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6edb

Crystal structure of SRY.hcGAS-21bp dsDNA complex

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

Sex-determining region Y protein,Cyclic GMP-AMP synthase

Homo sapiens

UniProt Q05066

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1hry 1hrz 1j46 1j47 6edb 7yho 7yhp 7yhq 9bvd 9bvd 9bvd

11 assemblies

View Construct and Data Evidence
UniProt name SRY_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–76； UniProt 56–130 Author chain B； PDBConstruct 2–76； UniProt 56–130

Sex-determining region Y protein,Cyclic GMP-AMP synthase

Homo sapiens

UniProt Q8N884

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Insufficient information Homooligomer Protein 2 DNA 2 ;DNA (5'-D(*CP*GP*AP*TP*CP*CP*GP*GP*GP*AP*TP*CP*TP*AP*AP*AP*CP*AP*AP*TP*G)-3') ; × 1 ;DNA (5'-D(*GP*CP*AP*TP*TP*GP*TP*TP*TP*AP*GP*AP*TP*CP*CP*CP*GP*GP*AP*TP*C)-3') ; × 1 ZINC ION × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
4km5 4lev 4lev 4lew 4lew 4mkp 4o67 4o67 4o68 4o69 5vdo 5vdo

106 assemblies; showing the first 12

Homodimer
4lev 4o67 5v8o 6lrc 6lre 6lri 6lrj 6lrk 6lrl 8ime 8imf 8img

15 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6ct9 6cta 6edb 6edc 6y5d 6y5e 7c0m 7ccq 7ccr 7ftn 8okx 8ol1

12 assemblies

View Construct and Data Evidence
UniProt name CGAS_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 90–455； UniProt 157–522 Author chain B； PDBConstruct 90–455； UniProt 157–522

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_id6edb
Deposition date deposition_date2018-08-09
Structure title titleCrystal structure of SRY.hcGAS-21bp dsDNA complex
Keywords keywordsSRY human cGAS DNA complex, Transferase-DNA complex; Transferase/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.

6edb__assembly_1__model_1

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

Download this curve (.dat)

6edb__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.

6edb__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）30.62 Å
Rg (electron density)30.68 Å
Total Rg31.03 Å
Atom count4379
Residues466
Excluded volume75651 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6edb__assembly_1__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 (4)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6edbA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1410 — Poly(a)-polymerase, middle domain
Homologous superfamily homologous superfamily40 —
Domain ID domain_id6edbA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily90 —
Domain ID domain_id6edbB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology30 — DNA Binding (I), subunit A
Homologous superfamily homologous superfamily10 — High mobility group box domain
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7. Citations (1)