SAXSdb — 3zzy

▼

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

POLYPYRIMIDINE TRACT-BINDING PROTEIN 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 156–285	Fragment：RNA RECOGNITION MOTIF 2, RESIDUES 172-301	RIBONUCLEOPROTEIN PTB-BINDING 1 × 1 （Q9CW46）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；SEE PAPER., pH 6.5	Resolution 1.40 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 156–285	Fragment：RNA RECOGNITION MOTIF 2, RESIDUES 172-301	RIBONUCLEOPROTEIN PTB-BINDING 1 × 1 （Q9CW46）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；SEE PAPER., pH 6.5	Resolution 1.40 Å R-free 0.234

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 3ZZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1QM9 NMR, REPRESENTATIVE STRUCTURE Deposited 1999-09-22	Different construct 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 335–531（197 aa） Fragment：RNA BINDING FRAGMENT	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；302 K	Resolution not provided
1SJQ NMR Structure of RRM1 from Human Polypyrimidine Tract Binding Protein Isoform 1 (PTB1) Deposited 2004-03-04	Different construct 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 54–147（94 aa） Fragment：RRM1, residues 54-147	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.3 M；Pressure ambient NMR sample composition 1 mM PTB1-1 U-15N,13C, 50 mM Na phosphate buffer, 100 mM NaCl, 2 mM NaN3,10% D2O \| 100 mM NaCl, 2 mM NaN3,10% D2O	Resolution not provided
1SJR NMR Structure of RRM2 from Human Polypyrimidine Tract Binding Protein Isoform 1 (PTB1) Deposited 2004-03-04	Different construct 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 147–301（155 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.3 M；Pressure ambient NMR sample composition 0.25 mM PTB1-2, U-15N, 13C, 50 mM Na phosphate buffer, 100 mM NaCl, 10 mM DTT, 2 mM NaN3,10% D2O \| 10% D2O	Resolution not provided
2AD9 Solution structure of Polypyrimidine Tract Binding protein RBD1 complexed with CUCUCU RNA Deposited 2005-07-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 49–146（98 aa） Fragment：RBD1	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 30mM；Pressure ambient NMR sample composition 1.5mM PTB RBD1 15N, 13C; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD1 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD1 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 100% D2O	Resolution not provided
2ADB Solution structure of Polypyrimidine Tract Binding protein RBD2 complexed with CUCUCU RNA Deposited 2005-07-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 172–298（127 aa） Fragment：RBD2	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.5；313 K；Ionic strength (raw mmCIF value) 30mM；Pressure ambient NMR sample composition 1.5mM PTB RBD2 15N, 13C; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD2 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD2 15N; 1.5mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 100% D2O	Resolution not provided
2ADC Solution structure of Polypyrimidine Tract Binding protein RBD34 complexed with CUCUCU RNA Deposited 2005-07-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 324–531（208 aa） Fragment：RBD34	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 30mM；Pressure ambient NMR sample composition 1.5mM PTB RBD34 15N, 13C; 3mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD34 15N; 3mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 90% H2O/10% D2O NMR sample composition 1.5mM PTB RBD34 15N; 3mM CUCUCU-RNA; 20mM phosphate buffer; 10mM NaCl \| 100% D2O	Resolution not provided
2EVZ Structure of RNA Binding Domains 3 and 4 of Polypyrimidine Tract Binding Protein Deposited 2005-11-01	Different construct 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 324–531（208 aa） Fragment：RNA BINDING DOMAINS 3 AND 4	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20mM NaCl, 10mM Na-phosphate；Pressure 1 NMR sample composition 1mM PTB RBD34 15N; 20mM NaCl; 10mM sodium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM PTB RBD34 15N, 13C; 20mM NaCl; 10mM sodium phosphate; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM PTB RBD34 15N; 20mM NaCl; 10mM sodium phosphate; 100% D2O \| 100% D2O NMR sample composition 1mM PTB RBD34 15N, 13C; 20mM NaCl; 10mM sodium phosphate; 100% D2O \| 100% D2O NMR sample composition 1mM PTB RBD3 15N, 13C, RBD4 unlabeled; 20mM NaCl; 10mM sodium phosphate; 100% D2O \| 100% D2O NMR sample composition 1mM PTB RBD3 unlabeled, RBD4 13C, 15N; 20mM NaCl; 10mM sodium phosphate; 100% D2O \| 100% D2O	Resolution not provided
