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3mdi

Crystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA

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

Cleavage and polyadenylation specificity factor subunit 5

Homo sapiens

UniProt O43809

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Homooligomer Protein 2 RNA 1 ;RNA (5'-R(*UP*GP*UP*AP*AP*A)-3') ; × 1 GLYCEROL × 2 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
5r4q 5r4q 5r4r 5r4r 5r4s 5r4s

6 assemblies

Homodimer
2cl3 2j8q 3bap 3bho 5r4p 5r4p 5r4t 5r4t 5r4u 5r4u 5r64 5r64

18 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3mdg 3mdi 3n9u 3p5t 3p5t 3p5t 3p6y 3p6y 3p6y 3p6y 3q2s 3q2t

12 assemblies

View Construct and Data Evidence
UniProt name CPSF5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–227； UniProt 1–227 Author chain B； PDBConstruct 1–227； UniProt 1–227

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_id3mdi
Deposition date deposition_date2010-03-30
Structure title titleCrystal Structure of the 25kDa Subunit of Human Cleavage factor Im in complex with RNA UGUAAA
Keywords keywordsCPSF5, CF Im, mRNA processing, cleavage factor, Nudix protein, protein-RNA complex, RNA binding protein, RNA binding-RNA complex; RNA binding/RNA
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.

3mdi__assembly_1__model_1

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

Download this curve (.dat)

3mdi__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3mdi__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）24.34 Å
Rg (electron density)22.88 Å
Total Rg23.87 Å
Atom count3472
Residues412
Excluded volume62034 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3mdi__assembly_1__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id3mdiA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
Domain ID domain_id3mdiB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology79 — Nucleoside Triphosphate Pyrophosphohydrolase
Homologous superfamily homologous superfamily10 — Nucleoside Triphosphate Pyrophosphohydrolase
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7. Citations (1)