SAXSdb — 5kw6

▼

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

Poly(U)-binding-splicing factor PUF60

Homo sapiens

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–DNA Homooligomer Protein × 2 DNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 118–316 Chain B； UniProt 118–316	Fragment：unp residues 118-316 Mutation：R123G, C129S, C255A	DNA (30-MER) × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；0.1 M Tris-HCl, 25% PEG 4000, 5-10 mM barium chloride dihydrate, pH 8.7, mixed with 10 mg/ml protein-nucleic acid mixture in 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 20 micromolar EDTA	Resolution 1.91 Å R-free 0.226

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 5KW6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KXF Solution structure of the first two RRM domains of FBP-interacting repressor (FIR) Deposited 2010-05-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 119–314（196 aa） Fragment：UNP residues 119-314	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；310 K；Ionic strength (raw mmCIF value) 0.06；Pressure ambient NMR sample composition 0.3-0.4 mM [U-15N] entity-1, 10 mM TRIS-HCl pH 8.0-2, 50 mM sodium chloride-3, 2 mM TCEP-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.4 mM [U-13C; U-15N] entity-5, 10 mM TRIS-HCl pH 8.0-6, 50 mM sodium chloride-7, 2 mM TCEP-8, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.4 mM [U-13C; U-15N; U70%-2H] entity-9, 10 mM TRIS-HCl pH 8.0-10, 50 mM sodium chloride-11, 2 mM TCEP-12, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KXH Solution structure of the first two RRM domains of FIR in the complex with FBP Nbox peptide Deposited 2010-05-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 119–314（196 aa） Fragment：UNP residues 119-314	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；310 K；Ionic strength (raw mmCIF value) 0.06；Pressure ambient NMR measurement conditions pH 8；318 K；Ionic strength (raw mmCIF value) 0.06；Pressure ambient NMR sample composition 0.6 mM [U-15N] protein_1-1, 10 mM TRIS-HCl pH 8.0-2, 50 mM sodium chloride-3, 2 mM TCEP-4, 1.25 mM protein_2-5, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition mM [U-13C; U-15N] protein_1-6, 10 mM TRIS-HCl pH 8.0-7, 50 mM sodium chloride-8, 2 mM TCEP-9, mM protein_2-10, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3 mM [U-13C; U-15N] protein_2-11, 10 mM TRIS-HCl pH 8.0-12, 50 mM sodium chloride-13, 2 mM TCEP-14, mM protein_1-15, 100% D2O \| 100% D2O NMR sample composition mM [U-13C; U-15N] protein_1-16, 10 mM TRIS-HCl pH 8.0-17, 50 mM sodium chloride-18, 2 mM TCEP-19, mM protein_2-20, 100% D2O \| 100% D2O	Resolution not provided
3DXB Structure of the UHM domain of Puf60 fused to thioredoxin Deposited 2008-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain F 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.271
3DXB Structure of the UHM domain of Puf60 fused to thioredoxin Deposited 2008-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain D 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.271
3DXB Structure of the UHM domain of Puf60 fused to thioredoxin Deposited 2008-07-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain G 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.271
3DXB Structure of the UHM domain of Puf60 fused to thioredoxin Deposited 2008-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain H 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559	Not recorded	CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.271
3DXB Structure of the UHM domain of Puf60 fused to thioredoxin Deposited 2008-07-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain B 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain C 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain D 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain E 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain F 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain G 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 Chain H 460–499（40 aa） Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559	Not recorded	CL CHLORIDE ION × 4 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.271
3UE2 Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 1.23 A resolution Deposited 2011-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 443–559（117 aa） Fragment：RNA binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；2.4 M ammonium sulfate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.23 Å R-free 0.160
3US5 Crystal structure of a RNA-binding domain of a poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 1.38 A resolution Deposited 2011-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 443–559（117 aa） Fragment：RRM 3 domain residues 443-559	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；2.40M ammonium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.38 Å R-free 0.181
3UWT Crystal structure of a RNA binding domain of poly-U binding splicing factor 60KDa (PUF60) from Homo sapiens at 2.50 A resolution Deposited 2011-12-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–316（199 aa） Fragment：RNA binding domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；0.2M sodium chloride, 1.26M ammonium sulfate, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.240
