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- PDB-5a76: KSHV LANA (ORF73) C-terminal domain, open non-ring conformation: ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5a76
TitleKSHV LANA (ORF73) C-terminal domain, open non-ring conformation: orthorhombic crystal form
ComponentsORF 73
KeywordsDNA BINDING PROTEIN / DNA / VIRAL / PROTEIN FOLDING / PROTEIN STRUCTURE / TERTIARY / RHADINOVIRUS / VIRAL PROTEINS / VIRUS LATENCY
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
ORF 73 / Kaposi's sarcoma-associated herpes-like virus ORF73 homolog
Similarity search - Component
Biological speciesHUMAN HERPESVIRUS 8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsPonnusamy, R. / Mcvey, C.E.
CitationJournal: Nucleic Acids Res / Year: 2015
Title: KSHV but not MHV-68 LANA induces a strong bend upon binding to terminal repeat viral DNA.
Authors: Rajesh Ponnusamy / Maxim V Petoukhov / Bruno Correia / Tania F Custodio / Franceline Juillard / Min Tan / Marta Pires de Miranda / Maria A Carrondo / J Pedro Simas / Kenneth M Kaye / Dmitri ...Authors: Rajesh Ponnusamy / Maxim V Petoukhov / Bruno Correia / Tania F Custodio / Franceline Juillard / Min Tan / Marta Pires de Miranda / Maria A Carrondo / J Pedro Simas / Kenneth M Kaye / Dmitri I Svergun / Colin E McVey /
Abstract: Latency-associated nuclear antigen (LANA) is central to episomal tethering, replication and transcriptional regulation of γ2-herpesviruses. LANA binds cooperatively to the terminal repeat (TR) ...Latency-associated nuclear antigen (LANA) is central to episomal tethering, replication and transcriptional regulation of γ2-herpesviruses. LANA binds cooperatively to the terminal repeat (TR) region of the viral episome via adjacent LANA binding sites (LBS), but the molecular mechanism by which LANA assembles on the TR remains elusive. We show that KSHV LANA and MHV-68 LANA proteins bind LBS DNA using strikingly different modes. Solution structure of LANA complexes revealed that while kLANA tetramer is intrinsically bent both in the free and bound state to LBS1-2 DNA, mLANA oligomers instead adopt a rigid linear conformation. In addition, we report a novel non-ring kLANA structure that displays more flexibility at its assembly interface than previously demonstrated. We identified a hydrophobic pivot point located at the dimer-dimer assembly interface, which gives rotational freedom for kLANA to adopt variable conformations to accommodate both LBS1-2 and LBS2-1-3 DNA. Alterations in the arrangement of LBS within TR or at the tetramer assembly interface have a drastic effect on the ability of kLANA binding. We also show kLANA and mLANA DNA binding functions can be reciprocated. Although KSHV and MHV-68 are closely related, the findings provide new insights into how the structure, oligomerization, and DNA binding of LANA have evolved differently to assemble on the TR DNA.
History
DepositionJul 2, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references / Refinement description
