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- PDB-4blg: Crystal structure of MHV-68 Latency-associated nuclear antigen (L... -

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Basic information

Entry
Database: PDB / ID: 4blg
TitleCrystal structure of MHV-68 Latency-associated nuclear antigen (LANA) C-terminal DNA binding domain
ComponentsLATENCY-ASSOCIATED NUCLEAR ANTIGEN
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell nucleus / DNA binding / identical protein binding
Similarity search - Function
: / Protein LANA1-like, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain / Epstein Barr virus nuclear antigen-1, DNA-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 73 protein
Similarity search - Component
Biological speciesMurid herpesvirus 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCorreia, B. / Cerqueira, S.A. / Beauchemin, C. / Pires De Miranda, M. / Li, S. / Ponnusamy, R. / Rodrigues, L. / Schneider, T.R. / Carrondo, M.A. / Kaye, K.M. ...Correia, B. / Cerqueira, S.A. / Beauchemin, C. / Pires De Miranda, M. / Li, S. / Ponnusamy, R. / Rodrigues, L. / Schneider, T.R. / Carrondo, M.A. / Kaye, K.M. / Simas, J.P. / McVey, C.E.
CitationJournal: Plos Pathog. / Year: 2013
Title: Crystal Structure of the Gamma-2 Herpesvirus Lana DNA Binding Domain Identifies Charged Surface Residues which Impact Viral Latency
Authors: Correia, B. / Cerqueira, S.A. / Beauchemin, C. / Pires De Miranda, M. / Li, S. / Ponnusamy, R. / Rodrigues, L. / Schneider, T.R. / Carrondo, M.A. / Kaye, K.M. / Simas, J.P. / Mcvey, C.E.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Data collection
Revision 1.2Mar 7, 2018Group: Advisory / Data collection / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LATENCY-ASSOCIATED NUCLEAR ANTIGEN
B: LATENCY-ASSOCIATED NUCLEAR ANTIGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6289
Polymers31,9632
Non-polymers6657
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-69.4 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.575, 61.680, 63.678
Angle α, β, γ (deg.)90.00, 99.36, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9981, 0.01007, 0.06091), (-0.004532, -0.9959, 0.09037), (0.06157, 0.08992, 0.994)
Vector: -9.289, -25.06, 1.376)

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Components

#1: Protein LATENCY-ASSOCIATED NUCLEAR ANTIGEN / IMMEDIATE-EARLY PROTEIN


Mass: 15981.517 Da / Num. of mol.: 2 / Fragment: DNA-BINDNG DOMAIN, RESIDUES 140-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murid herpesvirus 4 (Murine herpesvirus 68)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): STAR PRARE2 / References: UniProt: O41974
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.26 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M NA/K PHOSPHATE PH 7.0, 0.1 M LITHIUM SULPHATE, 22 % W/V PEG 3350 AND 4 % V/V 1,4 DIOXANE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.129
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.129 Å / Relative weight: 1
ReflectionResolution: 2.2→37 Å / Num. obs: 17333 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 7.5 % / Biso Wilson estimate: 41.78 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHI

1vhi


Resolution: 2.2→30.84 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.58 / Stereochemistry target values: ML / Details: RESIDUES 262-272 WERE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2032 864 5 %
Rwork0.1714 --
obs0.1731 17331 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→30.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 35 62 2027
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072017
X-RAY DIFFRACTIONf_angle_d1.1682739
X-RAY DIFFRACTIONf_dihedral_angle_d13.652757
X-RAY DIFFRACTIONf_chiral_restr0.06300
X-RAY DIFFRACTIONf_plane_restr0.005335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33780.27741340.22262753X-RAY DIFFRACTION100
2.3378-2.51820.25191390.20432703X-RAY DIFFRACTION100
2.5182-2.77150.22281580.19482741X-RAY DIFFRACTION100
2.7715-3.17220.26231350.19632737X-RAY DIFFRACTION100
3.1722-3.99530.22611380.16542739X-RAY DIFFRACTION100
3.9953-30.8430.15321600.14832794X-RAY DIFFRACTION100
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)
12.7894-0.79460.2312.6549-1.17722.5447-0.282-0.3159-0.60620.24890.25540.06160.37260.16770.04160.34050.14040.04610.30550.04080.34944.6465-23.144911.0277
21.3740.4283-0.86720.46910.46262.16110.6443-0.34280.9785-0.2732-0.1765-0.9376-2.34891.1005-0.5210.8655-0.1586-0.03110.40880.02080.89463.61993.68116.7101
33.0293-0.7727-1.25571.3658-0.1363.9879-0.5514-0.6274-0.40830.38750.3225-0.1060.34240.24190.1530.35380.18040.03330.32110.05730.28283.84-17.535317.2762
42.22981.32721.29357.5011-1.6421.66840.01840.21640.6372-0.71090.3058-0.13290.66740.8236-0.3920.45330.2914-0.01020.6016-0.03030.5118-21.55423.90297.6862
52.1267-1.94920.66984.17471.0122.233-0.8209-0.21671.99410.30920.215-0.8674-0.9364-0.09960.40640.66060.2299-0.14750.5406-0.08980.6455-8.31557.285416.8009
63.67252.50693.55972.55182.81287.7961-0.3731-0.39010.04620.35580.05960.47070.5771-0.27810.29720.31710.18380.06960.32950.04010.2613-12.8639-11.20613.6989
79.3413-1.9004-0.47018.38312.18032.1108-0.7956-0.0416-0.0039-0.34590.33210.80220.1154-0.20880.45840.29210.0689-0.02280.28080.00920.3497-16.2171-7.28744.134
84.0457-1.3925-0.0394.375-0.21333.612-0.1305-0.20160.10370.10220.29370.08150.0452-0.0959-0.1490.22030.06010.00940.22-0.00650.1892-8.4706-9.469410.0038
92.1559-1.2725-0.55072.77112.08682.0899-0.1257-0.6587-2.3855-0.54060.38191.67952.2179-2.2215-0.24930.8869-0.29440.01270.73510.00661.1813-15.1971-26.8666.5555
103.08860.88150.85763.00211.71745.5451-0.2415-0.46060.14940.1243-0.2250.4713-0.3616-0.55310.44170.24380.1302-0.02670.2895-0.03910.2625-8.3848-7.432913.0284
116.35730.88433.09572.28140.30625.8008-0.513-0.92030.64380.81510.24060.6228-0.1997-0.450.26550.39660.20930.0710.4528-0.0570.428-19.1278-4.01119.1996
128.04070.6457.32912.802-0.30836.97980.19930.2571-0.4430.64480.38970.50930.70610.0786-0.14190.30310.20950.1290.5232-0.03590.3327-17.4415-11.916315.1228
139.42-2.84453.76081.3482-2.53065.4817-0.7044-0.68940.84260.54090.2497-0.2826-0.79020.50350.30790.45420.138-0.07490.3606-0.15810.36862.5466-4.401319.1194
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 141 THROUGH 203 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 204 THROUGH 214 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 215 THROUGH 261 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 142 THROUGH 153 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 154 THROUGH 169 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 170 THROUGH 178 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 179 THROUGH 188 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 189 THROUGH 208 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 209 THROUGH 214 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 215 THROUGH 223 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 224 THROUGH 241 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 242 THROUGH 251 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 252 THROUGH 260 )

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