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- PDB-7nxq: Structure of the pentameric C-terminal domain of the capsid prote... -

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Basic information

Entry
Database: PDB / ID: 7nxq
TitleStructure of the pentameric C-terminal domain of the capsid protein from Kaposi's sarcoma-associated herpesvirus (KSHV)
ComponentsCapsid vertex component 2
KeywordsVIRAL PROTEIN / herpesvirus / capsid / KSHV / assembly
Function / homology
Function and homology information


viral genome packaging / viral release from host cell / viral penetration into host nucleus / viral capsid / symbiont entry into host cell / host cell nucleus
Similarity search - Function
Herpesvirus UL25 / Herpesvirus UL25 family
Similarity search - Domain/homology
ACETATE ION / ORF 19
Similarity search - Component
Biological speciesHuman herpesvirus 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.422 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid vertex component 2
B: Capsid vertex component 2
C: Capsid vertex component 2
D: Capsid vertex component 2
E: Capsid vertex component 2
F: Capsid vertex component 2
G: Capsid vertex component 2
H: Capsid vertex component 2
I: Capsid vertex component 2
J: Capsid vertex component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)491,82130
Polymers490,64010
Non-polymers1,18120
Water35,6701980
1
A: Capsid vertex component 2
D: Capsid vertex component 2
E: Capsid vertex component 2
H: Capsid vertex component 2
J: Capsid vertex component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,91115
Polymers245,3205
Non-polymers59010
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13610 Å2
ΔGint-60 kcal/mol
Surface area81140 Å2
MethodPISA
2
B: Capsid vertex component 2
C: Capsid vertex component 2
F: Capsid vertex component 2
G: Capsid vertex component 2
I: Capsid vertex component 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,91115
Polymers245,3205
Non-polymers59010
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13910 Å2
ΔGint-63 kcal/mol
Surface area80850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.51, 239.138, 264.402
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Capsid vertex component 2


Mass: 49064.035 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human herpesvirus 8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q76RI7
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1980 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5 1.69 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 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: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.42→48.36 Å / Num. obs: 229532 / % possible obs: 99.1 % / Redundancy: 13.3 % / CC1/2: 0.998 / Χ2: 0.93 / Net I/σ(I): 10.4
Reflection shellResolution: 2.42→2.48 Å / Num. unique obs: 14955 / CC1/2: 0.352 / % possible all: 88.1

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.422→48.36 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.515 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.544 / SU Rfree Blow DPI: 0.274 / SU Rfree Cruickshank DPI: 0.275
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 8712 -RANDOM
Rwork0.2069 ---
obs0.2083 174243 75.8 %-
Displacement parametersBiso mean: 60.87 Å2
Baniso -1Baniso -2Baniso -3
1-4.919 Å20 Å20 Å2
2---0.0547 Å20 Å2
3----4.8643 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.422→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31860 0 80 1980 33920
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00632747HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8144538HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d10905SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes5501HARMONIC5
X-RAY DIFFRACTIONt_it32747HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion4264SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact24977SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion15.97
LS refinement shellResolution: 2.422→2.48 Å
RfactorNum. reflection% reflection
Rfree0.3229 172 -
Rwork0.2774 --
obs--22.89 %
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)
11.17360.2579-0.21391.3747-0.7735.28410.03470.1579-0.19610.1579-0.0449-0.0705-0.1961-0.07050.0102-0.04090.06250.0254-0.1204-0.0209-0.1219-117.96921.035-12.9848
21.314-0.07750.55631.6128-0.36783.3292-0.00560.4743-0.14070.47430.0730.0089-0.14070.0089-0.06730.20590.25950.02610.06660.0171-0.1544-164.57619.2724-2.0861
31.3494-0.2710.28553.3727-1.45613.1491-0.0345-0.215-0.2317-0.215-0.13650.3651-0.23170.36510.1710.0262-0.07290.0167-0.01650.0577-0.0538-167.04745.4538-75.157
40.99820.2487-0.18324.653-0.00183.0977-0.1398-0.0090.4159-0.0090.0558-0.04990.4159-0.04990.084-0.0865-0.00120.038-0.0312-0.1242-0.0045-121.977-17.5804-40.6802
51.37360.2220.16214.5004-0.1192.8483-0.07740.3544-0.5830.35440.0310.0022-0.5830.00220.04640.14470.0886-0.0719-0.02520.0027-0.0287-114.15659.9173-41.127
61.5323-0.13610.82032.53080.40875.95670.164-0.36390.5679-0.3639-0.0590.39320.56790.3932-0.105-0.04250.0967-0.00160.0391-0.0809-0.0864-165.079-2.6114-76.549
70.99480.08650.2484.14111.71113.5755-0.2384-0.2378-0.6495-0.23780.21790.4211-0.64950.42110.02060.1228-0.0358-0.12880.0175-0.0447-0.0383-166.74559.1385-28.7143
80.9981-0.2146-0.19212.75741.06875.67470.00630.03490.37760.0349-0.09720.06160.37760.06160.091-0.1014-0.1266-0.03920.1719-0.131-0.0268-117.523-3.1143-86.9965
91.07660.1158-0.00525.78950.4361.8932-0.11650.41190.21060.41190.2849-0.11390.2106-0.1139-0.1684-0.11120.06740.01340.0105-0.00060.0083-163.131-19.3851-31.463
101.1261-0.0873-0.28353.9977-1.41232.5349-0.0193-0.45020.0079-0.45020.0501-0.30410.0079-0.3041-0.03080.11330.0093-0.09330.12170.0034-0.0634-111.55845.1636-87.1052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|126 - A|550 A|601 - A|602 }A126 - 550
2X-RAY DIFFRACTION1{ A|126 - A|550 A|601 - A|602 }A601 - 602
3X-RAY DIFFRACTION2{ B|126 - B|550 B|601 - B|602 }B126 - 550
4X-RAY DIFFRACTION2{ B|126 - B|550 B|601 - B|602 }B601 - 602
5X-RAY DIFFRACTION3{ C|126 - C|550 C|601 - C|602 }C126 - 550
6X-RAY DIFFRACTION3{ C|126 - C|550 C|601 - C|602 }C601 - 602
7X-RAY DIFFRACTION4{ D|126 - D|550 D|601 - D|602 }D126 - 550
8X-RAY DIFFRACTION4{ D|126 - D|550 D|601 - D|602 }D601 - 602
9X-RAY DIFFRACTION5{ E|126 - E|550 E|601 - E|602 }E126 - 550
10X-RAY DIFFRACTION5{ E|126 - E|550 E|601 - E|602 }E601 - 602
11X-RAY DIFFRACTION6{ F|126 - F|550 F|601 - F|602 }F126 - 550
12X-RAY DIFFRACTION6{ F|126 - F|550 F|601 - F|602 }F601 - 602
13X-RAY DIFFRACTION7{ G|126 - G|550 G|601 - G|602 }G126 - 550
14X-RAY DIFFRACTION7{ G|126 - G|550 G|601 - G|602 }G601 - 602
15X-RAY DIFFRACTION8{ H|126 - H|550 H|601 - H|602 }H126 - 550
16X-RAY DIFFRACTION8{ H|126 - H|550 H|601 - H|602 }H601 - 602
17X-RAY DIFFRACTION9{ I|126 - I|550 I|601 - I|602 }I126 - 550
18X-RAY DIFFRACTION9{ I|126 - I|550 I|601 - I|602 }I601 - 602
19X-RAY DIFFRACTION10{ J|126 - J|550 J|601 - J|602 }J126 - 550
20X-RAY DIFFRACTION10{ J|126 - J|550 J|601 - J|602 }J601 - 602

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