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- PDB-7nxp: Structure of the C-terminal domain of the pUL77 capsid protein fr... -

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Basic information

Entry
Database: PDB / ID: 7nxp
TitleStructure of the C-terminal domain of the pUL77 capsid protein from human cytomegalovirus (HCMV)
ComponentsCapsid vertex component 2
KeywordsVIRAL PROTEIN / herpesvirus / capsid / HCMV / assembly
Function / homologyHerpesvirus UL25 / Herpesvirus UL25 family / viral genome packaging / viral capsid / UL77 protein
Function and homology information
Biological speciesHuman cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsNaniima, P. / Legrand, P. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchGerman Center for Infection Research (DZIF) - TTU 07.704 Germany
CitationJournal: Plos Biol. / Year: 2021
Title: Assembly of infectious Kaposi's sarcoma-associated herpesvirus progeny requires formation of a pORF19 pentamer.
Authors: Naniima, P. / Naimo, E. / Koch, S. / Curth, U. / Alkharsah, K.R. / Stroh, L.J. / Binz, A. / Beneke, J.M. / Vollmer, B. / Boning, H. / Borst, E.M. / Desai, P. / Bohne, J. / Messerle, M. / ...Authors: Naniima, P. / Naimo, E. / Koch, S. / Curth, U. / Alkharsah, K.R. / Stroh, L.J. / Binz, A. / Beneke, J.M. / Vollmer, B. / Boning, H. / Borst, E.M. / Desai, P. / Bohne, J. / Messerle, M. / Bauerfeind, R. / Legrand, P. / Sodeik, B. / Schulz, T.F. / Krey, T.
History
DepositionMar 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid vertex component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8553
Polymers53,6711
Non-polymers1842
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area520 Å2
ΔGint-0 kcal/mol
Surface area19380 Å2
Unit cell
Length a, b, c (Å)163.907, 163.907, 50.965
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Capsid vertex component 2


Mass: 53670.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus / Gene: CVC2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G6XKK5
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.56 Å3/Da / Density % sol: 65.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Na-Cacodylate pH 6.5 16% PEG 8000 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. obs: 55350 / % possible obs: 99.5 % / Redundancy: 8.6 % / CC1/2: 0.999 / Net I/σ(I): 16.66
Reflection shellResolution: 1.896→2.01 Å / Num. unique obs: 8600 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F5U

2f5u


Resolution: 1.896→46.65 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.109 / SU Rfree Blow DPI: 0.101 / SU Rfree Cruickshank DPI: 0.101
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 2812 -RANDOM
Rwork0.1915 ---
obs0.1923 55350 99.5 %-
Displacement parametersBiso mean: 42.55 Å2
Baniso -1Baniso -2Baniso -3
1--3.7027 Å20 Å20 Å2
2---3.7027 Å20 Å2
3---7.4054 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.896→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 12 184 3598
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013522HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.884797HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1169SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes592HARMONIC5
X-RAY DIFFRACTIONt_it3522HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2529SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion14.99
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.347 51 -
Rwork0.3382 --
obs0.3386 1107 81.75 %
Refinement TLS params.

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)
10.55350.22-0.14010.3042-0.16110.57860.12570.0854-0.06340.0854-0.06520.0108-0.06340.0108-0.06060.0032-0.0422-0.022-0.02160.0284-0.0165-36.552566.21712.3286
20.22710.07881.32841.24262.83550.7318-0.0025-0.1347-0.072-0.1347-0.14510.102-0.0720.1020.14770.05610.04790.06030.11720.0936-0.0662-16.72174.5571-24.1272
30.5573-0.03970.32652.75610.90220.49370.0189-0.1513-0.0299-0.15130.12150.1271-0.02990.1271-0.14040.00410.01030.00180.07190.0053-0.0544-22.184964.5576-20.8916
40-0.62830.7910.66511.01168.30950.05490.03510.54420.0351-0.11840.03150.54420.03150.06350.03630.0487-0.0552-0.04410.02680.0258-16.219247.6948-8.2209
50.85410.30360.96150.34140.8481.82940.2205-0.0449-0.0125-0.0449-0.04930.1008-0.01250.1008-0.1712-0.07140.0189-0.06020.05230.01280.026-8.913956.1702-0.4357
60.05521.44831.02191.62460.02511.19260.2289-0.140.1069-0.14-0.03680.10520.10690.1052-0.1921-0.0310.10290.01010.0486-0.03020.0165-9.300357.9151-16.8192
75.64672.33782.55920-0.24710-0.1666-0.0237-0.0812-0.02370.11630.0986-0.08120.09860.0503-0.08240.0349-0.02910.1472-0.0245-0.03745.344261.3034-12.8416
80.5022-0.2008-2.33525.87522.71235.20910.19630.1942-0.07380.1942-0.27170.1621-0.07380.16210.0754-0.1088-0.0133-0.0210.03210.09190.0666-8.408775.2797-11.2968
90.5617-0.09480.10990.2587-0.11390.30190.0606-0.0530.0306-0.0530.00530.01450.03060.0145-0.0659-0.004-0.0249-0.02250.00190.0264-0.01-31.365364.8914-8.765
100.4712-0.44551.162901.44023.36750.0854-0.0564-0.0327-0.0564-0.0983-0.1848-0.0327-0.18480.0129-0.0403-0.0515-0.03930.02840.08140.015-27.742456.050812.258
112.33180.06262.91040.52360.06983.51850.12530.0327-0.09410.0327-0.17840.3327-0.09410.33270.0532-0.0361-0.0712-0.02480.11640.0341-0.0518-19.936760.897714.9649
121.04240.1796-0.039100.08760.83510.0547-0.00280.1089-0.0028-0.0156-0.03980.1089-0.0398-0.0392-0.0048-0.035-0.0436-0.02130.02730.0113-36.46256.3515-5.3848
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 114}A1 - 114
2X-RAY DIFFRACTION2{A|115 - 122}A115 - 122
3X-RAY DIFFRACTION3{A|123 - 144}A123 - 144
4X-RAY DIFFRACTION4{A|145 - 168}A145 - 168
5X-RAY DIFFRACTION5{A|169 - 186}A169 - 186
6X-RAY DIFFRACTION6{A|187 - 201}A187 - 201
7X-RAY DIFFRACTION7{A|202 - 221}A202 - 221
8X-RAY DIFFRACTION8{A|222 - 242}A224 - 242
9X-RAY DIFFRACTION9{A|243 - 362}A243 - 362
10X-RAY DIFFRACTION10{A|363 - 400}A363 - 400
11X-RAY DIFFRACTION11{A|401 - 406}A401 - 406
12X-RAY DIFFRACTION12{A|407 - 466}A407 - 465

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