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- PDB-4uzb: KSHV LANA (ORF73) C-terminal domain mutant bound to LBS1 DNA (R10... -

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Basic information

Entry
Database: PDB / ID: 4uzb
TitleKSHV LANA (ORF73) C-terminal domain mutant bound to LBS1 DNA (R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D)
Components
  • (LANA BINDING SITE 1 DNA) x 2
  • ORF 73
KeywordsVIRAL PROTEIN/DNA / VIRAL PROTEIN-DNA COMPLEX / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / HHV-8 / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE / TUMOR VIRUS / CANCER
Function / homology
Function and homology information


viral life cycle / : / host cell nucleus / DNA 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
: / DNA / DNA (> 10) / ORF 73 / Protein LANA1
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.865 Å
AuthorsHellert, J. / Krausze, J. / Luhrs, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: The 3D Structure of Kaposi Sarcoma Herpesvirus Lana C-Terminal Domain Bound to DNA.
Authors: Hellert, J. / Weidner-Glunde, M. / Krausze, J. / Lunsdorf, H. / Ritter, C. / Schulz, T.F. / Luhrs, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Crystallization, Room-Temperature X-Ray Diffraction and Preliminary Analysis of Kaposi'S Sarcoma Herpesvirus Lana Bound to DNA.
Authors: Hellert, J. / Krausze, J. / Schulz, T.F. / Luhrs, T.
History
DepositionSep 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Data collection / Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation ...Data collection / Experimental preparation / Other / Structure summary
Category: entity / exptl_crystal_grow ...entity / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_biol
Item: _entity.pdbx_mutation / _exptl_crystal_grow.method ..._entity.pdbx_mutation / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: ORF 73
B: ORF 73
C: LANA BINDING SITE 1 DNA
D: LANA BINDING SITE 1 DNA


Theoretical massNumber of molelcules
Total (without water)44,0684
Polymers44,0684
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-61.4 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.840, 177.840, 177.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.14212, 0.53378, 0.83359), (0.52853, -0.67112, 0.51986), (0.83693, 0.51446, -0.18674)
Vector: 21.95846, 33.56675, -43.61832)

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Components

#1: Protein ORF 73 / LATENCY-ASSOCIATED NUCLEAR ANTIGEN / LANA-1 / KSHV LANA


Mass: 15896.087 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, RESIDUES 1008-1146
Mutation: R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Plasmid: PET-BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76SB0, UniProt: Q9QR71*PLUS
#2: DNA chain LANA BINDING SITE 1 DNA


Mass: 6137.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 8 / References: GenBank: 1841835
#3: DNA chain LANA BINDING SITE 1 DNA


Mass: 6137.932 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN HERPESVIRUS 8 / References: GenBank: 1841835
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 5.33 Å3/Da / Density % sol: 79.4 % / Description: NONE
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.9 UL OF 1.60 MM LANA(1008-1146) MUTANT, 0.96 MM DSDNA, 10 MM BISTRIS PH 6.5, 0.9 M NACL, AND 5 MM DTT WERE ADDED TO 0.9 UL OF RESERVOIR SOLUTION CONTAINING 50 MM MES PH 6.6, 27% PEG4000, ...Details: 0.9 UL OF 1.60 MM LANA(1008-1146) MUTANT, 0.96 MM DSDNA, 10 MM BISTRIS PH 6.5, 0.9 M NACL, AND 5 MM DTT WERE ADDED TO 0.9 UL OF RESERVOIR SOLUTION CONTAINING 50 MM MES PH 6.6, 27% PEG4000, AND 0.3 M AMMONIUM ACETATE IN A HANGING DROP SETUP. CRYSTALS GREW WITHIN FIVE DAYS AT 24 DEGREES CENTIGRADE.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.00004
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2013 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.87→47.53 Å / Num. obs: 21605 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 79.32 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.65
Reflection shellResolution: 2.87→3.04 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.99 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXPHASER-MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPY

2ypy


Resolution: 2.865→47.53 Å / SU ML: 0.38 / σ(F): 1.36 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1547 1074 5 %
Rwork0.1218 --
obs0.1234 21618 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.5 Å2
Refinement stepCycle: LAST / Resolution: 2.865→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2188 814 0 105 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083180
X-RAY DIFFRACTIONf_angle_d1.0594498
X-RAY DIFFRACTIONf_dihedral_angle_d22.7351240
X-RAY DIFFRACTIONf_chiral_restr0.043464
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8654-2.99580.35631280.29442563X-RAY DIFFRACTION100
2.9958-3.15370.23681330.20492524X-RAY DIFFRACTION100
3.1537-3.35130.19321350.15362561X-RAY DIFFRACTION100
3.3513-3.60990.16541330.11752527X-RAY DIFFRACTION100
3.6099-3.9730.15741350.11382571X-RAY DIFFRACTION100
3.973-4.54760.1361350.09622566X-RAY DIFFRACTION100
4.5476-5.72790.11931360.10422587X-RAY DIFFRACTION100
5.7279-47.53630.13741390.11142645X-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)
16.42963.1765-1.86652.0489-0.92933.80120.27512.0364-0.4414-0.9226-0.9131.46830.5098-0.71120.4460.82560.2507-0.25861.104-0.62881.34324.92067.4117-23.4673
28.46925.5735-1.05245.90671.60096.56970.1360.9034-0.8474-1.0447-0.73113.0131-0.0318-0.88180.67930.79080.2932-0.3011.0784-0.45951.56084.097320.6353-16.7637
35.0004-6.7531-1.97089.10272.52925.7019-0.49913.02081.0167-0.149-1.08230.08170.0446-0.671.32471.36990.6007-0.16061.4826-0.19381.196-3.696536.0175-22.6341
48.4464-5.3964-4.48494.85626.18162.05820.40791.3195-1.0893-0.6001-2.25551.2642-0.1587-0.47471.74111.58760.5875-0.11671.25-0.1291.4269-5.237436.9698-15.4927
58.1315-3.82096.88585.6194-2.32517.5456-0.11272.9894-0.9688-0.8661-0.64390.98780.11360.41520.78011.01710.379-0.31921.6744-0.43151.35394.207422.8538-23.549
62.6009-3.6844-4.79948.56436.97948.4925-0.75710.7899-1.28011.1214-0.27860.73041.4877-0.54471.13821.08520.2867-0.14711.0946-0.53571.606317.71579.7136-18.0633
72.33180.9923-4.08964.75560.44288.2915-0.96091.6861-1.7626-0.4118-0.56411.67841.118-0.67381.53831.03470.2891-0.01431.3605-0.62811.408832.81261.3362-27.4821
82.431-6.54050.61644.46030.11653.986-0.426-0.5014-1.03650.25040.32531.40850.3257-0.51740.05740.74210.04230.06640.7916-0.11971.481417.472210.8542-7.3208
94.64873.1724.72488.35744.46584.86240.3371-0.1089-1.17340.4301-0.2879-0.10180.9541-0.1378-0.03870.56990.07270.12730.6254-0.08110.884333.9085.9623-3.4278
106.9382.6562-0.97579.0063-5.29085.9886-0.4986-1.8758-0.06742.50820.41750.2466-0.2579-1.0991-0.01611.31870.16860.14051.3004-0.04630.721328.286117.883910.1095
114.7284-1.0711.38625.6728-1.13930.86690.07950.4686-0.7185-0.3674-0.11470.3175-0.2054-0.2133-0.00050.55010.1220.05470.6469-0.17880.648229.08816.4296-9.2916
122.9849-0.5475-1.8284.98546.44328.74120.1773.61491.0067-3.6536-0.17751.396-1.77862.31920.06041.45750.1424-0.09671.48820.20450.905628.630830.5957-22.9217
135.3143-2.420.47848.24781.52474.74770.1356-0.1172-0.28180.0258-0.1441-0.0237-0.21380.1283-0.02730.41930.01240.04730.5393-0.03570.521234.687718.4241-4.7053
147.7214-5.7848-0.6144.27050.59210.13960.9541.35370.0849-2.6368-0.4785-0.6836-0.3849-0.3615-0.2941.38470.44610.01441.1695-0.08120.834218.621531.0588-22.9311
153.38533.91983.92117.31982.69366.0070.36240.54221.4644-0.1817-0.47510.5191-0.8344-0.40410.14050.95960.30630.17010.7436-0.06170.891217.318645.7438-12.0377
162.2468-0.72921.3725.0251-5.06255.25230.36360.79871.9657-0.374-0.9152-1.8878-1.07621.32550.75411.0798-0.00460.31130.94320.10281.449935.644841.6989-12.5902
173.1899-0.99860.81836.61690.03663.59390.34720.2969-0.0182-0.3015-0.25950.4125-0.5633-0.5893-0.10660.67540.15980.08590.6894-0.14580.698318.685633.0899-9.1352
184.87220.54394.24558.4395-3.05295.26281.3383-2.3583-2.7390.5878-0.44842.30853.3271-0.8203-0.90591.3623-0.08390.00481.05410.17211.40515.601916.15840.1049
192.952-1.63770.67156.21620.86582.95710.29090.0540.19510.0358-0.17840.2973-0.5935-0.3192-0.0860.68270.10260.16740.5779-0.11460.595119.886638.2138-3.1052
202.9257-1.60480.17764.47523.744.06660.26690.9141-0.2354-1.17750.2048-0.9343-1.73071.3081-0.16040.94430.01970.24140.8537-0.05990.839736.370931.2782-10.6701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'C' AND (RESID 2 THROUGH 11 )
2X-RAY DIFFRACTION2CHAIN 'C' AND (RESID 12 THROUGH 16 )
3X-RAY DIFFRACTION3CHAIN 'C' AND (RESID 17 THROUGH 21 )
4X-RAY DIFFRACTION4CHAIN 'D' AND (RESID -21 THROUGH -17 )
5X-RAY DIFFRACTION5CHAIN 'D' AND (RESID -16 THROUGH -12 )
6X-RAY DIFFRACTION6CHAIN 'D' AND (RESID -11 THROUGH -7 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID -6 THROUGH -2 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 1010 THROUGH 1028 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 1029 THROUGH 1046 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 1047 THROUGH 1055 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 1056 THROUGH 1087 )
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 1088 THROUGH 1099 )
13X-RAY DIFFRACTION13CHAIN 'A' AND (RESID 1100 THROUGH 1146 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 1010 THROUGH 1028 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 1029 THROUGH 1046 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 1047 THROUGH 1055 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 1056 THROUGH 1087 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 1088 THROUGH 1099 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 1100 THROUGH 1138 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 1139 THROUGH 1146 )

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