5KVY CRYSTAL STRUCTURE OF THE TWO TANDEM RRM DOMAINS OF PUF60 BOUND TO A PORTION OF AN ADML PRE-MRNA 3' SPLICE SITE ANALOG Deposited 2016-07-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 118–316（199 aa） Fragment：tandem RRM domains Chain B 118–316（199 aa） Fragment：tandem RRM domains	Mutation：R123G, C129S, C255A Mutation：R123G, C129S, C255A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；0.1 M TRIS-HCl, 25% PEG 4000, 5-10 mM Barium Chloride Dihydrate, pH 8.7, mixed with 10 mg/ml protein-nucleic acid mixture in 50 mM TRIS-HCl, pH 8.0, 150 mM NaCl, 20 micromolar EDTA.	Resolution 1.95 Å R-free 0.232
5KW1 Crystal Structure of the Two Tandem RRM Domains of PUF60 Bound to a Modified AdML Pre-mRNA 3' Splice Site Analogue Deposited 2016-07-15	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 118–316（199 aa） Fragment：unp residues 118-316 Chain B 118–316（199 aa） Fragment：unp residues 118-316	Mutation：R123G, C129S, C255A Mutation：R123G, C129S, C255A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.7；293 K；0.1 M Tris-HCl, 25% PEG 4000, 5-10 mM barium chloride dihydrate, pH 8.7, mixed with 10 mg/ml protein-nucleic acid mixture in 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 20 micromolar EDTA	Resolution 2.10 Å R-free 0.237
5KWQ Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60 Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 118–316（199 aa）	Mutation：R106G, C112S, C238A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1M Lithium sulfate, 0.1M HEPES (pH 7.5), 5% glycerol, mixed with an equal volume of 10 mg/ml protein	Resolution 2.80 Å R-free 0.256
5KWQ Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60 Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 118–316（199 aa）	Mutation：R106G, C112S, C238A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1M Lithium sulfate, 0.1M HEPES (pH 7.5), 5% glycerol, mixed with an equal volume of 10 mg/ml protein	Resolution 2.80 Å R-free 0.256
5KWQ Two Tandem RRM Domains of FBP-Interacting Repressor (FIR), also Known as PUF60 Deposited 2016-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 118–316（199 aa） Chain B 118–316（199 aa）	Mutation：R106G, C112S, C238A Mutation：R106G, C112S, C238A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；1M Lithium sulfate, 0.1M HEPES (pH 7.5), 5% glycerol, mixed with an equal volume of 10 mg/ml protein	Resolution 2.80 Å R-free 0.256
6LUR Human PUF60 UHM domain (thioredoxin fusion) in complex with a small molecule binder Deposited 2020-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 460–559（100 aa） Chain B 460–559（100 aa） Chain C 460–559（100 aa） Chain D 460–559（100 aa） Chain E 460–559（100 aa） Chain F 460–559（100 aa） Chain G 460–559（100 aa） Chain H 460–559（100 aa）	Not recorded	EVU 4-[2-[4-(aminomethyl)phenyl]phenyl]piperazin-2-one × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.3-1.6M AmSO4, 0.2M potassium formate	Resolution 2.00 Å R-free 0.253
6SLO Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 417–516（100 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate,	Resolution 1.94 Å R-free 0.207
6SLO Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 417–516（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate,	Resolution 1.94 Å R-free 0.207
6SLO Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 417–516（100 aa）	Not recorded	LJT 2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl)propyl]piperazin-1-yl]ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate,	Resolution 1.94 Å R-free 0.207
6SLO Crystal structure of PUF60 UHM domain in complex with 7,8 dimethoxyperphenazine Deposited 2019-08-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 417–516（100 aa）	Not recorded	LJT 2-[4-[3-(8-chloranyl-2,3-dimethoxy-phenothiazin-10-yl)propyl]piperazin-1-yl]ethanol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；1.4M ammonium sulfate, 0.05M K-formate,	Resolution 1.94 Å R-free 0.207
7Q8A Crystal structure of tandem domain RRM1-2 of FUBP-interacting repressor (FIR) bound to FUSE ssDNA fragment Deposited 2021-11-10	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 114–310（197 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；25% w/v PEG3350, 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris , pH5.5	Resolution 2.05 Å R-free 0.247
7Q8A Crystal structure of tandem domain RRM1-2 of FUBP-interacting repressor (FIR) bound to FUSE ssDNA fragment Deposited 2021-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 114–310（197 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；25% w/v PEG3350, 0.2M Sodium acetate trihydrate, 0.1M Bis-Tris , pH5.5	Resolution 2.05 Å R-free 0.247
7Z3X Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 114–308（195 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG3350 0.1M Bis-Tris, pH5.5	Resolution 1.65 Å R-free 0.214
7Z3X Crystal structure of FIR RRM1-2 Y115F mutant bound to FUSE ssDNA Deposited 2022-03-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 114–308（195 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；25% PEG3350 0.1M Bis-Tris, pH5.5	Resolution 1.65 Å R-free 0.214

