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- PDB-2yq1: MHV-68 LANA (ORF73) C-terminal domain: triclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 2yq1
TitleMHV-68 LANA (ORF73) C-terminal domain: triclinic crystal form
ComponentsORF73
KeywordsVIRAL PROTEIN / MUHV-4 / MURID HERPESVIRUS 68 / LATENCY- ASSOCIATED NUCLEAR ANTIGEN / LANA-1 / MLANA / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS / KSHV / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE
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
Biological speciesMURID HERPESVIRUS 4 (Murine herpesvirus 68)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHellert, J. / Krausze, J. / Luhrs, T.
CitationJournal: Plos Pathog. / Year: 2013
Title: A Structural Basis for Brd2/4-Mediated Host Chromatin Interaction and Oligomer Assembly of Kaposi Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Lana Proteins.
Authors: Hellert, J. / Weidner-Glunde, M. / Krausze, J. / Richter, U. / Adler, H. / Fedorov, R. / Pietrek, M. / Ruckert, J. / Ritter, C. / Schulz, T.F. / Luhrs, T.
History
DepositionNov 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Derived calculations / Other
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
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: ORF73
B: ORF73
C: ORF73
D: ORF73


Theoretical massNumber of molelcules
Total (without water)63,8744
Polymers63,8744
Non-polymers00
Water3,693205
1
C: ORF73
D: ORF73


Theoretical massNumber of molelcules
Total (without water)31,9372
Polymers31,9372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area13230 Å2
MethodPISA
2
A: ORF73
B: ORF73


Theoretical massNumber of molelcules
Total (without water)31,9372
Polymers31,9372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-34.7 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.958, 53.395, 70.859
Angle α, β, γ (deg.)106.00, 93.47, 109.80
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.21361, -0.26954, 0.939), (0.28261, -0.90304, -0.32351), (0.93515, -0.33448, 0.11672)-23.99054, 21.51538, 26.31948
2given(0.99977, 0.00649, -0.02067), (0.00642, -0.99997, -0.00333), (-0.02069, 0.0032, -0.99978)0.5938, 12.90218, 77.05668
3given(-0.21832, -0.27131, 0.9374), (0.28213, 0.90201, 0.32677), (-0.9342, 0.33581, -0.12038)-23.77854, -8.78445, 51.0144

