3vam

Structure of U2AF65 variant with BrU5C2 DNA

Method: X-RAY DIFFRACTION D_max: 107.1 Å Quality: GOOD

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

Splicing factor U2AF 65 kDa subunit

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 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 148–237 Chain A； UniProt 258–336 Chain B； UniProt 148–237 Chain B； UniProt 258–336	Fragment：RNA Binding Domains 1 and 2	;DNA (5'-D(UPCPUPUP(BRU)PUPU)-3') ; × 2 DIO* 1,4-DIETHYLENE DIOXIDE × 5 SO4 SULFATE ION × 5 GOL GLYCEROL × 2 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.237

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 3VAM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JMT X-ray Structure of a Core U2AF65/U2AF35 Heterodimer Deposited 2001-07-19	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 B 85–112（28 aa）	Not recorded	HEZ HEXANE-1,6-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.3；277 K；PEG mme5000, sodium acetate, 1,6-hexanediol, MES, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.20 Å R-free 0.238
1O0P Solution Structure of the third RNA Recognition Motif (RRM) of U2AF65 in complex with an N-terminal SF1 peptide Deposited 2003-02-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 372–475（104 aa） Fragment：C-terminal RRM domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；295 K；Ionic strength (raw mmCIF value) 50mM salt；Pressure ambient NMR sample composition 1mM 15N,13C U2AF65-RRM3 + 1mM unlabeled SF1_10-25, 30mM phosphate buffer, 20mM NaCL, 3mM DTT \| 90% H2O/10% D2O NMR sample composition 1mM 15N,13C U2AF65-RRM3 + 1mM unlabeled SF1_10-25, 30mM phosphate buffer, 20mM NaCL, 3mM DTT \| 100% D2O	Resolution not provided
1OPI SOLUTION STRUCTURE OF THE THIRD RNA RECOGNITION MOTIF (RRM) OF U2AF65 IN COMPLEX WITH AN N-TERMINAL SF1 PEPTIDE Deposited 2003-03-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 372–475（104 aa） Fragment：C-TERMINAL RRM DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；295 K；Ionic strength (raw mmCIF value) 50mM SALT；Pressure AMBIENT NMR sample composition 1MM 15N,13C U2AF65-RRM3 + 1MM UNLABELED SF1_10-25, 30MM PHOSPHATE BUFFER, 20MM NACL, 3MM DTT \| D2O	Resolution not provided
1U2F SOLUTION STRUCTURE OF THE FIRST RNA-BINDING DOMAIN OF HU2AF65 Deposited 1999-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–237（90 aa） Fragment：FIRST RNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K	Resolution not provided
2G4B Structure of U2AF65 variant with polyuridine tract Deposited 2006-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA binding domain Chain A 258–336（79 aa） Fragment：RNA binding domain	Mutation：deletion of residues 238-258 Mutation：deletion of residues 238-258	DIO 1,4-DIETHYLENE DIOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；.6 M ammonium sulfate, 100 mM 2-(N-morpholino) ethanesulfonic acid, sodium salt (MES) pH 6.5, 10% dioxane, 200 mM non-detergent sulfobetaine (NDSB) 195 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.276
2HZC Crystal structure of the N-terminal RRM of the U2AF large subunit Deposited 2006-08-08	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 148–229（82 aa） Fragment：RRM 1	Not recorded	ZN ZINC ION × 2 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；21% PEGmme550, 200mM Zn acetate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.47 Å R-free 0.226
2HZC Crystal structure of the N-terminal RRM of the U2AF large subunit Deposited 2006-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–229（82 aa） Fragment：RRM 1	Not recorded	ZN ZINC ION × 4 P6G HEXAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；21% PEGmme550, 200mM Zn acetate, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.47 Å R-free 0.226
2M0G Structure, phosphorylation and U2AF65 binding of the Nterminal Domain of splicing factor 1 during 3 splice site Recognition Deposited 2012-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 372–475（104 aa） Fragment：RRM 3 domain residues 372-475	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 100-600 uM [U-15N] protein, 100-600 uM [U-13C; U-15N] entity, 100-600 uM [U-13C; U-15N; U-2H] entity, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2U2F SOLUTION STRUCTURE OF THE SECOND RNA-BINDING DOMAIN OF HU2AF65 Deposited 1999-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 258–342（85 aa） Fragment：SECOND RNA-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K	Resolution not provided
2YH0 Solution structure of the closed conformation of human U2AF65 tandem RRM1 and RRM2 domains Deposited 2011-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–342（195 aa） Fragment：TANDEM RRM1 AND RRM2 DOMAINS JOINED BY NATIVE LINKER, RESIDUES 148-342	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 70；Pressure 1.0 NMR sample composition 90% WATER/10% D2O	Resolution not provided
2YH1 Model of human U2AF65 tandem RRM1 and RRM2 domains with eight-site uridine binding Deposited 2011-04-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 148–342（195 aa） Fragment：TANDEM RRM1 AND RRM2 DOMAINS JOINED BY NATIVE LINKER, RESIDUES 148-342	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 70；Pressure 1.0 NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 70；Pressure 1.0 NMR measurement conditions pH 6.5；295 K；Ionic strength (raw mmCIF value) 70；Pressure 1.0 NMR sample composition 90% WATER/10% D2O	Resolution not provided
