SAXSdb — 1ik9

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA REPAIR PROTEIN XRCC4

Homo sapiens

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 IV × 1 （P49917） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	XRCC4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–213； UniProt 1–213 Author chain B； PDBConstruct 1–213； UniProt 1–213

DNA LIGASE IV

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNL4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–37； UniProt 748–784

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_id	1ik9
Deposition date deposition_date	2001-05-03
Structure title title	CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
Keywords keywords	;DNA end joining, double-strand break repair, V(D)J recombination, protein-protein complex, coiled coil, GENE REGULATION-LIGASE COMPLEX ;; GENE REGULATION/LIGASE
Experimental Method method	X-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.

1ik9__assembly_1__model_1

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

Download this curve (.dat)

1ik9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ik9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	41.41 Å
Rg (electron density)	42.51 Å
Total Rg	42.37 Å
Atom count	3512
Residues	430
Excluded volume	62494 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ik9__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 (3)

Entity 1 Entity 1 polymer

Description description	DNA REPAIR PROTEIN XRCC4
Molecular weight formula_weight	24466.6 kDa
Mutation mutation	C93A,C128A,C130A,C165A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3736

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESAYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELIAYALDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKAVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA LIGASE IV
Molecular weight formula_weight	4323.7 kDa
EC 编号 ec_number	6.5.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PSTKEHFAREYDCYGDSYFIDTDLNQLKEVFSGIKNS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	224

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ik9a1
Class class	b — All beta proteins
Fold Fold fold	b.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamily	b.59.1 — XRCC4, N-terminal domain
Family Family family	b.59.1.1 — XRCC4, N-terminal domain

Domain ID domain_id	d1ik9a2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.11 — XRCC4, C-terminal oligomerization domain
Family Family family	h.1.11.1 — XRCC4, C-terminal oligomerization domain

Domain ID domain_id	d1ik9b1
Class class	b — All beta proteins
Fold Fold fold	b.59 — XRCC4, N-terminal domain
Superfamily Superfamily superfamily	b.59.1 — XRCC4, N-terminal domain
Family Family family	b.59.1.1 — XRCC4, N-terminal domain

Domain ID domain_id	d1ik9b2
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.11 — XRCC4, C-terminal oligomerization domain
Family Family family	h.1.11.1 — XRCC4, C-terminal oligomerization domain

CATH v4.4 (4 domains)

Domain ID domain_id	1ik9A01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	1ik9A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	1ik9B01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	210 — Dna Repair Protein Xrcc4; Chain: A, domain 1
Homologous superfamily homologous superfamily	10 — DNA double-strand break repair and VJ recombination XRCC4, N-terminal

Domain ID domain_id	1ik9B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	370 —

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Unit-cell length a length_a	45.062 Å
Unit-cell length b length_b	79.628 Å
Unit-cell length c length_c	242.142 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	33.260 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2660

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA REPAIR PROTEIN XRCC4

State in the Current Structure

Other States of the Same Protein in the Database

DNA LIGASE IV

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ik9__assembly_1__model_1

1ik9__assembly_1__model_1 | I(q)

1ik9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA REPAIR PROTEIN XRCC4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA LIGASE IV

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1ik9__assembly_1__model_1

1ik9__assembly_1__model_1 | I(q)

1ik9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)