Revision 1.3Jan 10, 2024Group: 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: ORF 73
D: ORF 73
E: ORF 73
F: ORF 73
G: ORF 73
H: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,12512
Polymers121,0288
Non-polymers974
Water00
1
E: ORF 73
F: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,2572
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-23.2 kcal/mol
Surface area12220 Å2
MethodPISA
2
C: ORF 73
D: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,2572
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-22.6 kcal/mol
Surface area11950 Å2
MethodPISA
3
A: ORF 73
B: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,2572
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-21.5 kcal/mol
Surface area11810 Å2
MethodPISA
4
G: ORF 73
H: ORF 73
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2813
Polymers30,2572
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-20.7 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.224, 200.224, 83.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA1029 - 114513 - 129
21ALAALALEULEUBB1029 - 114513 - 129
12ALAALALEULEUAA1029 - 114513 - 129
22ALAALALEULEUCC1029 - 114513 - 129
13ALAALALEULEUAA1029 - 114513 - 129
23ALAALALEULEUDD1029 - 114513 - 129
14ALAALALEULEUAA1029 - 114513 - 129
24ALAALALEULEUEE1029 - 114513 - 129
15ALAALALEULEUAA1029 - 114513 - 129
25ALAALALEULEUFF1029 - 114513 - 129
16ALAALALEULEUAA1029 - 114513 - 129
26ALAALALEULEUGG1029 - 114513 - 129
17ALAALALEULEUAA1029 - 114513 - 129
27ALAALALEULEUHH1029 - 114513 - 129
18ALAALALEULEUBB1029 - 114513 - 129
28ALAALALEULEUCC1029 - 114513 - 129
19PROPROPROPROBB1028 - 114412 - 128
29PROPROPROPRODD1028 - 114412 - 128
110ALAALAGLNGLNBB1029 - 114713 - 131
210ALAALAGLNGLNEE1029 - 114713 - 131
111ALAALATHRTHRBB1029 - 114613 - 130
211ALAALATHRTHRFF1029 - 114613 - 130
112ALAALALEULEUBB1029 - 114513 - 129
212ALAALALEULEUGG1029 - 114513 - 129
113ALAALATHRTHRBB1029 - 114613 - 130
213ALAALATHRTHRHH1029 - 114613 - 130
114ALAALALEULEUCC1029 - 114513 - 129
214ALAALALEULEUDD1029 - 114513 - 129
115ALAALAPROPROCC1029 - 114413 - 128
215ALAALAPROPROEE1029 - 114413 - 128
116ALAALALEULEUCC1029 - 114513 - 129
216ALAALALEULEUFF1029 - 114513 - 129
117ALAALALEULEUCC1029 - 114513 - 129
217ALAALALEULEUGG1029 - 114513 - 129
118ALAALALEULEUCC1029 - 114513 - 129
218ALAALALEULEUHH1029 - 114513 - 129
119ALAALAPROPRODD1029 - 114413 - 128
219ALAALAPROPROEE1029 - 114413 - 128
120ALAALALEULEUDD1029 - 114513 - 129
220ALAALALEULEUFF1029 - 114513 - 129
121ALAALALEULEUDD1029 - 114513 - 129
221ALAALALEULEUGG1029 - 114513 - 129
122ALAALALEULEUDD1029 - 114513 - 129
222ALAALALEULEUHH1029 - 114513 - 129
123ALAALATHRTHREE1029 - 114613 - 130
223ALAALATHRTHRFF1029 - 114613 - 130
124ALAALALEULEUEE1029 - 114513 - 129
224ALAALALEULEUGG1029 - 114513 - 129
125ALAALATHRTHREE1029 - 114613 - 130
225ALAALATHRTHRHH1029 - 114613 - 130
126ALAALALEULEUFF1029 - 114513 - 129
226ALAALALEULEUGG1029 - 114513 - 129
127ALAALATHRTHRFF1029 - 114613 - 130
227ALAALATHRTHRHH1029 - 114613 - 130
128ALAALALEULEUGG1029 - 114513 - 129
228ALAALALEULEUHH1029 - 114513 - 129

