9r3d

Cryo-EM structure of the human pre-Bact-OTS complex (whole map)

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

U5 small nuclear ribonucleoprotein 200 kDa helicase

OrganismNot specified

UniProt O75643

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 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 3
Chains and sequence ranges Author chain B; PDBConstruct 1–2136; UniProt 1–2136

116 kDa U5 small nuclear ribonucleoprotein component

OrganismNot specified

UniProt Q15029

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 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 4
Chains and sequence ranges Author chain C; PDBConstruct 1–972; UniProt 1–972

Pre-mRNA-splicing factor 38A

OrganismNot specified

UniProt Q8NAV1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PR38A_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I; PDBConstruct 1–312; UniProt 1–312

Microfibrillar-associated protein 1

OrganismNot specified

UniProt P55081

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name MFAP1_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain K; PDBConstruct 1–439; UniProt 1–439

Protein BUD31 homolog

OrganismNot specified

UniProt P41223

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name BUD31_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain Q; PDBConstruct 1–144; UniProt 1–144

Transcription elongation regulator 1

OrganismNot specified

UniProt O14776

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name TCRG1_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain T; PDBConstruct 1–1098; UniProt 1–1098

WW domain-binding protein 11

OrganismNot specified

UniProt Q9Y2W2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name WBP11_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain X; PDBConstruct 1–641; UniProt 1–641

Ubiquitin-like protein 5

OrganismNot specified

UniProt Q9BZL1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name UBL5_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain q; PDBConstruct 1–73; UniProt 1–73

Zinc finger matrin-type protein 2

OrganismNot specified

UniProt Q96NC0

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name ZMAT2_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain r; PDBConstruct 1–199; UniProt 1–199

Pre-mRNA-processing factor 17

OrganismNot specified

UniProt O60508

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PRP17_HUMAN
Isoform —
PDB entities 13
Chains and sequence ranges Author chain P7; PDBConstruct 1–579; UniProt 1–579

Pre-mRNA-processing-splicing factor 8

OrganismNot specified

UniProt Q6P2Q9

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 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 14
Chains and sequence ranges Author chain A; PDBConstruct 1–2335; UniProt 1–2335

Pre-mRNA-splicing factor RBM22

OrganismNot specified

UniProt Q9NW64

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBM22_HUMAN
Isoform —
PDB entities 15
Chains and sequence ranges Author chain P; PDBConstruct 1–420; UniProt 1–420

RING-type E3 ubiquitin-protein ligase PPIL2

OrganismNot specified

UniProt Q13356

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) SNW domain-containing protein 1 × 1 (Q13573) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name PPIL2_HUMAN
Isoform —
PDB entities 16
Chains and sequence ranges Author chain t; PDBConstruct 1–520; UniProt 1–520

SNW domain-containing protein 1

OrganismNot specified

UniProt Q13573

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Heteromer Protein 14 RNA 3 U5 snRNA × 1 U6 snRNA × 1 U5 small nuclear ribonucleoprotein 200 kDa helicase × 1 (O75643) 116 kDa U5 small nuclear ribonucleoprotein component × 1 (Q15029) Pre-mRNA-splicing factor 38A × 1 (Q8NAV1) Microfibrillar-associated protein 1 × 1 (P55081) Protein BUD31 homolog × 1 (P41223) Transcription elongation regulator 1 × 1 (O14776) WW domain-binding protein 11 × 1 (Q9Y2W2) pre-mRNA × 1 Ubiquitin-like protein 5 × 1 (Q9BZL1) Zinc finger matrin-type protein 2 × 1 (Q96NC0) Pre-mRNA-processing factor 17 × 1 (O60508) Pre-mRNA-processing-splicing factor 8 × 1 (Q6P2Q9) Pre-mRNA-splicing factor RBM22 × 1 (Q9NW64) RING-type E3 ubiquitin-protein ligase PPIL2 × 1 (Q13356) INOSITOL HEXAKISPHOSPHATE × 1 Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name SNW1_HUMAN
Isoform —
PDB entities 17
Chains and sequence ranges Author chain S1; PDBConstruct 1–526; UniProt 1–526

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_id9r3d
Deposition date deposition_date2025-05-04
Structure title titleCryo-EM structure of the human pre-Bact-OTS complex (whole map)
Keywords keywordsspliceosome, 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.

9r3d__assembly_1__model_1

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

Download this curve (.dat)

9r3d__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.

9r3d__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)65.15 Å
Rg (electron density)65.21 Å
Total Rg64.67 Å
Atom count41855
Residues5336
Excluded volume720810 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9r3d__assembly_1__model_1 17-meric (17) 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 (18)

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7. Citations (1)