717100
3.5052-4.01230.22421500.160715651715100
4.0123-5.0550.22171520.134915791731100
5.055-74.79840.20261600.183616671827100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.24380.17250.15620.14030.11930.4211-0.05190.09020.10640.1078-0.0282-0.1761-0.2548-0.34480.00290.35290.0767-0.06660.2832-0.0250.2997-20.7115-5.3127-27.4247
20.12220.04470.05740.1107-0.12340.2197-0.1301-0.0457-0.07050.05070.104-0.05-0.15870.1044-0.01310.2323-0.0276-0.04130.2457-0.00350.1957-16.8475-9.6504-32.6916
30.30320.06640.38650.31260.07950.455-0.17540.01060.0849-0.03640.05790.0119-0.28650.1191-0.01870.21280.0157-0.04010.1675-0.00110.187-22.368-10.6486-39.4062
41.2704-0.1992-0.19930.2540.00680.0349-0.34330.3268-0.2004-0.1570.1094-0.0046-0.72260.4668-0.32740.4318-0.2501-0.06980.43920.04610.2721-7.9683-1.2813-39.271
50.39810.0081-0.16560.0397-0.08970.8988-0.2375-0.42840.0980.05110.3293-0.05430.24620.27390.06670.18590.0501-0.03720.3079-0.040.2834-12.6721-22.5286-35.7915
60.01-0.00560.0570.0065-0.04490.1758-0.17060.13260.18130.14680.17280.1686-0.0693-0.09880.00510.15270.0029-0.05840.20940.01420.2087-6.699-17.7264-6.5075
70.1909-0.13410.07970.6608-0.31420.3685-0.08270.10370.0108-0.02710.05060.0003-0.0255-0.2097-0.0050.1483-0.0019-0.03180.1779-0.01550.1627-12.8244-21.3843-10.5282
80.4911-0.3666-0.85120.27430.63411.4820.0719-0.14390.3648-0.16410.28820.26110.10960.01750.15810.224-0.00290.03940.13030.02190.2614-4.2168-43.673-8.5244
90.11950.1509-0.22580.1422-0.20960.6295-0.07380.0670.0246-0.0464-0.0091-0.0576-0.0665-0.0382-0.00020.1374-0.0104-0.02840.08170.00560.1387-10.6848-23.3847-6.7706
100.0729-0.13560.00270.2564-0.01750.1424-0.0497-0.0458-0.0035-0.1695-0.01230.0795-0.0779-0.113500.20690.0235-0.05090.2995-0.0290.2273-19.6632-24.7212-12.9502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 40 )A3 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 73 )A41 - 73
3X-RAY DIFFRACTION3chain 'A' and (resid 74 through 148 )A74 - 148
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 176 )A149 - 176
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 196 )A177 - 196
6X-RAY DIFFRACTION6chain 'B' and (resid 4 through 22 )B4 - 22
7X-RAY DIFFRACTION7chain 'B' and (resid 23 through 86 )B23 - 86
8X-RAY DIFFRACTION8chain 'B' and (resid 87 through 100 )B87 - 100
9X-RAY DIFFRACTION9chain 'B' and (resid 101 through 160 )B101 - 160
10X-RAY DIFFRACTION10chain 'B' and (resid 161 through 196 )B161 - 196

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