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3ii6

Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.

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

DNA repair protein XRCC4

Homo sapiens

UniProt Q13426

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA ligase 4 × 1 （P49917） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA ligase 4 × 1 （P49917） CHLORIDE ION × 2 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
3sr2 3sr2 3w03

3 assemblies

Homotetramer
1fu1 1fu1

2 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ik9 3ii6 3ii6 3mud 3q4f 3q4f 3rwr 3sr2 4xa4 5chx 5chx 5cj0

36 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name XRCC4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–203； UniProt 1–203 Author chain B； PDBConstruct 1–203； UniProt 1–203 Author chain C； PDBConstruct 1–203； UniProt 1–203 Author chain D； PDBConstruct 1–203； UniProt 1–203

DNA ligase 4

Homo sapiens

UniProt P49917

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA repair protein XRCC4 × 2 （Q13426） water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA repair protein XRCC4 × 2 （Q13426） CHLORIDE ION × 2 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2e2w 3vnn 3w5o 3w5o 4hto 7d9k 7d9y

7 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1ik9 3ii6 3ii6 3w1b 3w1g 4htp 4htp 6bkf 6bkg 7lsy 7lt3 7nfc

27 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DNLI4_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain X； PDBConstruct 6–263； UniProt 654–911 Author chain Y； PDBConstruct 6–263； UniProt 654–911

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_id3ii6
Deposition date deposition_date2009-07-31
Structure title titleStructure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
Keywords keywords;XRCC4, DNA LIGASE IV, NHEJ, DNA REPAIR, BRCT, Alternative splicing, Coiled coil, DNA damage, DNA recombination, Isopeptide bond, Nucleus, Phosphoprotein, Polymorphism, Ubl conjugation, ATP-binding, Cell cycle, Cell division, Disease mutation, DNA replication, Ligase, Magnesium, Metal-binding, Nucleotide-binding, SCID, LIGASE-DNA BINDING PROTEIN COMPLEX ;; LIGASE/DNA BINDING PROTEIN
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.

3ii6__assembly_1__model_1

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

Download this curve (.dat)

3ii6__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.

3ii6__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）43.16 Å
Rg (electron density)43.74 Å
Total Rg43.64 Å
Atom count5318
Residues653
Excluded volume94601 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3ii6__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3ii6__assembly_2__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) 22 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3ii6a1
Class classb — All beta proteins
Fold Fold foldb.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamilyb.59.1 — XRCC4, N-terminal domain
Family Family familyb.59.1.1 — XRCC4, N-terminal domain
Domain ID domain_idd3ii6a2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.11 — XRCC4, C-terminal oligomerization domain
Family Family familyh.1.11.1 — XRCC4, C-terminal oligomerization domain
Domain ID domain_idd3ii6b1
Class classb — All beta proteins
Fold Fold foldb.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamilyb.59.1 — XRCC4, N-terminal domain
Family Family familyb.59.1.1 — XRCC4, N-terminal domain
Domain ID domain_idd3ii6b2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.11 — XRCC4, C-terminal oligomerization domain
Family Family familyh.1.11.1 — XRCC4, C-terminal oligomerization domain
Domain ID domain_idd3ii6c1
Class classb — All beta proteins
Fold Fold foldb.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamilyb.59.1 — XRCC4, N-terminal domain
Family Family familyb.59.1.1 — XRCC4, N-terminal domain
Domain ID domain_idd3ii6c2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.11 — XRCC4, C-terminal oligomerization domain
Family Family familyh.1.11.1 — XRCC4, C-terminal oligomerization domain
Domain ID domain_idd3ii6d1
Class classb — All beta proteins
Fold Fold foldb.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamilyb.59.1 — XRCC4, N-terminal domain
Family Family familyb.59.1.1 — XRCC4, N-terminal domain
Domain ID domain_idd3ii6d2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.11 — XRCC4, C-terminal oligomerization domain
Family Family familyh.1.11.1 — XRCC4, C-terminal oligomerization domain

CATH v4.4 (14 domains)

Domain ID domain_id3ii6A01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal
Domain ID domain_id3ii6A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily370 —
Domain ID domain_id3ii6B01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal
Domain ID domain_id3ii6B02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily370 —
Domain ID domain_id3ii6C01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal
Domain ID domain_id3ii6C02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily370 —
Domain ID domain_id3ii6D01
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal
Domain ID domain_id3ii6D02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily370 —
Domain ID domain_id3ii6X01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ii6X02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily520 —
Domain ID domain_id3ii6X03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ii6Y01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
Domain ID domain_id3ii6Y02
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily520 —
Domain ID domain_id3ii6Y03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10190 — BRCT domain
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7. Citations (1)