SAXSdb — 2ypy

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ORF 73

HUMAN HERPESVIRUS 8 TYPE M

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 G； UniProt 1013–1149 Chain H； UniProt 1013–1149	Fragment：C-TERMINAL DOMAIN, RESIDUES 1013-1149	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
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	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
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	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
4	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	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
5	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	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

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 2YPY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YPZ KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic 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 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	No recorded non-water small molecule	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
2YPZ KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic 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	No recorded non-water small molecule	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
2YPZ KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic 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	No recorded non-water small molecule	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
2YPZ KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic 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 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	No recorded non-water small molecule	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
2YPZ KSHV LANA (ORF73) C-terminal domain, decameric ring: orthorhombic 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 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	No recorded non-water small molecule	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
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ypy
Deposition date deposition_date	2012-11-02
Structure title title	KSHV LANA (ORF73) C-terminal domain, decameric ring: monoclinic crystal form
Keywords keywords	;VIRAL PROTEIN, VIRAL PROTEIN N, 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 method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.43 Å
Radius of gyration Rg (electron density) rg_electron	43.46 Å
Forward intensity I(0) i0	332427000.00
Molecular weight molecular_weight	154030.0 kDa
Excluded volume excluded_volume	194160 Å³
Envelope volume envelope_volume	288850 Å³
Hydration-shell volume shell_volume	53616 Å³
Envelope diameter envelope_diameter	122.4 Å
Shell Rg shell_rg	52.63 Å
Envelope Rg envelope_rg	40.72 Å
Shape Rg shape_rg	43.49 Å
Total Rg total_rg	43.76 Å
Total atoms total_atoms	10843
Residues n_residues	1345
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	125.4 Å
Rg (real space) rg_real	44.17 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	3.3240e+08
I(0) uncertainty (real space) i0_real_error	5.4450e+06
Rg (reciprocal space) rg_reciprocal	44.43 Å
I(0) (reciprocal space) i0_reciprocal	332500000.0000
Solution quality estimate total_estimate	0.8666
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	73.1 Å
Skewness Skewness skewness	-0.167
Kurtosis Kurtosis kurtosis	-0.977
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17040000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.845; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.734

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ORF 73
Molecular weight formula_weight	15760.2 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	11040

GSRYQQPPVPYRQIDDCPAKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPGPDQSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPLTQPG

来源 Source

来源生物 organism	HUMAN HERPESVIRUS 8 TYPE M
NCBI Class编号 ncbi_taxonomy_id	435895
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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7. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	2ypyA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyE00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

Domain ID domain_id	2ypyJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	390 — Epstein Barr virus nuclear antigen-1, DNA-binding domain

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8. Citations (1)

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Unit-cell length a length_a	51.740 Å
Unit-cell length b length_b	175.920 Å
Unit-cell length c length_c	97.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.453 Å
Low-resolution limit resolution_low	19.652 Å
R factor r_factor	0.2224
R_work r_work	0.2207
R_free r_free	0.2522

fit	/app/data/saxs_computation/yp/2ypy/2ypy.fit
pddf	/app/data/pr_computation/yp/2ypy/2ypy.pr.out
profile	/app/data/saxs_computation/yp/2ypy/2ypy.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

ORF 73

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction