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- PDB-4p3h: Crystal structure of Kaposi's sarcoma-associated herpesvirus (KSH... -

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Basic information

Entry
Database: PDB / ID: 4p3h
TitleCrystal structure of Kaposi's sarcoma-associated herpesvirus (KSHV) protease in complex with 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-25G / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / pdbx_validate_symm_contact / software / struct_ref
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_oper_list.symmetry_operation / _software.classification / _struct_ref.biol_id
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)43,9928
Polymers42,3862
Non-polymers1,6066
Water5,657314
1
A: KSHV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6462
Polymers21,1931
Non-polymers4531
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KSHV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3476
Polymers21,1931
Non-polymers1,1535
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)87,98416
Polymers84,7724
Non-polymers3,21212
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 area10430 Å2
ΔGint-37 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.120, 95.892, 119.342
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-348-

HOH

21B-366-

HOH

31B-374-

HOH

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: 21193.111 Da / Num. of mol.: 2 / Fragment: UNP residues 1-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Gene: ORF17 / Production host: Escherichia coli (E. coli) / References: UniProt: O36607
#2: Chemical ChemComp-25G / N-[2-benzyl-4-(1H-tetrazol-5-yl)phenyl]-6-(cyclohexylmethyl)pyridine-2-carboxamide


Mass: 452.551 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H28N6O
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
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: 1.43→59.812 Å / Num. all: 1497653 / Num. obs: 135014 / % possible obs: 100 % / Redundancy: 10.2 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.102 / Rsym value: 0.096 / Net I/av σ(I): 4.214 / Net I/σ(I): 13.1 / Num. measured all: 748120
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs
1.43-1.5180.9190.784478106140.3620.9192.1
1.51-1.680.5051.480419100480.20.5053.4
1.6-1.7180.32.47574294430.1180.35
1.71-1.858.10.2012.97171288230.0780.2017.6
1.85-2.029.20.1922.77494181300.0660.19212.1
2.02-2.2611.30.1813.28332573860.0560.18117.8
2.26-2.6114.70.1723.59566565250.0470.17222.5
2.61-3.214.80.1025.78235155660.0280.10228.2
3.2-4.5215.10.078.16547443410.0190.0738.1
4.52-59.81213.60.0589.33401325030.0180.05836.8

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Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
PHENIXPhenix 1.8.4 Phaser 2.1phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NJQ

