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- PDB-8qdo: Crystal structure of the tegument protein UL82 (pp71) from Human ... -

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Basic information

Entry
Database: PDB / ID: 8qdo
TitleCrystal structure of the tegument protein UL82 (pp71) from Human Cytomegalovirus
ComponentsProtein pp71
KeywordsVIRAL PROTEIN / dUTPase fold / tegument protein / transactivator
Function / homology
Function and homology information


DNA-templated viral transcription / viral tegument / : / host cell endoplasmic reticulum / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host innate immune response / host cell nucleus
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus
Similarity search - Domain/homology
Biological speciesHuman betaherpesvirus 5
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsBresch, I.P. / Eberhage, J. / Reubold, T.F. / Eschenburg, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390874280 Germany
CitationJournal: Protein Sci. / Year: 2024
Title: Crystal structure of the tegument protein UL82 (pp71) from human cytomegalovirus.
Authors: Eberhage, J. / Bresch, I.P. / Ramani, R. / Viohl, N. / Buchta, T. / Rehfeld, C.L. / Hinse, P. / Reubold, T.F. / Brinkmann, M.M. / Eschenburg, S.
History
DepositionAug 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein pp71
B: Protein pp71
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,1883
Polymers124,9942
Non-polymers1941
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-1 kcal/mol
Surface area39240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.610, 137.440, 275.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 13 through 539)
d_2ens_1(chain "B" and (resid 13 through 147 or resid 155 through 396 or resid 479 through 539))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERPROPROAA13 - 53918 - 544
d_21SERSERARGARGBB13 - 14718 - 152
d_22PROPROASNASNBB155 - 396160 - 401
d_23GLYGLYPROPROBB479 - 539484 - 544

NCS oper: (Code: givenMatrix: (-0.0203818160206, -0.989007489787, 0.146453974755), (-0.988595928809, -0.00192484142211, -0.150580159806), (0.149206806539, -0.147852900314, -0.977689546201)Vector: 59. ...NCS oper: (Code: given
Matrix: (-0.0203818160206, -0.989007489787, 0.146453974755), (-0.988595928809, -0.00192484142211, -0.150580159806), (0.149206806539, -0.147852900314, -0.977689546201)
Vector: 59.3099119186, 87.8043726797, 194.060673777)

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Components

#1: Protein Protein pp71


Mass: 62496.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human betaherpesvirus 5 / Strain: AD169 / Gene: UL82 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06726
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 6.5, 0.2 M MgCl2, 7.25% w/v PEG4000

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)10.978565
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)21.00522
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELAug 17, 2021
DECTRIS PILATUS 6M2PIXELAug 17, 2021
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MSINGLE WAVELENGTHMx-ray1
2MSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9785651
21.005221
ReflectionResolution: 2.7→48.614 Å / Num. obs: 47593 / % possible obs: 100 % / Redundancy: 13.76 % / Biso Wilson estimate: 85.38 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.075 / Rsym value: 0.072 / Net I/σ(I): 22.55
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 4846 / CC1/2: 0.793 / Rrim(I) all: 1.209 / Rsym value: 1.167 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.61 Å / SU ML: 0.4785 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.8578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 2380 5 %
Rwork0.2067 45206 -
obs0.2079 47586 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.72 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7001 0 13 43 7057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00457183
X-RAY DIFFRACTIONf_angle_d0.70089775
X-RAY DIFFRACTIONf_chiral_restr0.04911110
X-RAY DIFFRACTIONf_plane_restr0.00621283
X-RAY DIFFRACTIONf_dihedral_angle_d11.95162668
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.861718070637 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.760.58821370.53572605X-RAY DIFFRACTION99.96
2.76-2.820.46421390.45122631X-RAY DIFFRACTION99.96
2.82-2.880.41051370.36272610X-RAY DIFFRACTION100
2.88-2.950.35651390.30442638X-RAY DIFFRACTION99.96
2.95-3.030.28061390.26052645X-RAY DIFFRACTION100
3.03-3.120.27861380.25622620X-RAY DIFFRACTION100
3.12-3.220.29661400.24692652X-RAY DIFFRACTION100
3.22-3.340.29481380.26072633X-RAY DIFFRACTION100
3.34-3.470.32061390.28832631X-RAY DIFFRACTION100
3.47-3.630.24731390.21492652X-RAY DIFFRACTION100
3.63-3.820.25691400.21162658X-RAY DIFFRACTION100
3.82-4.060.23181390.20552636X-RAY DIFFRACTION100
4.06-4.370.21011400.18862663X-RAY DIFFRACTION100
4.37-4.810.20771410.15882684X-RAY DIFFRACTION100
4.81-5.510.18331420.16722697X-RAY DIFFRACTION100
5.51-6.940.20841430.19612716X-RAY DIFFRACTION100
6.94-48.610.16291500.16232835X-RAY DIFFRACTION99.83

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