3VAF Structure of U2AF65 variant with BrU3 DNA Deposited 2011-12-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 4 SO4 SULFATE ION × 6 GOL GLYCEROL × 1 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.49 Å R-free 0.289
3VAG Structure of U2AF65 variant with BrU3C2 DNA Deposited 2011-12-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 6 SO4 SULFATE ION × 7 GOL GLYCEROL × 2 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.19 Å R-free 0.232
3VAH Structure of U2AF65 variant with BrU3C4 DNA Deposited 2011-12-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 4 SO4 SULFATE ION × 5 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.259
3VAI Structure of U2AF65 variant with BrU3C5 DNA Deposited 2011-12-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 5 SO4 SULFATE ION × 7 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.250
3VAJ Structure of U2AF65 variant with BrU5C6 DNA Deposited 2011-12-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 5 SO4 SULFATE ION × 6 GOL GLYCEROL × 2 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.236
3VAK Structure of U2AF65 variant with BrU5 DNA Deposited 2011-12-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 5 SO4 SULFATE ION × 7 GOL GLYCEROL × 4 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, Deoxy-Big Chap, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.17 Å R-free 0.229
3VAL Structure of U2AF65 variant with BrU5C1 DNA Deposited 2011-12-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 4 PDB declaration: octameric	Chain A 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain A 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain B 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain D 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain D 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2 Chain I 148–237（90 aa） Fragment：RNA Binding Domains 1 and 2 Chain I 258–336（79 aa） Fragment：RNA Binding Domains 1 and 2	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 4 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M Ammonium sulfate, 10% Dioxane, 0.1M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.271
4FXW Structure of phosphorylated SF1 complex with U2AF65-UHM domain Deposited 2012-07-03	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 A 375–475（101 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.29 Å R-free 0.281
4FXW Structure of phosphorylated SF1 complex with U2AF65-UHM domain Deposited 2012-07-03	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 C 375–475（101 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；0.2 M Lithium sulfate, 20% PEG 3350 and 0.1 M Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.29 Å R-free 0.281
4TU7 Structure of U2AF65 D231V variant with BrU5 DNA Deposited 2014-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–336（189 aa） Chain B 148–336（189 aa）	Mutation：D231V Mutation：D231V	DIO 1,4-DIETHYLENE DIOXIDE × 4 SO4 SULFATE ION × 6 GOL GLYCEROL × 4 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1.6M AMMONIUM SULFATE, 10% DIOXANE, 0.1M MES PH 6.0, DEOXY-BIG CHAP	Resolution 2.09 Å R-free 0.223
4TU8 STRUCTURE OF U2AF65 VARIANT WITH BRU5A6 DNA Deposited 2014-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–336（189 aa） Fragment：UNP residues 148-336 Chain B 148–336（189 aa） Fragment：UNP residues 148-336	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 7 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 9 SO4 SULFATE ION × 3 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M AMMONIUM SULFATE, 10% DIOXANE, 0.1M MES PH 6.5, ETHYLENE GLYCOL, DEOXY-BIG CHAP	Resolution 1.92 Å R-free 0.218
4TU9 STRUCTURE OF U2AF65 VARIANT WITH BRU5G6 DNA Deposited 2014-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 148–336（189 aa） Fragment：UNP residues 148-336 Chain B 148–336（189 aa） Fragment：UNP residues 148-336	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 5 SO4 SULFATE ION × 6 GOL GLYCEROL × 2 CPQ N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6M AMMONIUM SULFATE, 10% DIOXANE, 0.1M MES PH 6.5, DEOXY-BIG CHAP	Resolution 1.99 Å R-free 0.234
5EV1 Structure I of Intact U2AF65 Recognizing a 3' Splice Site Signal Deposited 2015-11-19	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 141–341（201 aa） Fragment：UNP residues 141-341	Not recorded	NA SODIUM ION × 2 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM phosphate-citrate buffer, 40% Peg400, 10% dioxane	Resolution 2.04 Å R-free 0.228
5EV2 Structure II of Intact U2AF65 Recognizing the 3' Splice Site Signal Deposited 2015-11-19	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 141–341（201 aa） Fragment：UNP residues 141-341	Not recorded	DIO 1,4-DIETHYLENE DIOXIDE × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；200 mM LiCl, 100 mM sodium citrate, 8% PEG 6000, 10% PEG 300, 10% Dioxane, Deoxy-BigCHAP	Resolution 1.86 Å R-free 0.188
5EV3 Structure III of Intact U2AF65 Recognizing the 3' Splice Site Signal Deposited 2015-11-19	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 141–341（201 aa） Fragment：UNP residues 141-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；1M Succinic Acid, 0.1M, 1% PEG MME 2000	Resolution 1.50 Å R-free 0.186