3njq


Resolution: 1.45→59.812 Å / FOM work R set: 0.8371 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.58 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1948 6826 5.06 %
Rwork0.1729 128188 -
obs0.1741 72871 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.14 Å2 / Biso mean: 38.35 Å2 / Biso min: 11.47 Å2
Refinement stepCycle: final / Resolution: 1.45→59.812 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2900 0 217 314 3431
Biso mean--32.72 40.3 -
Num. residues----375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123202
X-RAY DIFFRACTIONf_angle_d1.4574394
X-RAY DIFFRACTIONf_chiral_restr0.075497
X-RAY DIFFRACTIONf_plane_restr0.008558
X-RAY DIFFRACTIONf_dihedral_angle_d16.0771184
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46650.3321920.32934184437698
1.4665-1.48380.27652310.30934212444398
1.4838-1.50180.31842230.29684267449098
1.5018-1.52090.32792530.2924212446599
1.5209-1.54090.3271970.28594221441899
1.5409-1.5620.32512370.26354297453499
1.562-1.58430.27482380.24364289452799
1.5843-1.60790.24762560.22884176443299
1.6079-1.63310.24132380.2164221445999
1.6331-1.65990.22762390.21374270450999
1.6599-1.68850.25821850.20474337452299
1.6885-1.71920.22242500.1934286453699
1.7192-1.75230.18612150.18774274448999
1.7523-1.7880.26442100.18454322453299
1.788-1.82690.17572500.186542234473100
1.8269-1.86940.20592330.18343224555100
1.8694-1.91620.23972040.18214251445599
1.9162-1.9680.23522240.17843044528100
1.968-2.02590.19212230.17642494472100
2.0259-2.09130.18662050.171843514556100
2.0913-2.1660.18232180.165942884506100
2.166-2.25270.16972850.16142354520100
2.2527-2.35530.20152400.166542594499100
2.3553-2.47950.1872200.17143314551100
2.4795-2.63480.20932250.172742954520100
2.6348-2.83820.19382100.173542684478100
2.8382-3.12380.21672140.172443594573100
3.1238-3.57580.16222300.154542864516100
3.5758-4.50490.15322580.133142684526100
4.5049-59.86330.17882230.159643314554100
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)
18.49780.7023-2.4796.25411.34187.3814-0.2163-0.4880.80540.346-0.01110.3848-0.7236-0.4240.14940.31720.105-0.16320.293-0.04940.1815-25.0421-5.9866-29.4314
23.80690.78861.32585.38392.60164.4125-0.2074-0.08680.31240.34630.1518-0.2321-0.49650.20860.00080.30770.0218-0.0780.21690.01890.1475-18.2463-9.3922-27.103
32.5869-0.7837-0.51167.51830.77042.1509-0.1912-0.02220.63390.02140.0777-0.3043-0.72850.57390.11760.3544-0.1073-0.11350.29940.010.2988-13.1356-5.2812-32.7522
45.542-2.4822.48183.5423-2.19156.09890.0180.1797-0.0016-0.0592-0.0773-0.0821-0.0810.49770.04140.1079-0.0305-0.00320.1811-0.01540.1182-20.9639-16.9653-52.0066
51.621-0.4511.04232.47552.89867.6674-0.2921-0.13240.2150.15290.1192-0.0612-0.5319-0.06630.10920.24660.0215-0.06510.1565-0.01150.1859-23.0518-8.0825-35.2513
62.64810.83021.97381.71620.87781.479-0.5746-0.24950.59370.06460.0808-0.0068-0.9675-0.42110.39330.42260.1165-0.14170.2501-0.07070.2843-22.507-5.1539-27.0614
74.3944.13820.94166.10540.97650.2149-0.56210.95040.4713-0.11970.1324-0.6184-1.20941.10480.2230.5972-0.3075-0.16090.54360.14740.4152-10.3011-2.6776-43.2289
84.36372.76461.22314.06161.35031.0579-0.1635-0.10380.12790.0608-0.0832-0.1959-0.28260.3659-0.12230.5109-0.798-0.3090.85340.05450.5019-3.8211-0.8056-33.5486
94.8532-0.7827-0.77917.1198-1.52525.5140.046-0.02960.25490.0970.05-0.93160.11031.1091-0.03230.12430.05150.00580.3857-0.01250.2784-11.7843-22.0202-35.0663
107.5984.36512.97277.24862.31893.4508-0.60180.340.623-0.38410.30450.0185-0.75560.30050.22830.2586-0.0152-0.0720.2110.04640.1721-6.5433-16.4722-4.7649
112.7983-0.59380.00722.23140.79593.5704-0.0967-0.21010.25520.1071-0.03030.1316-0.3395-0.36070.11880.18610.0609-0.03810.2063-0.00940.1595-15.4481-18.031-9.1546
123.0079-4.12354.13546.2568-6.69477.3830.29720.2182-0.3826-0.7097-0.1420.19450.5427-0.151-0.12270.25360.0011-0.01250.2192-0.04620.2227-6.8161-36.9752-20.2408
139.22840.1974.53528.32742.49066.86850.0589-0.637-0.4950.3403-0.04010.36080.6236-0.4652-0.03770.2979-0.03170.0420.19850.01620.2373-3.8352-43.336-9.8203
144.0763-3.07730.34774.71960.26395.1603-0.00170.0222-0.17310.0778-0.0029-0.0390.2575-0.16350.00920.086-0.02250.00170.1225-0.00490.0926-7.9658-31.3979-8.0711
155.26081.7747-0.60624.43981.84454.1542-0.28540.17271.0926-0.0231-0.1328-0.1885-1.2517-0.04030.21350.57530.056-0.19460.18220.01030.4625-9.6777-5.1342-8.5664
162.47980.0655-0.3021.7053-0.12173.84010.0035-0.0184-0.04360.0467-0.05080.1640.1303-0.42050.05190.13330.013-0.01240.1684-0.01610.1295-13.5921-27.9721-3.6244
177.6998-1.2752-2.01577.18734.33442.9643-0.00980.30750.106-0.0926-0.10050.4085-0.1873-0.6930.14270.13680.0071-0.01340.50930.01510.353-28.6881-23.9513-4.7172
185.2089-5.47380.26557.59320.04027.28780.15640.6950.1660.0006-0.10050.1734-0.0479-0.4405-0.04980.2237-0.0108-0.03890.1287-0.00990.1019-12.8138-24.5027-22.6152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 26 )A4 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 52 )A27 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 73 )A53 - 73
4X-RAY DIFFRACTION4chain 'A' and (resid 74 through 100 )A74 - 100
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 122 )A101 - 122
6X-RAY DIFFRACTION6chain 'A' and (resid 123 through 148 )A123 - 148
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 165 )A149 - 165
8X-RAY DIFFRACTION8chain 'A' and (resid 166 through 178 )A166 - 178
9X-RAY DIFFRACTION9chain 'A' and (resid 179 through 193 )A179 - 193
10X-RAY DIFFRACTION10chain 'B' and (resid 4 through 26 )B4 - 26
11X-RAY DIFFRACTION11chain 'B' and (resid 27 through 73 )B27 - 73
12X-RAY DIFFRACTION12chain 'B' and (resid 74 through 86 )B74 - 86
13X-RAY DIFFRACTION13chain 'B' and (resid 87 through 100 )B87 - 100
14X-RAY DIFFRACTION14chain 'B' and (resid 101 through 116 )B101 - 116
15X-RAY DIFFRACTION15chain 'B' and (resid 117 through 133 )B117 - 133
16X-RAY DIFFRACTION16chain 'B' and (resid 134 through 165 )B134 - 165
17X-RAY DIFFRACTION17chain 'B' and (resid 166 through 178 )B166 - 178
18X-RAY DIFFRACTION18chain 'B' and (resid 179 through 196 )B179 - 196

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