2N3O Structure of PTB RRM1(41-163) bound to an RNA stemloop containing a structured loop derived from viral internal ribosomal entry site RNA Deposited 2015-06-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 41–163（123 aa） Fragment：UNP residues 41-163	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 0.020；Pressure ambient NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.020；Pressure ambient NMR measurement conditions pH 6.5；278 K；Ionic strength (raw mmCIF value) 0.020；Pressure ambient NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 0.020；Pressure ambient NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-99% 13C; U-99% 15N] RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-13C; U-15N]-ribose-Cyt9,Ura11,Ura13,Gua15 RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-13C; U-15N]-Ura7,Ura10,Cyt11,Ura12,Ura13,Ura14,Cyt15,Cyt16,Ura20,Cyt21,Cyt22,Cyt23 RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] PTBRRM1, 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-99% 13C; U-99% 15N] RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-13C; U-15N]-ribose-Ura10,Ura12,Ura14 RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 13C; U-99% 15N] PTBRRM1, 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 13 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-99% 13C; U-99% 15N] RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 13 mg/mL Pf1 phage, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-99% 15N] PTBRRM1, 1 mM [U-99% 13C; U-99% 15N] RNA, 10 mM sodium phosphate, 20 mM sodium chloride, 13 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3ZZZ Crystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2 Deposited 2011-09-06	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 156–285（130 aa） Fragment：RNA RECOGNITION MOTIF 2, RESIDUES 156-285	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；SEE PAPER., pH 6.5	Resolution 1.55 Å R-free 0.224
3ZZZ Crystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2 Deposited 2011-09-06	Different construct Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 156–285（130 aa） Fragment：RNA RECOGNITION MOTIF 2, RESIDUES 156-285	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；SEE PAPER., pH 6.5	Resolution 1.55 Å R-free 0.224
8BGF NMR solution structure of the N-terminal RRM and flanking linker regions of Polypyrimidine tract binding protein 1 using the CYANA CONSENSUS method. Deposited 2022-10-27	Different construct 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 41–163（123 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 33.3；Pressure 1 NMR measurement conditions pH 6.5；313 K；Ionic strength (raw mmCIF value) 33.3；Pressure 1 NMR measurement conditions pH 6.5；293 K；Ionic strength (raw mmCIF value) 33.3；Pressure 1 NMR sample composition 0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-13C,15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-15N]-99% Polypyrimidine-tract binding protein N-terminal RNA recognition motif, 10 mM NaH2PO4/NaOH buffer, 20 mM sodium chloride, 0.8 mM [U-13C,15N]-99% UCUUU-SL-RNA, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 5 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 2 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 1 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 13 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 14 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 15 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 1 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 16 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 1 NH2 AMINO GROUP × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 2 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 2 NH2 AMINO GROUP × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 3 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 57–140（84 aa）	Not recorded	SO4 SULFATE ION × 1 NH2 AMINO GROUP × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
8BWF PTBP1 RRM1 bound to an allosteric inhibitor Deposited 2022-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 57–140（84 aa）	Not recorded	NH2 AMINO GROUP × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.86；298 K；1.89M Ammoniumsulfate, 0.1 M HEPES, 2 v/v% PEG400	Resolution 2.90 Å R-free 0.340
9LGQ The crystal structure of SARS-CoV-2 NSP5 in complex with PTBP1 Deposited 2025-01-10	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 316–325（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.1 M MES pH 5.6, 7% PEG 6000, and 6% dimethyl sulfoxide (DMSO)	Resolution 1.82 Å R-free 0.218

12 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PTBP1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 156–285 Author chain B； PDBConstruct 1–130； UniProt 156–285