5EV4 Structure IV of Intact U2AF65 Recognizing the 3' Splice Site Signal Deposited 2015-11-19	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 141–341（201 aa） Fragment：UNP RESIDUES 141-341	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；1M Succinic Acid, 0.1M HEPES, 3% PEG MME 2000	Resolution 1.57 Å R-free 0.176
5W0G Structure of U2AF65 (U2AF2) RRM1 at 1.07 resolution Deposited 2017-05-30	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 148–229（82 aa） Fragment：RNA RECOGNITION motif 1 (RRM1), residues 148-229	Not recorded	ZN ZINC ION × 2 ACT ACETATE ION × 1 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；21% (w/v) PEG MME 550, 210 mM zinc acetate, 100 mM MES	Resolution 1.07 Å R-free 0.153
5W0H Structure of U2AF65 (U2AF2) RRM2 at 1.11 Angstrom Resolution Deposited 2017-05-30	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 258–336（79 aa） Fragment：RNA Recognition Motif 2 (RRM2), residues 258-336	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；26% (w/v) PEG 8000, 0.1 M NaOAc, 0.2 mM TCEP, 10% (v/v) dioxane, 0.2 ul BigCHAP, 0.05 M potassium phosphate monobasic	Resolution 1.11 Å R-free 0.168
6TR0 Solution structure of U2AF2 RRM1,2 Deposited 2019-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 140–342（203 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.5 mM [U-13C; U-15N] U2AF2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6XLV Crystal structure of leukemia-associated N196K mutant of U2AF65 bound to AdML splice site Deposited 2020-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 141–341（201 aa）	Mutation：N196K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG 3350, 3.4 M sodium malonate pH 7, sucrose, LDAO	Resolution 1.40 Å R-free 0.169
6XLW Crystal structure of U2AF65 bound to AdML splice site sequence Deposited 2020-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 141–341（201 aa）	Not recorded	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 1 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；1M Succinic Acid, 0.1M HEPES pH 7, 3% PEG MME 2000	Resolution 1.50 Å R-free 0.153
6XLX Crystal structure of cancer-associated G301D mutant of U2AF65 bound to AdML splice site Deposited 2020-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 141–341（201 aa）	Mutation：G301D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；25% PEG 3350, 0.24 M Na malonate pH 7, 5% sucrose, Lauryldimethylamine oxide	Resolution 1.70 Å R-free 0.194
7S3A Crystal structure of intact U2AF65 RRM-region bound to AdML-C5 oligonucleotide Deposited 2021-09-05	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 141–341（201 aa）	Not recorded	NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；0.60 M succinic acid, 0.10 M Hepes pH 7.0, 2% Peg MME 2000	Resolution 1.48 Å R-free 0.157
7S3B Crystal structure of intact U2AF65 RRM-region bound to AdML-G5 oligonucleotide Deposited 2021-09-05	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 141–341（201 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277.15 K；0.24 M Na Malonate, 26% Peg 3350, n-dodecyl-N,N-dimethylamine-N-oxide (=LDAO)	Resolution 1.89 Å R-free 0.200
7S3C Crystal structure of intact U2AF65 RRM-region bound to AdML-A5 oligonucleotide Deposited 2021-09-05	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 141–341（201 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；0.24 M malonate, 26% Peg 3350, 10% sucrose, LDAO	Resolution 1.51 Å R-free 0.190
7SN6 U2AF65 UHM BOUND TO SF3B155 ULM5 Deposited 2021-10-27	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 A 375–475（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 15% V/V 2-PROPANOL, 20% PEG 4000	Resolution 1.80 Å R-free 0.217
7SN6 U2AF65 UHM BOUND TO SF3B155 ULM5 Deposited 2021-10-27	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 B 375–475（101 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M SODIUM CITRATE TRIBASIC DIHYDRATE PH 5.6, 15% V/V 2-PROPANOL, 20% PEG 4000	Resolution 1.80 Å R-free 0.217
8P25 Solution structure of a chimeric U2AF2 RRM2 / FUBP1 N-Box Deposited 2023-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 231–342（112 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure 1 NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] Chimeric construct of U2AF2 linker-RRM2 and FUBP1 N-box, 100% D2O \| 100% D2O	Resolution not provided
9C7A Crystal structure of R149W neurodevelopmental disease-associated U2AF2 variant Deposited 2024-06-10	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 141–341（201 aa）	Mutation：R149W	GOL GLYCEROL × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；24 M sodium malonate pH 7.0, 5% w/v sucrose, 25% w/v PEG 3350, with addition of 0.1 uL of 5% w/v LDAO detergent	Resolution 1.40 Å R-free 0.159
9C7B Crystal structure of R150H neurodevelopmental disease-associated U2AF2 variant Deposited 2024-06-10	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 141–341（201 aa）	Mutation：R150H	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277.15 K；24 M sodium malonate pH 7.0, 5% w/v sucrose, 25% w/v PEG 3350, with addition of 0.1 uL of 5% w/v LDAO detergent	Resolution 1.40 Å R-free 0.167
9DWU CoREST complex bound to U2AF2 Deposited 2024-10-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 257–336（80 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.14 Å

