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- PDB-2yq0: KSHV LANA (ORF73) C-terminal domain, octameric ring: cubic crysta... -

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Basic information

Entry
Database: PDB / ID: 2yq0
TitleKSHV LANA (ORF73) C-terminal domain, octameric ring: cubic crystal form
ComponentsORF 73
KeywordsVIRAL PROTEIN / LATENCY-ASSOCIATED NUCLEAR ANTIGEN / LANA-1 / DNA-BINDING DOMAIN / ORIGIN-BINDING DOMAIN / OLIGOMERIZATION DOMAIN / KAPOSI'S SARCOMA-ASSOCIATED HERPESVIRUS / GAMMAHERPESVIRUS / RHADINOVIRUS / PRIMARY EFFUSION LYMPHOMA / MULTICENTRIC CASTLEMAN'S DISEASE / TUMOR VIRUS / CANCER / MURID HERPESVIRUS 4 / MUHV-4 / MURID HERPESVIRUS 68 / MHV-68
Function / homology
Function and homology information


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
Biological speciesHUMAN HERPESVIRUS 8 TYPE M
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.911 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 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...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 / 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: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2662
Polymers18,1701
Non-polymers961
Water0
1
A: ORF 73
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)146,12916
Polymers145,3608
Non-polymers7698
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_556x,z,-y+11
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation19_566-x,-z+1,-y+11
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation20_565x,-z+1,y1
crystal symmetry operation18_555-x,z,y1
Buried area15810 Å2
ΔGint-251 kcal/mol
Surface area44250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.400, 107.400, 107.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein ORF 73 / KSHV LANA


Mass: 18170.047 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN, RESIDUES 996-1153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 TYPE M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76SB0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.85 Å3/Da / Density % sol: 56.8 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 1 UL OF 1 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 2 MM DTT WAS ADDED TO 1 UL OF 0.1 M SODIUM CITRATE, PH 2.5, 1.5 M AMMONIUM SULFATE. THE MIXTURE WAS INCUBATED AT 4 DEGREE CENTIGRADE IN A ...Details: 1 UL OF 1 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 2 MM DTT WAS ADDED TO 1 UL OF 0.1 M SODIUM CITRATE, PH 2.5, 1.5 M AMMONIUM SULFATE. THE MIXTURE WAS INCUBATED AT 4 DEGREE CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM CITRATE, PH 2.5, 1.5 M AMMONIUM SULFATE, 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: 3.91→50 Å / Num. obs: 2178 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Biso Wilson estimate: 140.76 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.73
Reflection shellResolution: 3.91→4.01 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 3.92 / % possible all: 100

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Processing

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

2ypy


Resolution: 3.911→33.963 Å / SU ML: 0.41 / σ(F): 2.01 / Phase error: 36.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3166 109 5 %
Rwork0.2595 --
obs0.2623 2178 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 198.3 Å2
Refinement stepCycle: LAST / Resolution: 3.911→33.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms946 0 5 0 951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003980
X-RAY DIFFRACTIONf_angle_d0.7461324
X-RAY DIFFRACTIONf_dihedral_angle_d12.361366
X-RAY DIFFRACTIONf_chiral_restr0.054134
X-RAY DIFFRACTIONf_plane_restr0.003167
LS refinement shellResolution: 3.9113→33.9641 Å
RfactorNum. reflection% reflection
Rfree0.3166 109 -
Rwork0.2595 2069 -
obs--100 %
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)
12.0683-7.0726-7.11642.24282.85763.796-0.31680.15460.98490.6095-0.8652-4.86720.9520.80250.35432.3971-0.2906-0.34511.65660.49251.8599.595845.059117.1916
22.04880.8679-0.17482.0212-5.68692.1209-2.41062.10891.35411.1208-0.1514-2.63310.7010.79264.38851.9875-0.0845-0.12721.9720.3122.52415.634844.417134.2914
32.3309-0.3265-4.94092.9316-0.76562.77272.07150.4839-1.6661.7104-0.5104-1.0188-1.4051-1.6211-1.61342.1903-0.4958-0.15841.22710.03751.32290.852336.628223.8304
42.0045-5.0673-5.16941.86171.92311.9432-0.90432.4707-2.1892-4.8149-1.50031.11297.74262.98042.89862.96010.48460.08252.27030.03081.2885-13.755828.406627.2438
54.7844-3.3338-0.92942.73910.99786.1119-0.6445-0.88450.01430.382-0.00390.50340.5877-1.37880.60891.9136-0.2957-0.00621.02460.28581.4837-0.746944.685325.8393
62.0573-8.8696-4.11022.06680.87968.3456-0.31336.1045-1.62223.1533-0.1043-1.3259-1.6260.67191.06482.3765-0.5761-0.43722.3392-0.09611.93669.699336.153439.396
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1024 THROUGH 1046 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1047 THROUGH 1055 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1056 THROUGH 1089 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1090 THROUGH 1099 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 1100 THROUGH 1138 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 1139 THROUGH 1146 )

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