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Components

#1: Protein
ORF73 / MHV-68 LANA / IMMEDIATE-EARLY PROTEIN


Mass: 15968.619 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 124-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MURID HERPESVIRUS 4 (Murine herpesvirus 68)
Strain: 68 / Plasmid: PET BASED / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O41974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 1.9 Å3/Da / Density % sol: 35.37 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.5 UL OF 0.3 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 5 MM DTT WERE ADDED TO 1.5 UL OF 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 20 DEGREE CENTIGRADE IN A HANGING ...Details: 1.5 UL OF 0.3 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 5 MM DTT WERE ADDED TO 1.5 UL OF 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 20 DEGREE CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 2.0 M SODIUM FORMATE, 15% (W/V) PEG 6000, 25% (V/V) GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 24125 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 2.03 % / Biso Wilson estimate: 21.93 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.4
Reflection shellResolution: 2.14→2.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.34 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.062 Å / SU ML: 0.29 / σ(F): 1.99 / Phase error: 24.99 / Stereochemistry target values: ML
Details: DATA UP TO 2.3 A RESOLUTION WERE INCLUDED FOR REFINEMENT.
RfactorNum. reflection% reflection
Rfree0.2456 993 5 %
Rwork0.2001 --
obs0.2024 19866 95.24 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.709 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.8435 Å2-1.93 Å2-3.643 Å2
2---5.5569 Å2-2.0527 Å2
3---6.4004 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 0 0 205 4350
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054279
X-RAY DIFFRACTIONf_angle_d1.0095810
X-RAY DIFFRACTIONf_dihedral_angle_d12.291647
X-RAY DIFFRACTIONf_chiral_restr0.056637
X-RAY DIFFRACTIONf_plane_restr0.005732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.42130.27541410.242689X-RAY DIFFRACTION95
2.4213-2.57280.30961420.22372695X-RAY DIFFRACTION95
2.5728-2.77120.28991420.22732686X-RAY DIFFRACTION96
2.7712-3.04960.25551440.212737X-RAY DIFFRACTION96
3.0496-3.48970.23261410.19072693X-RAY DIFFRACTION95
3.4897-4.39230.21261430.16912704X-RAY DIFFRACTION95
4.3923-24.06290.22731400.19722669X-RAY DIFFRACTION95
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)
10.2910.5839-0.48361.0867-0.93490.808-0.15980.00620.4541-0.0265-0.272-0.5970.02740.26170.23540.35230.034-0.04610.4927-0.11990.7084.9181-6.924623.6991
22.61340.41491.88241.43780.59384.5701-0.21530.0805-0.27460.01990.1793-0.0250.46670.27020.06410.35590.01540.06690.20740.04950.2056-7.5272-14.906822.8528
30.83750.2738-0.11281.1630.08961.54750.05260.0161-0.1134-0.11310.1874-0.15510.14960.4565-0.26950.1610.0257-0.01290.1503-0.00630.2497-6.5454-3.507815.6299
41.09680.18510.27611.6470.29551.04360.12-0.0654-0.37150.02060.0245-0.38960.0353-0.1788-0.05160.15450.01820.00170.1871-0.03560.0896-3.9695-2.230723.1318
53.21651.081.33334.4934-1.90561.88030.0789-0.59480.4110.6340.02410.4404-0.1615-0.2979-0.05880.4580.0901-0.08030.1443-0.05760.6563-12.351318.623535.1361
61.0078-0.04590.01261.76190.68233.2263-0.070.0612-0.09880.1306-0.22980.1626-0.062-0.34740.27570.1121-0.026-0.00890.1828-0.01010.1111-9.40915.843425.8643
72.35270.5158-0.69623.7966-2.35815.7580.02010.0051-0.10320.1259-0.12560.36190.2961-0.25010.12410.2291-0.0103-0.04630.238-0.08090.2818-16.3569-5.75818.9903
82.35890.2591-0.50714.7603-3.54766.77630.0366-0.347-0.03280.01560.07630.435-0.0414-0.0438-0.04620.18470.0536-0.01240.1402-0.00160.1906-14.90641.589123.2444
93.22272.3043-0.00413.7831-0.83837.4982-0.33230.14680.0526-0.3-0.3486-0.29910.0139-0.15830.35730.27260.0044-0.03460.2075-0.00130.2545-2.49428.81569.897
101.57130.7426-0.74551.8794-1.15121.94360.2921-0.43350.14570.9011-0.2179-0.0456-0.44330.4786-0.18370.3583-0.05810.00160.3123-0.05670.26881.38924.9830.9385
113.57222.26570.34022.9164-0.4820.7856-0.0567-0.43890.58160.747-0.15590.7941-0.1322-0.46920.17710.2612-0.01620.07520.3159-0.07470.3339-13.716326.222825.1052
122.00640.06180.32071.1734-0.07621.54420.1172-0.0019-0.24440.0436-0.01440.022-0.04870.0492-0.09810.1313-0.0284-0.00480.11250.01670.18480.1914.189322.3926
134.22391.01930.18062.02070.57372.12070.29210.3353-0.2147-0.2417-0.0921-0.1084-0.47220.071-0.18890.27030.0085-0.01770.18440.02380.2355-0.664622.30314.8999
143.78441.4412.18023.0053-2.14744.84950.0648-0.43510.1920.12340.07450.3441-0.0826-0.7536-0.08890.1290.0349-0.01060.2173-0.02140.2605-17.27111.743423.4125
150.2423-0.44830.40780.717-0.67210.6155-0.0855-0.0812-0.16530.44550.0257-0.57020.29740.2677-0.01320.4494-0.1461-0.06050.5641-0.15510.99644.950519.744453.6232
161.46-0.39310.66571.3069-0.29132.2682-0.24610.04150.01840.2826-0.1385-0.258-0.4278-0.10040.22340.29770.0448-0.0820.1378-0.01150.2534-6.374226.359359.945
170.9693-0.0479-0.17751.5021-0.26572.7181-0.020.0581-0.0815-0.0497-0.0582-0.05250.0488-0.00340.08380.05860.00510.00750.11960.00210.0958-6.836810.379953.4903
181.8523-0.68570.40892.9726-0.85661.99720.031-0.1218-0.04530.032-0.00530.147-0.1259-0.0284-0.02530.11010.00210.02510.1701-0.03690.1333-12.071313.350159.6204
191.03510.23170.26752.223-0.05371.9375-0.00780.3229-0.1406-0.602-0.0617-0.0860.08460.42660.08980.25190.0258-0.02840.2492-0.03290.32481.5931-12.102946.2621
203.8012-1.4012-0.15071.8699-0.65280.42080.02460.3733-1.0824-0.377-0.09590.21790.0554-0.22420.04820.3136-0.0719-0.0980.284-0.02770.3495-13.5151-13.44452.1529
211.88990.0090.29351.85020.31021.83920.0617-0.02070.0266-0.0776-0.0361-0.01560.17760.0661-0.03930.10790.01420.01990.08060.01280.111-1.6461-3.56257.2557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 130:140)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 141:153)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 154:180)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 181:203)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 204:208)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 209:223)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 224:241)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 242:251)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 252:259)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 130:153)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 154:169)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 170:223)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 224:251)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 252:260)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 130:140)
16X-RAY DIFFRACTION16CHAIN C AND (RESSEQ 141:163)
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 164:223)
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 224:260)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 130:153)
20X-RAY DIFFRACTION20CHAIN D AND (RESSEQ 154:169)
21X-RAY DIFFRACTION21CHAIN D AND (RESSEQ 170:260)

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