3sr2

Crystal Structure of Human XLF-XRCC4 Complex

Method: X-RAY DIFFRACTION

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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 8	Non-homologous end-joining factor 1 × 4 （Q9H9Q4）	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	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 6–145； UniProt 1–140 Author chain B； PDBConstruct 6–145； UniProt 1–140 Author chain E； PDBConstruct 6–145； UniProt 1–140 Author chain F； PDBConstruct 6–145； UniProt 1–140

Non-homologous end-joining factor 1

Homo sapiens

UniProt Q9H9Q4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA repair protein XRCC4 × 4 （Q13426）	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NHEJ1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 6–229； UniProt 1–224 Author chain D； PDBConstruct 6–229； UniProt 1–224 Author chain G； PDBConstruct 6–229； UniProt 1–224 Author chain H； PDBConstruct 6–229； UniProt 1–224

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	3sr2
Deposition date deposition_date	2011-07-06
Structure title title	Crystal Structure of Human XLF-XRCC4 Complex
Keywords keywords	;XRCC4, XLF, NHEJ, DNA Repair, DNA, DNA Ligases, DNA-Binding Proteins, Dimerization, Humans, Protein Structure, Quaternary, Complex, Non-Homologous End Joining (NHEJ), DNA ligase IV, Ku, XLF-XRCC4, Protein DNA-interaction, DNA BINDING PROTEIN-PROTEIN BINDING complex ;; DNA BINDING PROTEIN/PROTEIN BINDING
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.

3sr2__assembly_1__model_1

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

Download this curve (.dat)

3sr2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3sr2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.64 Å
Rg (electron density)	49.95 Å
Total Rg	49.70 Å
Atom count	11363
Residues	1432
Excluded volume	203510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3sr2__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3sr2__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3sr2__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3sr2__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3sr2__assembly_5__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 (2)

Entity 1 Entity 1 polymer

Description description	DNA repair protein XRCC4
Molecular weight formula_weight	16256.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F
Atom count atom_count	11363

GPLGSMERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTIAENQAK

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

Entity 2 Entity 2 polymer

Description description	Non-homologous end-joining factor 1
Molecular weight formula_weight	25868.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H

GPLGSMEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKELNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWNFHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLKTEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQ

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

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	3sr2A00
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	3sr2B00
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	3sr2C01
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	3sr2C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	3sr2D01
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	3sr2D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	3sr2E00
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	3sr2F00
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	3sr2G01
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	3sr2G02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

Domain ID domain_id	3sr2H01
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	3sr2H02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	450 — Helix hairpin bin

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Unit-cell length a length_a	110.017 Å
Unit-cell length b length_b	110.017 Å
Unit-cell length c length_c	763.680 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	3.971 Å
Low-resolution limit resolution_low	67.436 Å
R factor r_factor	0.3586
R_work r_work	0.3577
R_free r_free	0.3690

Crystal Structure of Human XLF-XRCC4 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

Non-homologous end-joining factor 1

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

3sr2__assembly_1__model_1

3sr2__assembly_1__model_1 | I(q)

3sr2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of Human XLF-XRCC4 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

Non-homologous end-joining factor 1

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

3sr2__assembly_1__model_1

3sr2__assembly_1__model_1 | I(q)

3sr2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)