← Back to search
1pqn

dominant negative human hDim1 (hDim1 1-128)

Method: SOLUTION NMR Dmax: 53.2 Å Quality: GOOD
▼

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

Spliceosomal U5 snRNP-specific 15 kDa protein

Homo sapiens

UniProt P83876

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–128 Fragment：dominant negative human hDim1 Mutation：deltaC14 No other associated polymer 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

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 1PQN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1QGV HUMAN SPLICEOSOMAL PROTEIN U5-15KD Deposited 1999-05-06 Different construct Different mutation/modification Different experimental method 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
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–142（142 aa）
Not recorded No recorded non-water small molecule 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
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–142（142 aa）
Not recorded No recorded non-water small molecule 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
1SYX The crystal structure of a binary U5 snRNP complex Deposited 2004-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–142（142 aa）
Not recorded No recorded non-water small molecule 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
3JCR 3D structure determination of the human*U4/U6.U5* tri-snRNP complex Deposited 2016-01-21 Different construct Different mutation/modification 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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 mutation/modification Different oligomeric state Different experimental method 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 38 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 1–127； UniProt 2–128

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1pqn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pqn
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1pqn
Deposition date deposition_date2003-06-18
Structure title titledominant negative human hDim1 (hDim1 1-128)
Keywords keywordsdim1, dominant negative, cell cycle, pre-mRNA splicing, snRNP, U5-15k SPLICEOSOMAL PROTEIN, THIOREDOXIN, TRANSCRIPTION, cleavage; CELL CYCLE
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier14.96 Å
Radius of gyration Rg (electron density) rg_electron14.61 Å
Forward intensity I(0) i01226660000.00
Molecular weight molecular_weight298960.0 kDa
Excluded volume excluded_volume374040 ų
Envelope volume envelope_volume40753 ų
Hydration-shell volume shell_volume19078 ų
Envelope diameter envelope_diameter61.4 Å
Shell Rg shell_rg24.26 Å
Envelope Rg envelope_rg17.94 Å
Shape Rg shape_rg14.61 Å
Total Rg total_rg14.78 Å
Total atoms total_atoms41480
Residues n_residues2540
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

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

Maximum dimension Dmax dmax53.2 Å
Rg (real space) rg_real14.87 Å
Rg uncertainty (real space) rg_real_error0.32 Å
I(0) (real space) i0_real1.2270e+09
I(0) uncertainty (real space) i0_real_error1.4710e+07
Rg (reciprocal space) rg_reciprocal14.87 Å
I(0) (reciprocal space) i0_reciprocal1227000000.0000
Solution quality estimate total_estimate0.8482
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.8 Å
Skewness Skewness skewness0.159
Kurtosis Kurtosis kurtosis-0.271
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha515400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.999
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pqna_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.47 — Thioredoxin fold
Superfamily Superfamily superfamilyc.47.1 — Thioredoxin-like
Family Family familyc.47.1.8 — spliceosomal protein U5-15Kd

CATH v4.4 (1 domains)

Domain ID domain_id1pqnA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
▶

8. Citations (2)

▶

9. Files and Curves (10)