1fu1

CRYSTAL STRUCTURE OF HUMAN XRCC4

Method: X-RAY DIFFRACTION D_max: 90.4 Å Quality: REASONABLE

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–203 Chain B； UniProt 1–203	Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203 Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Ammonium sulphate, magnesium acetate, DTT, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.70 Å R-free 0.263
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–203 Chain B； UniProt 1–203	Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203 Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Ammonium sulphate, magnesium acetate, DTT, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.70 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1FU1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IK9 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX Deposited 2001-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–213（213 aa） Fragment：XRCC4 FRAGMENT, RESIDUES 1-213 Chain B 1–213（213 aa） Fragment：XRCC4 FRAGMENT, RESIDUES 1-213	Mutation：C93A,C128A,C130A,C165A Mutation：C93A,C128A,C130A,C165A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.266
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–203（203 aa） Fragment：residues 1-203 Chain B 1–203（203 aa） Fragment：residues 1-203	Mutation：A60E, I134T Mutation：A60E, I134T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.280
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–203（203 aa） Fragment：residues 1-203 Chain D 1–203（203 aa） Fragment：residues 1-203	Mutation：A60E, I134T Mutation：A60E, I134T	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.280
3MUD Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle Deposited 2010-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–137（136 aa） Chain B 2–137（136 aa）	Mutation：I134T, L249N,I134T Mutation：I134T, L249N,I134T	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% MePEG 2000, 100 mM Bis-Tris, 120 mM MgSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.250
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 1–157（157 aa） Fragment：unp residues 1-157 Chain H 1–157（157 aa） Fragment：unp residues 1-157	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.50 Å R-free 0.309
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–157（157 aa） Fragment：unp residues 1-157 Chain D 1–157（157 aa） Fragment：unp residues 1-157	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 5.50 Å R-free 0.309
3RWR Crystal structure of the human XRCC4-XLF complex Deposited 2011-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–157（157 aa） Fragment：unp residues 1-157 Chain B 1–157（157 aa） Fragment：unp residues 1-157 Chain F 1–157（157 aa） Fragment：unp residues 1-157 Chain G 1–157（157 aa） Fragment：unp residues 1-157	Not recorded	TBR HEXATANTALUM DODECABROMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8M Ammonium citrate, pH 8.0, 20 mM Barium chloride dihydrate, 400 mM sodium thiocyanate, 0.5 mM tantalum bromide, 60% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.94 Å R-free 0.326
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–140（140 aa） Chain B 1–140（140 aa） Chain E 1–140（140 aa） Chain F 1–140（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–140（140 aa） Chain B 1–140（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–140（140 aa） Chain F 1–140（140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K	Resolution 3.97 Å R-free 0.369
3W03 XLF-XRCC4 complex Deposited 2012-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–164（164 aa） Fragment：UNP residues 1-164 Chain D 1–164（164 aa） Fragment：UNP residues 1-164	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris pH7.5, 2M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 8.49 Å R-free 0.360
4XA4 Crystal Structure of the coiled-coil surrounding Skip 3 of MYH7 Deposited 2014-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–147（146 aa） Fragment：UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609 Chain B 2–147（146 aa） Fragment：UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% (w/v) polyethylene glycol 1500, 250 mM tetramethylammonium chloride, 100 mM 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS)	Resolution 2.33 Å R-free 0.274
5CHX Crystal Structure of amino acids 1590-1657 of MYH7 Deposited 2015-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657 Chain B 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；16% (w/v) MEPEG 2000, 250 mM potassium nitrate, 100 mM 3-(N-morpholino)propanesulfonic acid (MOPS)	Resolution 2.30 Å R-free 0.265
5CHX Crystal Structure of amino acids 1590-1657 of MYH7 Deposited 2015-07-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657 Chain B 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；16% (w/v) MEPEG 2000, 250 mM potassium nitrate, 100 mM 3-(N-morpholino)propanesulfonic acid (MOPS)	Resolution 2.30 Å R-free 0.265
5CJ0 Crystal Structure of Amino Acids 1631-1692 of MYH7 Deposited 2015-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–142（141 aa） Fragment：UNP Q13426 residues 2-142, UNP P12883 residues 1631-1692 Chain B 2–142（141 aa） Fragment：UNP Q13426 residues 2-142, UNP P12883 residues 1631-1692	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；14% (w/v) MEPEG 5000, 200 mM glycine, 100 mM bistrispropane pH 7.0.	Resolution 2.30 Å R-free 0.238
5CJ4 Crystal Structure of Amino Acids 1562-1622 of MYH7 Deposited 2015-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622 Chain B 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；23% (w/v) PEG 4000, 500 mM NaCl, 100 mM triethanolamine pH 8.0.	Resolution 3.10 Å R-free 0.280
5CJ4 Crystal Structure of Amino Acids 1562-1622 of MYH7 Deposited 2015-07-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622 Chain D 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；23% (w/v) PEG 4000, 500 mM NaCl, 100 mM triethanolamine pH 8.0.	Resolution 3.10 Å R-free 0.280
5WJ7 Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Xrcc4 Deposited 2017-07-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797 Chain B 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；16% (w/v) Methyl-Ether PEG 5K, 300 mM glycine, 100 mM triethanolamine pH 7.5	Resolution 2.50 Å R-free 0.249
5WLZ Crystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac Myosin Fused to Xrcc4 Deposited 2017-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758 Chain B 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758 Chain C 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758 Chain D 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758	Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8-10% methyl-ether polyethylene glycol (MEPEG) 5K, 300 mM glycine, bis-tris propane pH 7.0, 1.5-3.0% (w/v) jeffamine M-600	Resolution 3.50 Å R-free 0.249
6ABO human XRCC4 and IFFO1 complex Deposited 2018-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–213（213 aa） Fragment：UNP residues 1-213	Not recorded	GOL GLYCEROL × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Sodium cacodylate pH6.0, 50mM Calcium acetate, 20-25% MPD, 1M Ammonium sulfate	Resolution 2.65 Å R-free 0.273
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric	Chain F 1–336（336 aa） Chain G 1–336（336 aa） Chain O 1–336（336 aa） Chain P 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.40 Å
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain F 1–336（336 aa） Chain G 1–336（336 aa） Chain O 1–336（336 aa） Chain P 1–336（336 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7M3P Xrcc4-Spc110p(164-207) fusion Deposited 2021-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–132（131 aa） Chain B 2–132（131 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；13% PEG3350 and 0.2 M magnesium formate	Resolution 2.00 Å R-free 0.247
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain K 1–336（336 aa） Chain L 1–336（336 aa） Chain N 1–336（336 aa） Chain O 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
7NFE Cryo-EM structure of NHEJ super-complex (monomer) Deposited 2021-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain H 1–336（336 aa） Chain I 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.29 Å
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain G 1–336（336 aa） Chain H 1–336（336 aa） Chain P 1–336（336 aa） Chain Q 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.55 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain K 1–336（336 aa） Chain L 1–336（336 aa） Chain N 1–336（336 aa） Chain O 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.51 Å
8BHY DNA-PK Ku80 mediated dimer bound to PAXX and XLF Deposited 2022-11-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain G 1–336（336 aa） Chain H 1–336（336 aa） Chain P 1–336（336 aa） Chain Q 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.33 Å
8BOT Cryo-EM structure of NHEJ supercomplex(trimer) Deposited 2022-11-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric	Chain K 1–336（336 aa） Chain L 1–336（336 aa） Chain N 1–336（336 aa） Chain O 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.76 Å
8EZA NHEJ Long-range complex with PAXX Deposited 2022-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric	Chain F 1–336（336 aa） Chain G 1–336（336 aa） Chain O 1–336（336 aa） Chain P 1–336（336 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.39 Å
8EZB NHEJ Long-range complex with ATP Deposited 2022-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain F 1–336（336 aa） Chain G 1–336（336 aa） Chain O 1–336（336 aa） Chain P 1–336（336 aa）	Not recorded	MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.90 Å
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9CQ6 The ligation complex in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9CQC The ligation complex like in the NHEJ pathway Deposited 2024-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain P 1–336（336 aa） Chain Q 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.25 Å
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–336（336 aa） Chain H 1–336（336 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.97 Å
9N81 A gap-filling complex with Pol mu engaged in the NHEJ Pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	MG MAGNESIUM ION × 1 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9N82 The ligation (AMP-Lys) complex in the NHEJ pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9N83 The ligation complex in the NHEJ pathway Deposited 2025-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric	Chain D 1–336（336 aa） Chain E 1–336（336 aa） Chain d 1–336（336 aa） Chain e 1–336（336 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