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
ORF 73


Mass: 15128.496 Da / Num. of mol.: 8 / Fragment: DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN HERPESVIRUS 8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PRARE2 / References: UniProt: Q76SB0, UniProt: Q98148*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 3.47 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growpH: 3
Details: 100 MM CITRIC ACID, PH 3.0, 1200 MM MAGNESIUM CHLORIDE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9725
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 3.8→47.19 Å / Num. obs: 16786 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.28 / Net I/σ(I): 5.2
Reflection shellResolution: 3.8→4.25 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4K2J

4k2j


Resolution: 3.8→141.58 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.894 / SU B: 90.988 / SU ML: 0.567 / Cross valid method: THROUGHOUT / ESU R Free: 0.709 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. FOLLOWING RESIDUES ARE DISORDERED IN THE CRYSTALS. CHAIN A, 1017-1028, 1048, 1049, 1091-1096, 1146-1150. CHAIN B, 1017-1027, 1049-1051, 1091-1094, 1148-1150. CHAIN ...Details: U VALUES WITH TLS ADDED. FOLLOWING RESIDUES ARE DISORDERED IN THE CRYSTALS. CHAIN A, 1017-1028, 1048, 1049, 1091-1096, 1146-1150. CHAIN B, 1017-1027, 1049-1051, 1091-1094, 1148-1150. CHAIN C, 1017-1028, 1091-1093, 1146-1150. CHAIN D, 1017-1027, 1051-1052, 1094-1096, 1146-1150. CHAIN E, 1017-1026, 1094-1096, 1148-1150. CHAIN F, 1017-1028, 1147-1150. CHAIN G, 1017-1028, 1095, 1146-1150. CHAIN H, 1017-1028, 1091-1094, 1147-1150.
RfactorNum. reflection% reflectionSelection details
Rfree0.26908 853 5.1 %RANDOM
Rwork0.22109 ---
obs0.22347 15922 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.722 Å2
Baniso -1Baniso -2Baniso -3
1--3.8 Å20 Å20 Å2
2---1.77 Å20 Å2
3---5.56 Å2
Refinement stepCycle: LAST / Resolution: 3.8→141.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7324 0 4 0 7328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197563
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9510198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9315896
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.76322.539319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.647151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3551547
X-RAY DIFFRACTIONr_chiral_restr0.0720.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0225727
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7494.1873638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.3786.2584516
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9494.5523923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.29238.5829914
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2240.2
12B2240.2
21A2460.18
22C2460.18
31A2220.2
32D2220.2
41A2340.19
42E2340.19
51A2300.18
52F2300.18
61A2480.18
62G2480.18
71A2300.13
72H2300.13
81B2320.21
82C2320.21
91B2360.16
92D2360.16
101B2300.25
102E2300.25
111B2460.2
112F2460.2
121B2300.19
122G2300.19
131B2320.18
132H2320.18
141C2300.21
142D2300.21
151C2360.2
152E2360.2
161C2380.19
162F2380.19
171C2460.19
172G2460.19
181C2500.24
182H2500.24
191D2360.19
192E2360.19
201D2480.17
202F2480.17
211D2360.14
212G2360.14
221D2460.14
222H2460.14
231E2460.22
232F2460.22
241E2540.21
242G2540.21
251E2460.22
252H2460.22
261F2560.18
262G2560.18
271F2520.17
272H2520.17
281G2540.15
282H2540.15
LS refinement shellResolution: 3.8→3.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 77 -
Rwork0.286 1138 -
obs--99.84 %
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)
15.7401-3.53370.37973.3532-1.31133.14870.23440.21630.0338-0.0705-0.24890.0735-0.3296-0.06340.01450.1315-0.01140.03140.2435-0.05590.4417-21.539-38.428-5.359
24.7334-0.29930.97652.53960.33711.1295-0.332-0.1464-0.24740.01040.3862-0.1806-0.1160.3495-0.05420.03040.0167-0.02260.3757-0.05990.7461-4.119-49.7231.772
33.8332-0.0710.63842.24110.63522.22320.26330.1067-0.1146-0.2534-0.18240.00090.2027-0.0355-0.0810.12520.1008-0.00770.33010.0620.5216-58.757-61.757-6.702
45.28450.1261-0.44371.1357-1.42681.8269-0.3325-0.02910.1667-0.01560.350.04090.0455-0.3713-0.01760.02480.02240.01360.30670.0280.751-76.612-50.5060.105
52.14292.1651-0.05822.7334-0.50873.1943-0.19430.2006-0.333-0.10570.385-0.0984-0.19490.1821-0.19070.0542-0.02520.03050.2045-0.06790.7721-28.634-69.053-5.635
61.6121-0.64620.42653.2118-0.92390.32440.3040.041-0.30680.1566-0.16360.20690.01960.087-0.14040.08950.0138-0.04460.0842-0.08881.0033-39.527-86.2561.138
73.73571.46240.18240.64980.42293.2725-0.22110.22280.0135-0.09820.1610.0883-0.0907-0.21970.06010.1488-0.04250.02010.25690.11030.673-51.588-31.147-6.197
83.8829-0.84060.23294.54981.57880.91720.25510.12480.37820.297-0.1313-0.1581-0.144-0.0962-0.12380.35730.02280.0420.09350.12110.6649-40.941-13.5261.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1029 - 1145
2X-RAY DIFFRACTION2B1028 - 1147
3X-RAY DIFFRACTION3C1029 - 1145
4X-RAY DIFFRACTION4D1028 - 1145
5X-RAY DIFFRACTION5E1029 - 1147
6X-RAY DIFFRACTION6F1029 - 1146
7X-RAY DIFFRACTION7G1029 - 1145
8X-RAY DIFFRACTION8H1029 - 1146

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