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7lsy

NHEJ Short-range synaptic complex

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

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 12 DNA 5 X-ray repair cross-complementing protein 5 × 2 （P13010） DNA (26-MER) × 1 ;DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') ; × 1 DNA repair protein XRCC4 × 4 （Q13426） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） ;DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') ; × 1 DNA (26-MER) × 1 ;DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') ; × 1 DNA ligase 4 × 2 （P49917） 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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–600； UniProt 1–600 Author chain J； PDBConstruct 1–600； UniProt 1–600

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 12 DNA 5 X-ray repair cross-complementing protein 6 × 2 （P12956） DNA (26-MER) × 1 ;DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') ; × 1 DNA repair protein XRCC4 × 4 （Q13426） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） ;DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') ; × 1 DNA (26-MER) × 1 ;DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') ; × 1 DNA ligase 4 × 2 （P49917） 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 2
Chains and sequence ranges Author chain B； PDBConstruct 1–732； UniProt 1–732 Author chain K； PDBConstruct 1–732； UniProt 1–732

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 12 DNA 5 X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） DNA (26-MER) × 1 ;DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') ; × 1 Non-homologous end-joining factor 1 × 2 （Q9H9Q4） ;DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') ; × 1 DNA (26-MER) × 1 ;DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') ; × 1 DNA ligase 4 × 2 （P49917） 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 F； PDBConstruct 1–336； UniProt 1–336 Author chain G； PDBConstruct 1–336； UniProt 1–336 Author chain O； PDBConstruct 1–336； UniProt 1–336 Author chain P； PDBConstruct 1–336； UniProt 1–336

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 12 DNA 5 X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） DNA (26-MER) × 1 ;DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') ; × 1 DNA repair protein XRCC4 × 4 （Q13426） ;DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') ; × 1 DNA (26-MER) × 1 ;DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') ; × 1 DNA ligase 4 × 2 （P49917） 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 6
Chains and sequence ranges Author chain H； PDBConstruct 1–299； UniProt 1–299 Author chain I； PDBConstruct 1–299； UniProt 1–299

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 12 DNA 5 X-ray repair cross-complementing protein 6 × 2 （P12956） X-ray repair cross-complementing protein 5 × 2 （P13010） DNA (26-MER) × 1 ;DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3') ; × 1 DNA repair protein XRCC4 × 4 （Q13426） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） ;DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3') ; × 1 DNA (26-MER) × 1 ;DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3') ; × 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 10
Chains and sequence ranges Author chain X； PDBConstruct 1–911； UniProt 1–911 Author chain Y； 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_id7lsy
Deposition date deposition_date2021-02-18
Structure title titleNHEJ Short-range synaptic complex
Keywords keywordsNHEJ, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

7lsy__assembly_1__model_1

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

Download this curve (.dat)

7lsy__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.

7lsy__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）76.16 Å
Rg (electron density)76.67 Å
Total Rg76.42 Å
Atom count37020
Residues4458
Excluded volume656910 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7lsy__assembly_1__model_1 heptadecameric （17） 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 (10)

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7. Citations (1)