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9iax

DNA-PK, LX4, XLF - Catalytic domain of L4

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-dependent protein kinase catalytic subunit

OrganismNot specified

UniProt P78527

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 2 X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
5w1r 6zfp 6zh2 6zh4 7k10 7k11 7otm 7otp 7otv 7otw 7oty

11 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5luq 5luq 5y3r 6zh6 6zh8 6zha 6zhe 7k0y 7k19 7k1b 7k1j 7k1k

37 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name PRKDC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–4128； UniProt 1–4128

X-ray repair cross-complementing protein 6

Homo sapiens

UniProt P12956

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 2 DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 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
1jeq 1jey 3rzx 5y3r 6erf 6erf 6erf 6erf 6erg 6erg 6erh 6erh

63 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name XRCC6_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–609； UniProt 1–609

X-ray repair cross-complementing protein 5

Homo sapiens

UniProt P13010

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Heteromer Protein 8 DNA 2 DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1q2z 1rw2

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1jeq 1jey 3rz9 5y3r 6erf 6erf 6erf 6erf 6erg 6erg 6erh 6erh

67 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name XRCC5_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–732； UniProt 1–732

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–DNA Heteromer Protein 8 DNA 2 DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer
2qm4 2qm4 2r9a 3sr2 3sr2 3w03

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3q4f 3q4f 3rwr 3sr2 6erg 6erg 6erh 6erh 7lsy 7lt3 7nfc 7nfe

26 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name NHEJ1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–299； UniProt 1–299 Author chain M； PDBConstruct 1–299； UniProt 1–299

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–DNA Heteromer Protein 8 DNA 2 DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 Consistent with all polymers

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 5
Chains and sequence ranges Author chain G； PDBConstruct 1–336； UniProt 1–336 Author chain H； PDBConstruct 1–336； UniProt 1–336

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–DNA Heteromer Protein 8 DNA 2 DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA × 1 DNA × 1 Consistent with all polymers

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 6
Chains and sequence ranges Author chain K； PDBConstruct 1–911； UniProt 1–911

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_id9iax
Deposition date deposition_date2025-02-11
Structure title titleDNA-PK, LX4, XLF - Catalytic domain of L4
Keywords keywordsKinase, NHEJ, cryo-EM, DNA-PK, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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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.

9iax__assembly_1__model_1

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

Download this curve (.dat)

9iax__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

9iax__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）74.12 Å
Rg (electron density)74.38 Å
Total Rg74.17 Å
Atom count51268
Residues6382
Excluded volume916910 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 9iax__assembly_1__model_1 decameric （10） 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 (8)

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7. Citations (1)