1syx

The crystal structure of a binary U5 snRNP complex

Method: X-RAY DIFFRACTION D_max: 141.8 Å Quality: REASONABLE

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

Spliceosomal U5 snRNP-specific 15 kDa protein

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 1–142	Not recorded	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–142	Not recorded	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 1–142	Not recorded	CD2 antigen cytoplasmic tail-binding protein 2 × 1 （O95400）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262

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 1SYX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PQN dominant negative human hDim1 (hDim1 1-128) Deposited 2003-06-18	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 2–128（127 aa） Fragment：dominant negative human hDim1	Mutation：deltaC14	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.65；310 K；Pressure ambient NMR sample composition 1mM hDim1 1-128,U-15N; 10mM phosphate buffer; 95% H2O, 5% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN3 \| 95% H2O/5% D2O NMR sample composition 1mM hDim1 1-128,U-15N,13C; 10mM phosphate buffer; 95% H2O, 5% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN3 \| 95% H2O/5% D2O NMR sample composition 1mM hDim1 1-128,U-13C; 10mM phosphate buffer; 100% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN3 \| 100% D2O	Resolution not provided
1QGV HUMAN SPLICEOSOMAL PROTEIN U5-15KD Deposited 1999-05-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–142（142 aa） Fragment：FULL-LENGTH	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；1.0 M AMMONIUM SULPHATE 0.2 M HEPES/NAOH, PH 7.6 AT 294 K, VAPOR DIFFUSION, HANGING DROP	Resolution 1.40 Å R-free 0.269
3JCR 3D structure determination of the humanU4/U6.U5 tri-snRNP complex Deposited 2016-01-21	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 36-meric	Chain E 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA；pH 7.9；20 mM HEPES, pH 7.9, 100 mM KCl, 5 mM MgCl2, 0.1 mM EDTA cryo-EM vitrification conditions Cryogen ETHANE；Plunged into liquid ethane (FEI VITROBOT MARK IV).	Resolution 7.00 Å
4BWQ Crystal structure of U5-15kD in a complex with PQBP1 Deposited 2013-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.252
4BWQ Crystal structure of U5-15kD in a complex with PQBP1 Deposited 2013-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.252
4BWQ Crystal structure of U5-15kD in a complex with PQBP1 Deposited 2013-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.252
4BWQ Crystal structure of U5-15kD in a complex with PQBP1 Deposited 2013-07-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.252
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 4–137（134 aa） Fragment：RESIDUES 4-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
4CDO Crystal structure of PQBP1 bound to spliceosomal U5-15kD Deposited 2013-11-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 4–137（134 aa） Fragment：RESIDUES 4-137,223-265	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.238
4CDO Crystal structure of PQBP1 bound to spliceosomal U5-15kD Deposited 2013-11-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–137（134 aa） Fragment：RESIDUES 4-137,223-265	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.238
5O9Z Cryo-EM structure of a pre-catalytic human spliceosome primed for activation (B complex) Deposited 2017-06-20	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain J 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6AH0 The Cryo-EM Structure of the Precusor of Human Pre-catalytic Spliceosome (pre-B complex) Deposited 2018-08-15	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain O 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
6AHD The Cryo-EM Structure of Human Pre-catalytic Spliceosome (B complex) at 3.8 angstrom resolution Deposited 2018-08-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain O 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6QW6 Structure of the human U5.U4/U6 tri-snRNP at 2.9A resolution. Deposited 2019-03-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric	Chain 5D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Wait 30s, blot for 2s to 3s.	Resolution 2.92 Å
6QX9 Structure of a human fully-assembled precatalytic spliceosome (pre-B complex). Deposited 2019-03-07	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 71-meric	Chain 5D 1–142（142 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
8H6E Cryo-EM structure of human exon-defined spliceosome in the late pre-B state. Deposited 2022-10-17	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4F 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8H6J Cryo-EM structure of human exon-defined spliceosome in the mature pre-B state. Deposited 2022-10-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain 4F 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
8H6K Cryo-EM structure of human exon-defined spliceosome in the mature B state. Deposited 2022-10-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 63-meric	Chain 4F 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8H6L Cryo-EM structure of human exon-defined spliceosome in the early B state. Deposited 2022-10-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 59-meric	Chain 4F 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8Q7N cryo-EM structure of the human spliceosomal B complex protomer (tri-snRNP core region) Deposited 2023-08-16	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: 21-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QO9 Cryo-EM structure of a human spliceosomal B complex protomer Deposited 2023-09-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 66 PDB declaration: 71-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.29 Å
8QOZ Cryo-EM Structure of Pre-B+5'ss+ATPgammaS Complex (core part) Deposited 2023-09-29	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 17-meric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QP8 Cryo-EM Structure of Pre-B Complex (core part) Deposited 2023-09-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: 15-meric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8QP9 Cryo-EM Structure of Pre-B+AMPPNP Complex (core part) Deposited 2023-09-30	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 16-meric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8QPA Cryo-EM Structure of Pre-B+5'ssLNG Complex (core part) Deposited 2023-10-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: heptadecameric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8QPB Cryo-EM Structure of Pre-B+ATP Complex (core part) Deposited 2023-10-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 17-meric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8QPE Cryo-EM Structure of Pre-B-like Complex (core part) Deposited 2023-10-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 15 PDB declaration: 20-meric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8QPK Cryo-EM Structure of Pre-B+5'ss Complex (core part) Deposited 2023-10-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 12 PDB declaration: hexadecameric	Chain D 1–142（142 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8QXD Cryo-EM structure of the cross-exon pre-B complex Deposited 2023-10-24	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 61-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.60 Å
8QZS Cryo-EM structure of the cross-exon B-like complex Deposited 2023-10-29	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 68-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8R08 Cryo-EM structure of the cross-exon pre-B+AMPPNP complex Deposited 2023-10-31	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 71-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.10 Å
8R09 Cryo-EM structure of the cross-exon pre-B+5'ss+ATPgammaS complex Deposited 2023-10-31	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
8R0A Cryo-EM structure of the cross-exon pre-B+5'ss complex Deposited 2023-10-31	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 62-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.80 Å
8R0B Cryo-EM structure of the cross-exon pre-B+ATP complex Deposited 2023-10-31	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
8RM5 Cryo-EM structure of the cross-exon pre-B+5'ssLNG+ATPyS complex Deposited 2024-01-05	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 60-meric	Chain D 1–142（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.90 Å