39 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	U2AF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–95； UniProt 148–237 Author chain A； PDBConstruct 96–174； UniProt 258–336 Author chain B； PDBConstruct 6–95； UniProt 148–237 Author chain B； PDBConstruct 96–174； UniProt 258–336

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3vam
Deposition date deposition_date	2011-12-29
Structure title title	Structure of U2AF65 variant with BrU5C2 DNA
Keywords keywords	RNA SPLICING FACTOR, RNA RECOGNITION MOTIF, RNA BINDING PROTEIN, RNA BINDING PROTEIN-DNA complex; RNA BINDING PROTEIN/DNA
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	28.51 Å
Radius of gyration Rg (electron density) rg_electron	28.88 Å
Forward intensity I(0) i0	33979200.00
Molecular weight molecular_weight	43090.0 kDa
Excluded volume excluded_volume	52984 Å³
Envelope volume envelope_volume	70913 Å³
Hydration-shell volume shell_volume	23058 Å³
Envelope diameter envelope_diameter	110.5 Å
Shell Rg shell_rg	32.01 Å
Envelope Rg envelope_rg	29.07 Å
Shape Rg shape_rg	28.91 Å
Total Rg total_rg	29.12 Å
Total atoms total_atoms	2999
Residues n_residues	356
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	107.1 Å
Rg (real space) rg_real	28.92 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	3.3980e+07
I(0) uncertainty (real space) i0_real_error	5.6510e+05
Rg (reciprocal space) rg_reciprocal	28.79 Å
I(0) (reciprocal space) i0_reciprocal	33980000.0000
Solution quality estimate total_estimate	0.7775
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.633
Kurtosis Kurtosis kurtosis	0.127
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7834000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.565; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.485; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Splicing factor U2AF 65 kDa subunit
Molecular weight formula_weight	19075.8 kDa
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	3150

GPLGSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRAS

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 (5'-D(UPCPUPUP(BRU)PUP*U)-3') ;
Molecular weight formula_weight	2064.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P,E

UCUUUUU

Entity 3 Entity 3 non-polymer

Description description	1,4-DIETHYLENE DIOXIDE
Molecular weight formula_weight	88.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE
Molecular weight formula_weight	862.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

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

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3vamA01
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	3vamA02
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	3vamB01
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	3vamB02
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

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8. Citations (1)

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Unit-cell length a length_a	166.108 Å
Unit-cell length b length_b	37.973 Å
Unit-cell length c length_c	101.974 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.49 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	41.520 Å
R factor r_factor	0.1980
R_work r_work	0.1938
R_free r_free	0.2375

fit	/app/data/saxs_computation/va/3vam/3vam.fit
pddf	/app/data/pr_computation/va/3vam/3vam.pr.out
profile	/app/data/saxs_computation/va/3vam/3vam.dat

Structure of U2AF65 variant with BrU5C2 DNA

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

Splicing factor U2AF 65 kDa subunit

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)