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- PDB-8j3s: Complex structure of human cytomegalovirus protease and a macrocy... -

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Basic information

Entry
Database: PDB / ID: 8j3s
TitleComplex structure of human cytomegalovirus protease and a macrocyclic peptide ligand
Components
  • Assemblin
  • PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY
KeywordsHYDROLASE / Protease
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
Capsid scaffolding protein
Similarity search - Component
Biological speciesHuman betaherpesvirus 5
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsYoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. ...Yoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. / Nishikawa, J. / Tachibana, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Authors: Yoshida, S. / Sako, Y. / Nikaido, E. / Ueda, T. / Kozono, I. / Ichihashi, Y. / Nakahashi, A. / Onishi, M. / Yamatsu, Y. / Kato, T. / Nishikawa, J. / Tachibana, Y.
History
DepositionApr 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Assemblin
B: Assemblin
C: Assemblin
D: Assemblin
E: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY
F: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY
G: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY


Theoretical massNumber of molelcules
Total (without water)121,6207
Polymers121,6207
Non-polymers00
Water41423
1
A: Assemblin
E: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY

A: Assemblin
E: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY


Theoretical massNumber of molelcules
Total (without water)61,6594
Polymers61,6594
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6270 Å2
ΔGint-36 kcal/mol
Surface area19820 Å2
MethodPISA
2
B: Assemblin
C: Assemblin
F: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY
G: PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY


Theoretical massNumber of molelcules
Total (without water)61,6594
Polymers61,6594
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-38 kcal/mol
Surface area18260 Å2
MethodPISA
3
D: Assemblin

D: Assemblin


Theoretical massNumber of molelcules
Total (without water)58,2612
Polymers58,2612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2780 Å2
ΔGint-23 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.184, 81.648, 198.095
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Assemblin / Protease


Mass: 29130.686 Da / Num. of mol.: 4 / Mutation: A143Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Gene: UL80 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G2TMR2, assemblin
#2: Protein/peptide PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY


Mass: 1698.983 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.05 M MES (pH 5.2), 0.15 M Mg acetate tetraydrate, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.09→50 Å / Num. obs: 22800 / % possible obs: 97.7 % / Redundancy: 6.7 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.067 / Rrim(I) all: 0.175 / Χ2: 0.924 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.1-3.156.40.48211820.8940.9720.2030.5230.89797
3.15-3.216.30.46110710.880.9680.1950.5010.88196.4
3.21-3.276.40.43211080.870.9650.1820.4690.9497.1
3.27-3.346.50.35611530.9220.9790.1490.3860.93196.8
3.34-3.416.60.32511230.9330.9830.1350.3520.96997.1
3.41-3.496.60.28311090.9490.9870.1170.3060.97997.4
3.49-3.586.80.25911550.9560.9890.1060.281.00597.3
3.58-3.686.80.23810820.9580.9890.0970.2571.00497.2
3.68-3.7870.22611780.9680.9920.0910.2431.04597.8
3.78-3.916.80.211060.980.9950.0820.2160.99697.8
3.91-4.046.70.1611430.9840.9960.0660.1730.97197.6
4.04-4.216.80.13211240.9910.9980.0540.1420.95998
4.21-4.46.90.1311690.9890.9970.0530.140.99298.2
4.4-4.636.80.10911180.9930.9980.0450.1180.92198.4
4.63-4.926.80.10911450.9940.9980.0440.1180.89498.6
4.92-5.36.80.11811650.9910.9980.0480.1280.84398.4
5.3-5.836.70.12911500.9890.9970.0530.140.84298.4
5.83-6.676.80.12211620.9920.9980.050.1320.88199.1
6.67-8.46.80.07411790.9960.9990.030.080.80899.3
8-106.80.04611780.99810.0190.050.74196.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.834 / SU B: 22.019 / SU ML: 0.397 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28885 1143 5 %RANDOM
Rwork0.22311 ---
obs0.22644 21648 97.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0 Å2-0.05 Å2
2--0.18 Å2-0 Å2
3----0.29 Å2
Refinement stepCycle: 1 / Resolution: 3.09→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 0 23 6452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196556
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9658919
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4755850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.86622.053263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.00815888
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4721559
X-RAY DIFFRACTIONr_chiral_restr0.0920.21012
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215039
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3216.4123466
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9969.5884294
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1016.1393089
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.1884.7579395
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.09→3.17 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 74 -
Rwork0.3 1548 -
obs--91.85 %

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