31 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TXN4A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–142； UniProt 1–142 Author chain C； PDBConstruct 1–142； UniProt 1–142 Author chain E； PDBConstruct 1–142； UniProt 1–142

CD2 antigen cytoplasmic tail-binding protein 2

Homo sapiens

UniProt O95400

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 B； UniProt 262–341	Fragment：86 amino acid C-terminal fragment	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 262–341	Fragment：86 amino acid C-terminal fragment	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 262–341	Fragment：86 amino acid C-terminal fragment	Spliceosomal U5 snRNP-specific 15 kDa protein × 1 （P83876）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；PEG 2000mme, MES, calcium acetate, 1,4-butanediol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.35 Å R-free 0.262

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1SYX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GYF GYF DOMAIN FROM HUMAN CD2BP2 PROTEIN Deposited 1999-04-30	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 280–341（62 aa） Fragment：CD2-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NAPO4 NMR sample composition 90% WATER/10%D2O	Resolution not provided
1L2Z CD2BP2-GYF domain in complex with proline-rich CD2 tail segment peptide Deposited 2002-02-26	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 280–341（62 aa） Fragment：Residue 1-62	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR measurement conditions pH 6.3；298 K；Ionic strength (raw mmCIF value) 50 mM NaPo4；Pressure 1 NMR sample composition 1 mM GYF domain U-deuterated, U-15N, 1mM Peptide, 50 mM phosphate buffer, pH 6.3, 100% D2O \| 100% D2O NMR sample composition 1 mM GYF domain, aromatic amino acids protonated only, 1 mM Peptide protonated \| 100% D2O	Resolution not provided
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 280–341（62 aa） Fragment：RESIDUES 280-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
4BWS Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD. Deposited 2013-07-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 280–341（62 aa） Fragment：RESIDUES 280-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.277
8Q7Q Structure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 2) Deposited 2023-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8Q7V Structure of the recycling U5 snRNP bound to chaperones CD2BP2 and TSSC4 (State 1) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8Q7W Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 3) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
8Q7X Structure of the recycling U5 snRNP bound to chaperone CD2BP2 (State 4) Deposited 2023-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain G 1–341（341 aa）	Not recorded	MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
8Q91 Structure of the human 20S U5 snRNP core Deposited 2023-08-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 13 PDB declaration: 14-meric	Chain F 1–341（341 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8RC0 Structure of the human 20S U5 snRNP Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 14 PDB declaration: 15-meric	Chain F 1–341（341 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CD2B2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 7–86； UniProt 262–341 Author chain D； PDBConstruct 7–86； UniProt 262–341 Author chain F； PDBConstruct 7–86； UniProt 262–341

