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2ypz

KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form

Method: X-RAY DIFFRACTION Dmax: 125.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

KSHV LANA

HUMAN HERPESVIRUS 8 TYPE M

UniProt Q76SB0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain I； UniProt 1013–1149 Chain J； UniProt 1013–1149 Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. 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 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL. Resolution 3.20 Å R-free 0.265
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1013–1149 Chain D； UniProt 1013–1149 Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. 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 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL. Resolution 3.20 Å R-free 0.265
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1013–1149 Chain B； UniProt 1013–1149 Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. 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 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL. Resolution 3.20 Å R-free 0.265
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 1013–1149 Chain H； UniProt 1013–1149 Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. 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 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL. Resolution 3.20 Å R-free 0.265
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1013–1149 Chain F； UniProt 1013–1149 Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；1.5 UL OF 0.8 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 200 MM LICL, 4 MM DTT WERE ADDED TO 1.5 UL OF 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350. 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 0.2 M LITHIUM CITRATE, PH 7.6, 20 % (W/V) PEG 3350, 30 % (V/V) GLYCEROL. Resolution 3.20 Å R-free 0.265

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2YPZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2YPY KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form Deposited 2012-11-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain H 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；285 K；1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.
Resolution 2.45 Å R-free 0.252
2YPY KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form Deposited 2012-11-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain D 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；285 K；1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.
Resolution 2.45 Å R-free 0.252
2YPY KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form Deposited 2012-11-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain B 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；285 K；1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.
Resolution 2.45 Å R-free 0.252
2YPY KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form Deposited 2012-11-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain F 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded CL CHLORIDE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；285 K；1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.
Resolution 2.45 Å R-free 0.252
2YPY KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form Deposited 2012-11-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain J 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；285 K；1.5 UL OF 2.0 MM PROTEIN IN 5 MM BISTRIS, PH 6.5, 10 MM DTT WERE ADDED TO 1.5 UL OF 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000. THE MIXTURE WAS INCUBATED AT 12 DEGREES CENTIGRADE IN A HANGING DROP SETUP. CRYSTALS GREW IN A FEW DAYS AND WERE CRYO-PROTECTED BY SHORT SOAKING IN 0.1 M SODIUM BICINE, PH 9.0, 1.0 M LITHIUM CHLORIDE, 7 % (W/V) PEG 6000, 25 % (V/V) GLYCEROL.
Resolution 2.45 Å R-free 0.252
2YQ0 KSHV LANA (ORF73) C-terminal domain, octameric ring: cubic crystal form Deposited 2012-11-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 996–1153（158 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 996-1153
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；277 K；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.
Resolution 3.91 Å R-free 0.317
4UZB KSHV LANA (ORF73) C-terminal domain mutant bound to LBS1 DNA (R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D) Deposited 2014-09-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1008–1146（139 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1008-1146
Chain B 1008–1146（139 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1008-1146
Mutation：R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D Mutation：R1039Q, R1040Q, K1055E, K1109A, D1110A, A1121E, K1138S, K1140D, K1141D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；297 K；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.
Resolution 2.87 Å R-free 0.155
4UZC KSHV LANA (ORF73) C-terminal domain, spiral: hexagonal crystal form Deposited 2014-09-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 48 PDB declaration: 48-meric
Chain A 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain B 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain C 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Chain D 1013–1149（137 aa） Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.4 UL OF 31.5 MG/ML PROTEIN IN 5 MM BISTRIS-CL, 5 MM DTT, PH 6.5 WERE AS SUCH EQUILIBRATED AGAINST A RESERVOIR SOLUTION OF 170 MM LITHIUM ACETATE AND 18% (W/V) PEG3350 IN A SITTING DROP SETUP AT 20 DEGREE CENTIGRADE. AFTER TWO DAYS, CRYSTALS WERE DETACHED FROM THE CARRIER PLASTIC BY ADDING 1 UL OF 2 M AMMONIUM FORMATE.
Resolution 3.70 Å R-free 0.239
5A76 KSHV LANA (ORF73) C-terminal domain, open non-ring conformation: orthorhombic crystal form Deposited 2015-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Chain F 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3；100 MM CITRIC ACID, PH 3.0, 1200 MM MAGNESIUM CHLORIDE.
Resolution 3.80 Å R-free 0.269
5A76 KSHV LANA (ORF73) C-terminal domain, open non-ring conformation: orthorhombic crystal form Deposited 2015-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Chain D 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3；100 MM CITRIC ACID, PH 3.0, 1200 MM MAGNESIUM CHLORIDE.
Resolution 3.80 Å R-free 0.269
5A76 KSHV LANA (ORF73) C-terminal domain, open non-ring conformation: orthorhombic crystal form Deposited 2015-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Chain B 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3；100 MM CITRIC ACID, PH 3.0, 1200 MM MAGNESIUM CHLORIDE.
Resolution 3.80 Å R-free 0.269
5A76 KSHV LANA (ORF73) C-terminal domain, open non-ring conformation: orthorhombic crystal form Deposited 2015-07-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Chain H 1018–1150（133 aa） Fragment：DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3；100 MM CITRIC ACID, PH 3.0, 1200 MM MAGNESIUM CHLORIDE.
Resolution 3.80 Å R-free 0.269
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain Q 23–32（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227
7BCY X-ray structure of WDR5delta24 bound to the Kaposi's sarcoma herpesvirus LANA win motif peptide Deposited 2020-12-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 23–32（10 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；294 K；100 mM Bis-Tris pH 5.5, 50 mM (NH4)2SO4, 25% PEG3350
Resolution 1.50 Å R-free 0.227

