8q91

Structure of the human 20S U5 snRNP core

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CD2 antigen cytoplasmic tail-binding protein 2

Homo sapiens

UniProt O95400

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name CD2B2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain F; PDBConstruct 1–341; UniProt 1–341

Pre-mRNA-processing-splicing factor 8

Homo sapiens

UniProt Q6P2Q9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PRP8_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A; PDBConstruct 1–2335; UniProt 1–2335

Pre-mRNA-processing factor 6

Homo sapiens

UniProt O94906

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PRP6_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain E; PDBConstruct 1–941; UniProt 1–941

Probable ATP-dependent RNA helicase DDX23

Homo sapiens

UniProt Q9BUQ8

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name DDX23_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain D; PDBConstruct 1–820; UniProt 1–820

116 kDa U5 small nuclear ribonucleoprotein component

Homo sapiens

UniProt Q15029

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name U5S1_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain C; PDBConstruct 1–972; UniProt 1–972

U5 small nuclear ribonucleoprotein 200 kDa helicase

Homo sapiens

UniProt O75643

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name U520_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain B; PDBConstruct 1–2136; UniProt 1–2136

Small nuclear ribonucleoprotein F

Homo sapiens

UniProt P62306

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RUXF_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain m; PDBConstruct 1–86; UniProt 1–86

Small nuclear ribonucleoprotein G

Homo sapiens

UniProt P62308

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RUXG_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain n; PDBConstruct 1–76; UniProt 1–76

Small nuclear ribonucleoprotein Sm D1

Homo sapiens

UniProt P62314

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SMD1_HUMAN
Isoform —
PDB entities 10
Chains and sequence ranges Author chain i; PDBConstruct 1–119; UniProt 1–119

Small nuclear ribonucleoprotein Sm D2

Homo sapiens

UniProt P62316

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SMD2_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain j; PDBConstruct 1–118; UniProt 1–118

Small nuclear ribonucleoprotein Sm D3

Homo sapiens

UniProt P62318

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SMD3_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain k; PDBConstruct 1–126; UniProt 1–126

;Small nuclear ribonucleoprotein-associated proteins B and B' ;

Homo sapiens

UniProt P14678

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) Small nuclear ribonucleoprotein E × 1 (P62304) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RSMB_HUMAN
Isoform —
PDB entities 13
Chains and sequence ranges Author chain h; PDBConstruct 1–240; UniProt 1–240

Small nuclear ribonucleoprotein E

Homo sapiens

UniProt P62304

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 13 RNA 1 CD2 antigen cytoplasmic tail-binding protein 2 × 1 (O95400) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) U5 snRNA × 1 Pre-mRNA-processing factor 6 × 1 (O94906) Probable ATP-dependent RNA helicase DDX23 × 1 (Q9BUQ8) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Small nuclear ribonucleoprotein F × 1 (P62306) Small nuclear ribonucleoprotein G × 1 (P62308) Small nuclear ribonucleoprotein Sm D1 × 1 (P62314) Small nuclear ribonucleoprotein Sm D2 × 1 (P62316) Small nuclear ribonucleoprotein Sm D3 × 1 (P62318) ;Small nuclear ribonucleoprotein-associated proteins B and B' ; × 1 (P14678) GUANOSINE-5'-TRIPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RUXE_HUMAN
Isoform —
PDB entities 14
Chains and sequence ranges Author chain l; PDBConstruct 1–92; UniProt 1–92

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id8q91
Deposition date deposition_date2023-08-19
Structure title titleStructure of the human 20S U5 snRNP core
Keywords keywordssnRNP, CD2BP2, spliceosome, U5, SPLICING; SPLICING
Experimental Method methodELECTRON MICROSCOPY
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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8q91__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8q91__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

8q91__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)58.13 Å
Rg (electron density)57.43 Å
Total Rg57.18 Å
Atom count26706
Residues3419
Excluded volume462510 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8q91__assembly_1__model_1 14-meric (14) Success 4.1.3-1-20251215 (887e7ef) View Download
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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (15)

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7. Citations (1)