RIBONUCLEOPROTEIN PTB-BINDING 1

MUS MUSCULUS

UniProt Q9CW46

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 496–507	Fragment：MOTIF PRI3, RESIDUES 496-507 Mutation：YES	POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 × 1 （P26599）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；SEE PAPER., pH 6.5	Resolution 1.40 Å R-free 0.234
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 496–507	Fragment：MOTIF PRI3, RESIDUES 496-507 Mutation：YES	POLYPYRIMIDINE TRACT-BINDING PROTEIN 1 × 1 （P26599）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；SEE PAPER., pH 6.5	Resolution 1.40 Å R-free 0.234

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 3ZZY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZZZ Crystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2 Deposited 2011-09-06	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 680–692（13 aa） Fragment：MOTIF PRI4, RESIDUES 680-692	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；SEE PAPER., pH 6.5	Resolution 1.55 Å R-free 0.224
3ZZZ Crystal structure of a Raver1 PRI4 peptide in complex with polypyrimidine tract binding protein RRM2 Deposited 2011-09-06	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 680–692（13 aa） Fragment：MOTIF PRI4, RESIDUES 680-692	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；SEE PAPER., pH 6.5	Resolution 1.55 Å R-free 0.224

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RAVR1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 5–16； UniProt 496–507 Author chain D； PDBConstruct 5–16； UniProt 496–507

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	3zzy
Deposition date deposition_date	2011-09-06
Structure title title	Crystal structure of a Raver1 PRI3 peptide in complex with polypyrimidine tract binding protein RRM2
Keywords keywords	PROTEIN BINDING, PEPTIDE BINDING, RNA RECOGNITION MOTIF; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.27 Å
Radius of gyration Rg (electron density) rg_electron	18.22 Å
Forward intensity I(0) i0	10116300.00
Molecular weight molecular_weight	24627.0 kDa
Excluded volume excluded_volume	31276 Å³
Envelope volume envelope_volume	36296 Å³
Hydration-shell volume shell_volume	16886 Å³
Envelope diameter envelope_diameter	63.2 Å
Shell Rg shell_rg	24.05 Å
Envelope Rg envelope_rg	18.38 Å
Shape Rg shape_rg	18.21 Å
Total Rg total_rg	19.23 Å
Total atoms total_atoms	1741
Residues n_residues	226
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	62.4 Å
Rg (real space) rg_real	19.20 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	1.0120e+07
I(0) uncertainty (real space) i0_real_error	1.2410e+05
Rg (reciprocal space) rg_reciprocal	19.21 Å
I(0) (reciprocal space) i0_reciprocal	10120000.0000
Solution quality estimate total_estimate	0.8177
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.4 Å
Skewness Skewness skewness	0.241
Kurtosis Kurtosis kurtosis	-0.383
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1281000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.875; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	POLYPYRIMIDINE TRACT-BINDING PROTEIN 1
Molecular weight formula_weight	14169.1 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	1932

SVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQALLQYADPVSAQHAKLSLDGQNIYNACCTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDS

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	RIBONUCLEOPROTEIN PTB-BINDING 1
Molecular weight formula_weight	1467.7 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GAMGPGVSLLGAPPKD

来源 Source

来源生物 organism	MUS MUSCULUS
通用名 common_name	HOUSE MOUSE
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3zzya_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

Domain ID domain_id	d3zzyb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.7 — RNA-binding domain, RBD, aka RNA recognition motif (RRM)
Family Family family	d.58.7.1 — Canonical RBD

CATH v4.4 (2 domains)

Domain ID domain_id	3zzyA00
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	3zzyB00
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 (1)

▶

Unit-cell length a length_a	74.233 Å
Unit-cell length b length_b	60.606 Å
Unit-cell length c length_c	60.842 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.51 °
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	1.400 Å
Low-resolution limit resolution_low	29.010 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2340

fit	/app/data/saxs_computation/zz/3zzy/3zzy.fit
pddf	/app/data/pr_computation/zz/3zzy/3zzy.pr.out
profile	/app/data/saxs_computation/zz/3zzy/3zzy.dat

Crystal structure of a Raver1 PRI3 peptide in complex with polypyrimidine tract binding protein RRM2

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

POLYPYRIMIDINE TRACT-BINDING PROTEIN 1

State in the Current Structure

Other States of the Same Protein in the Database

RIBONUCLEOPROTEIN PTB-BINDING 1

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

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)