6 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q76SB0_HHV8
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–139； UniProt 1013–1149 Author chain B； PDBConstruct 3–139； UniProt 1013–1149 Author chain C； PDBConstruct 3–139； UniProt 1013–1149 Author chain D； PDBConstruct 3–139； UniProt 1013–1149 Author chain E； PDBConstruct 3–139； UniProt 1013–1149 Author chain F； PDBConstruct 3–139； UniProt 1013–1149 Author chain G； PDBConstruct 3–139； UniProt 1013–1149 Author chain H； PDBConstruct 3–139； UniProt 1013–1149 Author chain I； PDBConstruct 3–139； UniProt 1013–1149 Author chain J； PDBConstruct 3–139； UniProt 1013–1149

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2ypz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2ypz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2ypz
Deposition date deposition_date2012-11-02
Structure title titleKSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic crystal form
Keywords keywords;VIRAL 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 ;; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier44.45 Å
Radius of gyration Rg (electron density) rg_electron43.45 Å
Forward intensity I(0) i0324170000.00
Molecular weight molecular_weight153420.0 kDa
Excluded volume excluded_volume194010 ų
Envelope volume envelope_volume287740 ų
Hydration-shell volume shell_volume53326 ų
Envelope diameter envelope_diameter125.3 Å
Shell Rg shell_rg52.69 Å
Envelope Rg envelope_rg40.75 Å
Shape Rg shape_rg43.48 Å
Total Rg total_rg43.77 Å
Total atoms total_atoms10837
Residues n_residues1347
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax125.4 Å
Rg (real space) rg_real44.19 Å
Rg uncertainty (real space) rg_real_error1.05 Å
I(0) (real space) i0_real3.2420e+08
I(0) uncertainty (real space) i0_real_error5.2700e+06
Rg (reciprocal space) rg_reciprocal44.45 Å
I(0) (reciprocal space) i0_reciprocal324300000.0000
Solution quality estimate total_estimate0.8600
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary75.2 Å
Skewness Skewness skewness-0.167
Kurtosis Kurtosis kurtosis-0.972
Angular range angular_range— – 0.1750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15620000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.646
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id2ypzA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzG00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzH00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
Domain ID domain_id2ypzJ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)