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6wea

YTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA

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

YTH domain-containing protein 1

Homo sapiens

UniProt Q96MU7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3') ; × 1 1,2-ETHANEDIOL × 6 SULFATE ION × 6 SODIUM ION × 1 water × 2 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3') ; × 1 1,2-ETHANEDIOL × 4 SULFATE ION × 4 water × 2 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3') ; × 1 1,2-ETHANEDIOL × 1 SULFATE ION × 1 water × 2 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 1 ;DNA (5'-D(*CP*GP*CP*GP*GP*(6MA)P*CP*TP*TP*C)-3') ; × 1 1,2-ETHANEDIOL × 1 SULFATE ION × 2 water × 2 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2yud 4r3h 4r3h 6syz 6syz 6sz1 6sz1 6sz2 6sz2 6sz3 6sz3 6sz7

201 assemblies; showing the first 12

Homodimer
6we8

1 assemblies

Homotetramer
9mb3

1 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
4r3i 6rt4 6rt4 6rt5 6rt5 6rt6 6rt6 6rt7 6rt7 6we9 6we9 6wea

20 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name YTDC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–166； UniProt 345–509 Author chain B； PDBConstruct 2–166； UniProt 345–509 Author chain C； PDBConstruct 2–166； UniProt 345–509 Author chain D； PDBConstruct 2–166； UniProt 345–509

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_id6wea
Deposition date deposition_date2020-04-01
Structure title titleYTH domain of human YTHDC1 with a 10mer Oligo Containing N6mA
Keywords keywordsN6-methyladenine binding protein domain, ssDNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

6wea__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wea__assembly_2__model_1 | I(q)

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

6wea__assembly_2__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）17.92 Å
Rg (electron density)16.37 Å
Total Rg17.43 Å
Atom count1520
Residues172
Excluded volume26510 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6wea__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6wea__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6wea__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6wea__assembly_4__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 (6)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6weaA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology590 — ph1033 like fold
Homologous superfamily homologous superfamily10 — ph1033 like domains
Domain ID domain_id6weaB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology590 — ph1033 like fold
Homologous superfamily homologous superfamily10 — ph1033 like domains
Domain ID domain_id6weaC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology590 — ph1033 like fold
Homologous superfamily homologous superfamily10 — ph1033 like domains
Domain ID domain_id6weaD00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology590 — ph1033 like fold
Homologous superfamily homologous superfamily10 — ph1033 like domains
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7. Citations (1)