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	1syx
Deposition date deposition_date	2004-04-02
Structure title title	The crystal structure of a binary U5 snRNP complex
Keywords keywords	GYF-domain; thioredoxin-like; spliceosomal proteins, TRANSLATION-IMMUNE SYSTEM COMPLEX; TRANSLATION/IMMUNE SYSTEM
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	43.56 Å
Radius of gyration Rg (electron density) rg_electron	44.77 Å
Forward intensity I(0) i0	72771700.00
Molecular weight molecular_weight	69430.0 kDa
Excluded volume excluded_volume	86867 Å³
Envelope volume envelope_volume	125760 Å³
Hydration-shell volume shell_volume	28794 Å³
Envelope diameter envelope_diameter	153.6 Å
Shell Rg shell_rg	38.85 Å
Envelope Rg envelope_rg	44.17 Å
Shape Rg shape_rg	44.76 Å
Total Rg total_rg	44.44 Å
Total atoms total_atoms	4890
Residues n_residues	591
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	141.8 Å
Rg (real space) rg_real	44.43 Å
Rg uncertainty (real space) rg_real_error	1.77 Å
I(0) (real space) i0_real	7.2770e+07
I(0) uncertainty (real space) i0_real_error	1.4660e+06
Rg (reciprocal space) rg_reciprocal	43.56 Å
I(0) (reciprocal space) i0_reciprocal	72700000.0000
Solution quality estimate total_estimate	0.6253
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.582
Kurtosis Kurtosis kurtosis	-0.637
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3017000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.336; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.121; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Spliceosomal U5 snRNP-specific 15 kDa protein
Molecular weight formula_weight	16807.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	5082

MSYMLPHLHNGWQVDQAILSEEDRVVVIRFGHDWDPTCMKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY

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	CD2 antigen cytoplasmic tail-binding protein 2
Molecular weight formula_weight	9875.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F

AEEELETPTPTQRGEAESRGDGLVDVMWEYKWENTGDAELYGPFTSAQMQTWVSEGYFPDGVYCRKLDPPGGQFYNSKRIDFDLYT

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1syxa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

Domain ID domain_id	d1syxc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

Domain ID domain_id	d1syxe_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.8 — spliceosomal protein U5-15Kd

Domain ID domain_id	d1syxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.76 — GYF/BRK domain-like
Superfamily Superfamily superfamily	d.76.1 — GYF domain
Family Family family	d.76.1.1 — GYF domain

CATH v4.4 (6 domains)

Domain ID domain_id	1syxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	1syxC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

Domain ID domain_id	1syxE00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	1syxF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	40 — GYF domain

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8. Citations (1)

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Unit-cell length a length_a	135.726 Å
Unit-cell length b length_b	75.913 Å
Unit-cell length c length_c	77.027 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.27 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.345 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.2181
R_work r_work	0.2158
R_free r_free	0.2625

fit	/app/data/saxs_computation/sy/1syx/1syx.fit
pddf	/app/data/pr_computation/sy/1syx/1syx.pr.out
profile	/app/data/saxs_computation/sy/1syx/1syx.dat

The crystal structure of a binary U5 snRNP complex

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

Spliceosomal U5 snRNP-specific 15 kDa protein

State in the Current Structure

Other States of the Same Protein in the Database

CD2 antigen cytoplasmic tail-binding protein 2

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

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)