13 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PUF60_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 18–216； UniProt 118–316 Author chain B； PDBConstruct 18–216； UniProt 118–316

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5kw6
Deposition date deposition_date	2016-07-15
Structure title title	Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Splice Site Analogue with a Modified Binding-Site Nucleic Acid Base
Keywords keywords	TANDEM RRMS, PROTEIN-NUCLEIC ACID COMPLEX, SPLICING FACTOR, splicing-dna complex; splicing/dna
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	23.49 Å
Radius of gyration Rg (electron density) rg_electron	22.38 Å
Forward intensity I(0) i0	35220300.00
Molecular weight molecular_weight	44637.0 kDa
Excluded volume excluded_volume	55528 Å³
Envelope volume envelope_volume	69308 Å³
Hydration-shell volume shell_volume	25494 Å³
Envelope diameter envelope_diameter	75.3 Å
Shell Rg shell_rg	29.55 Å
Envelope Rg envelope_rg	22.45 Å
Shape Rg shape_rg	22.35 Å
Total Rg total_rg	23.38 Å
Total atoms total_atoms	3136
Residues n_residues	405
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

▼

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

Maximum dimension Dmax dmax	74.3 Å
Rg (real space) rg_real	23.34 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	3.5220e+07
I(0) uncertainty (real space) i0_real_error	4.3890e+05
Rg (reciprocal space) rg_reciprocal	23.38 Å
I(0) (reciprocal space) i0_reciprocal	35220000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.0 Å
Skewness Skewness skewness	0.112
Kurtosis Kurtosis kurtosis	-0.449
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7212000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.967

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Poly(U)-binding-splicing factor PUF60
Molecular weight formula_weight	23408.5 kDa
Mutation mutation	R123G, C129S, C255A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3263

GSHMASMTGGQQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRVGKAVTPPMPLLTPATPG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (30-MER)
Molecular weight formula_weight	8862.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

GAUGUCAUACUUAUCCUGUCCCUUUUUUUU

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	127

▼

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5kw6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5kw6A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5kw6B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

Domain ID domain_id	5kw6B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	62.590 Å
Unit-cell length b length_b	62.590 Å
Unit-cell length c length_c	83.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	29.290 Å
R factor r_factor	—
R_work r_work	0.2110
R_free r_free	0.2260

fit	/app/data/saxs_computation/kw/5kw6/5kw6.fit
pddf	/app/data/pr_computation/kw/5kw6/5kw6.pr.out
profile	/app/data/saxs_computation/kw/5kw6/5kw6.dat

Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Splice Site Analogue with a Modified Binding-Site Nucleic Acid Base

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

Poly(U)-binding-splicing factor PUF60

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)