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4ngd

Structure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having 5'-p and UU-3' ends (1.95 Angstrom resolution)

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

Endoribonuclease Dicer

Homo sapiens

UniProt Q9UPY3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–RNA Monomer Protein 1 RNA 2 5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' × 2 SULFATE ION × 2 DI(HYDROXYETHYL)ETHER × 2 water × 3 Consistent with all polymers
2 Protein–RNA Homooligomer Protein 2 RNA 2 5'-R(P*GP*CP*GP*AP*AP*UP*UP*CP*GP*CP*UP*U)-3' × 2 SULFATE ION × 4 DI(HYDROXYETHYL)ETHER × 4 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
7xw3

1 assemblies

Homodimer
2eb1 2eb1

2 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
21cb 21cn 21cq 4ngb 4ngb 4ngc 4ngc 4ngd 4ngd 4ngf 4ngf 4ngf

31 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DICER_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–302； UniProt 765–1065

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_id4ngd
Deposition date deposition_date2013-11-01
Structure title titleStructure of human Dicer Platform-PAZ-Connector Helix cassette in complex with 12-mer siRNA having 5'-p and UU-3' ends (1.95 Angstrom resolution)
Keywords keywordsPAZ domain, platform domain, connector helix, siRNA, RNase III domain, endoribonuclease, pre-miRNA, HYDROLASE-RNA complex; HYDROLASE/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.

4ngd__assembly_1__model_1

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

Download this curve (.dat)

4ngd__assembly_1__model_1 | I(q)

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

4ngd__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）24.11 Å
Rg (electron density)22.97 Å
Total Rg23.88 Å
Atom count5363
Residues304
Excluded volume48696 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4ngd__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4ngd__assembly_2__model_1 tetrameric （4） 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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4ngdA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology260 — paz domain
Homologous superfamily homologous superfamily10 — paz domain
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7. Citations (1)