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3d9m

Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RNA-binding protein 16

Homo sapiens

UniProt Q9UPN6

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 CTD-PEPTIDE × 1 AMMONIUM ION × 1 SULFATE ION × 3 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 CTD-PEPTIDE × 1 AMMONIUM ION × 1 SULFATE ION × 4 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3d9i 3d9i 3d9j 3d9j 3d9o 9u9x

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3d9k 3d9k 3d9l 3d9l 3d9m 3d9m 3d9n 3d9n 3d9o 3d9p 3d9p

11 assemblies

View Construct and Data Evidence
UniProt name RBM16_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain B； PDBConstruct 1–136； UniProt 1–136

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_id3d9m
Deposition date deposition_date2008-05-27
Structure title titleSnapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
Keywords keywordsSCAF8, RNA POLYMERASE II CTD INTERACTING DOMAIN, ARM REPEATS, PHOSPHO-CTD, Phosphoprotein, RNA-binding, Transcription; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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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.

3d9m__assembly_1__model_1

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

Download this curve (.dat)

3d9m__assembly_1__model_1 | I(q)

10-2 10-1 105 106 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3d9m__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）16.07 Å
Rg (electron density)14.57 Å
Total Rg15.90 Å
Atom count1227
Residues148
Excluded volume22011 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3d9m__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3d9m__assembly_2__model_1 dimeric （2） 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 (5)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3d9mA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
Domain ID domain_id3d9mB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily90 —
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7. Citations (1)