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3dxb

Structure of the UHM domain of Puf60 fused to thioredoxin

Method: X-RAY DIFFRACTION Dmax: 115.1 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

thioredoxin N-terminally fused to Puf60(UHM)

Homo sapiens

UniProt P0AA27

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–109 Chain F； UniProt 1–109 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–109 Chain D； UniProt 1–109 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 No other associated polymer 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
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–109 Chain G； UniProt 1–109 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 No other associated polymer 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
4 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1–109 Chain H； UniProt 1–109 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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
5 Insufficient information Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–109 Chain B； UniProt 1–109 Chain C； UniProt 1–109 Chain D； UniProt 1–109 Chain E； UniProt 1–109 Chain F； UniProt 1–109 Chain G； UniProt 1–109 Chain H； UniProt 1–109 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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

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 3DXB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1T7P T7 DNA POLYMERASE COMPLEXED TO DNA PRIMER/TEMPLATE,A NUCLEOSIDE TRIPHOSPHATE, AND ITS PROCESSIVITY FACTOR THIOREDOXIN Deposited 1997-09-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 2–109（108 aa）
Not recorded DG3 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.20 Å R-free 0.279
5E4W Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail Deposited 2015-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 3–109（107 aa） Fragment：UNP residues 3-109
Not recorded GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 3350, 0.2 M Ca(OAc)2
Resolution 2.80 Å R-free 0.291
5E4W Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail Deposited 2015-10-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 3–109（107 aa） Fragment：UNP residues 3-109
Chain B 3–109（107 aa） Fragment：UNP residues 3-109
Not recorded GOL GLYCEROL × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 3350, 0.2 M Ca(OAc)2
Resolution 2.80 Å R-free 0.291
5E4W Crystal structure of cpSRP43 chromodomains 2 and 3 in complex with the Alb3 tail Deposited 2015-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 3–109（107 aa） Fragment：UNP residues 3-109
Not recorded GOL GLYCEROL × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20% PEG 3350, 0.2 M Ca(OAc)2
Resolution 2.80 Å R-free 0.291
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 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 1–109（109 aa）
Mutation：L107A CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–109（109 aa）
Mutation：L107A CU COPPER (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–109（109 aa）
Mutation：L107A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–109（109 aa）
Mutation：L107A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 1–109（109 aa）
Mutation：L107A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain F 1–109（109 aa）
Mutation：L107A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5HR1 Crystal structure of thioredoxin L107A mutant Deposited 2016-01-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 1–109（109 aa）
Mutation：L107A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；The drop was a 2:1 mix of protein (10 mg/ml in water) and reservoir solution (100 mM sodium acetate, 4 mM CuSO4, 18 % ethanol, pH 4.25), respectively.
Resolution 2.14 Å R-free 0.235
5IKN Crystal Structure of the T7 Replisome in the Absence of DNA Deposited 2016-03-03 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain K 4–108（105 aa）
Chain L 4–108（105 aa）
Chain M 4–108（105 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295.15 K；1.47-1.62M Sodium Formate 0.1M Tris pH 7.5
Resolution 4.80 Å R-free 0.318

4 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_ECO57
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 10–118； UniProt 1–109 Author chain B； PDBConstruct 10–118； UniProt 1–109 Author chain C； PDBConstruct 10–118； UniProt 1–109 Author chain D； PDBConstruct 10–118； UniProt 1–109 Author chain E； PDBConstruct 10–118； UniProt 1–109 Author chain F； PDBConstruct 10–118； UniProt 1–109 Author chain G； PDBConstruct 10–118； UniProt 1–109 Author chain H； PDBConstruct 10–118； UniProt 1–109

thioredoxin N-terminally fused to Puf60(UHM)

Homo sapiens

UniProt Q9UHX1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 460–499 Chain F； UniProt 460–499 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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
2 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 460–499 Chain D； UniProt 460–499 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 No other associated polymer 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
3 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 460–499 Chain G； UniProt 460–499 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 No other associated polymer 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
4 Insufficient information Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 460–499 Chain H； UniProt 460–499 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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
5 Insufficient information Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 460–499 Chain B； UniProt 460–499 Chain C； UniProt 460–499 Chain D； UniProt 460–499 Chain E； UniProt 460–499 Chain F； UniProt 460–499 Chain G； UniProt 460–499 Chain H； UniProt 460–499 Fragment：Chimera of Thioredoxin 1-109 and Puf60 C-terminal 460-559 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

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 3DXB 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
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 mutation/modification Different oligomeric state 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 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: 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
5KW6 Two Tandem RRM Domains of PUF60 Bound to an AdML Pre-mRNA 3' Splice Site Analogue with a Modified Binding-Site Nucleic Acid Base Deposited 2016-07-15 Different construct Different mutation/modification Different oligomeric state Different experimental conditions 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 No recorded non-water small molecule 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
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 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 20 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 123–162； UniProt 460–499 Author chain B； PDBConstruct 123–162； UniProt 460–499 Author chain C； PDBConstruct 123–162； UniProt 460–499 Author chain D； PDBConstruct 123–162； UniProt 460–499 Author chain E； PDBConstruct 123–162； UniProt 460–499 Author chain F； PDBConstruct 123–162； UniProt 460–499 Author chain G； PDBConstruct 123–162； UniProt 460–499 Author chain H； PDBConstruct 123–162； UniProt 460–499

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 3dxb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dxb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dxb
Deposition date deposition_date2008-07-24
Structure title titleStructure of the UHM domain of Puf60 fused to thioredoxin
Keywords keywordssplicing, FBP interacting repressor, UHM, RRM, Electron transport, Redox-active center, Transport, TRANSCRIPTION; SPLICING, TRANSCRIPTION
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_guinier38.37 Å
Radius of gyration Rg (electron density) rg_electron37.26 Å
Forward intensity I(0) i0520090000.00
Molecular weight molecular_weight186050.0 kDa
Excluded volume excluded_volume233080 ų
Envelope volume envelope_volume322330 ų
Hydration-shell volume shell_volume69465 ų
Envelope diameter envelope_diameter113.8 Å
Shell Rg shell_rg45.98 Å
Envelope Rg envelope_rg35.83 Å
Shape Rg shape_rg37.29 Å
Total Rg total_rg37.72 Å
Total atoms total_atoms13082
Residues n_residues1695
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 dmax115.1 Å
Rg (real space) rg_real38.04 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real5.2010e+08
I(0) uncertainty (real space) i0_real_error8.2140e+06
Rg (reciprocal space) rg_reciprocal38.25 Å
I(0) (reciprocal space) i0_reciprocal520200000.0000
Solution quality estimate total_estimate0.9024
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary50.5 Å
Skewness Skewness skewness0.014
Kurtosis Kurtosis kurtosis-0.601
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha103500000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id3dxbA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbD02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbF02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbG02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dxbH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3dxbH02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
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8. Citations (2)

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9. Files and Curves (10)