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- PDB-7tcz: Human cytomegalovirus protease mutant (C84A, C87A, C138A, C202A) ... -

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Basic information

Entry
Database: PDB / ID: 7tcz
TitleHuman cytomegalovirus protease mutant (C84A, C87A, C138A, C202A) in complex with inhibitor
ComponentsAssemblin
KeywordsHYRDROLASE/HYDROLASE INHIBITOR / Protease / VIRAL PROTEIN / HYRDROLASE-HYDROLASE INHIBITOR complex
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
Peptidase S21 / Herpesvirus protease superfamily / Assemblin (Peptidase family S21)
Similarity search - Domain/homology
Chem-GIT / Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsHulce, K.R. / Bohn, M. / Ongpipattanakul, C. / Jaishankar, P. / Renslo, A.R. / Craik, C.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM082250 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104659 United States
CitationJournal: Cell Chem Biol / Year: 2022
Title: Inhibiting a dynamic viral protease by targeting a non-catalytic cysteine.
Authors: Hulce, K.R. / Jaishankar, P. / Lee, G.M. / Bohn, M.F. / Connelly, E.J. / Wucherer, K. / Ongpipattanakul, C. / Volk, R.F. / Chuo, S.W. / Arkin, M.R. / Renslo, A.R. / Craik, C.S.
History
DepositionDec 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3262
Polymers28,9611
Non-polymers3641
Water724
1
A: Assemblin
hetero molecules

A: Assemblin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6524
Polymers57,9232
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_644y+1,x-1,-z-1/41
Buried area3120 Å2
ΔGint-18 kcal/mol
Surface area18620 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.673, 51.673, 215.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Assemblin / Protease


Mass: 28961.416 Da / Num. of mol.: 1 / Mutation: C84A, C87A, C138A, C202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Gene: UL80 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A126N917, assemblin
#2: Chemical ChemComp-GIT / [1-(2-oxopropyl)-4-phenyl-1H-1,2,3-triazol-5-yl]methyl benzylcarbamate


Mass: 364.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.26 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 40% v/v PEG 200, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11583 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 2.669→51.67 Å / Num. obs: 9026 / % possible obs: 99.35 % / Redundancy: 23.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.2958 / Rpim(I) all: 0.083 / Rrim(I) all: 0.306 / Net I/σ(I): 7.94
Reflection shellResolution: 2.669→2.766 Å / Redundancy: 24.7 % / Rmerge(I) obs: 3.171 / Num. unique obs: 871 / CC1/2: 0.814 / % possible all: 98.28

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NJT

1njt


Resolution: 2.67→51.67 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 444 4.95 %
Rwork0.2488 --
obs0.2507 8978 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→51.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 27 4 1661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091696
X-RAY DIFFRACTIONf_angle_d1.2232303
X-RAY DIFFRACTIONf_dihedral_angle_d22.773605
X-RAY DIFFRACTIONf_chiral_restr0.058254
X-RAY DIFFRACTIONf_plane_restr0.007302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-3.060.40071400.31592758X-RAY DIFFRACTION99
3.06-3.850.31661580.26342758X-RAY DIFFRACTION99
3.85-51.670.24791460.22813018X-RAY DIFFRACTION100

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