33 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

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

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1fu1
Deposition date deposition_date	2000-09-13
Structure title title	CRYSTAL STRUCTURE OF HUMAN XRCC4
Keywords keywords	helix-turn-helix, helix bundle, GENE REGULATION; GENE REGULATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.13 Å
Radius of gyration Rg (electron density) rg_electron	35.56 Å
Forward intensity I(0) i0	34364300.00
Molecular weight molecular_weight	44787.0 kDa
Excluded volume excluded_volume	55580 Å³
Envelope volume envelope_volume	78197 Å³
Hydration-shell volume shell_volume	22048 Å³
Envelope diameter envelope_diameter	137.1 Å
Shell Rg shell_rg	34.63 Å
Envelope Rg envelope_rg	37.36 Å
Shape Rg shape_rg	35.57 Å
Total Rg total_rg	35.43 Å
Total atoms total_atoms	3116
Residues n_residues	373
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.4 Å
Rg (real space) rg_real	30.22 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	3.2500e+07
I(0) uncertainty (real space) i0_real_error	4.2230e+05
Rg (reciprocal space) rg_reciprocal	34.50 Å
I(0) (reciprocal space) i0_reciprocal	34340000.0000
Solution quality estimate total_estimate	0.6671
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.462
Kurtosis Kurtosis kurtosis	-0.520
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.7649
Highest regularization parameter α highest_alpha	2780000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.004; Oscil: 0.949; Stabil: 0.992; Sysdev: 0.000; Positv: 1.000; Valcen: 0.882; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA REPAIR PROTEIN XRCC4
Molecular weight formula_weight	23782.4 kDa
Mutation mutation	T135I
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	3177

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMAMEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPAEVIRELICYCLDTTAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRFILVLNEKKTKIRSLHNKLLNAAQ

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1fu1a1
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	d1fu1a2
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	d1fu1b1
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	d1fu1b2
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	1fu1A01
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	1fu1A02
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	1fu1B01
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	1fu1B02
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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8. Citations (1)

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Unit-cell length a length_a	164.892 Å
Unit-cell length b length_b	74.793 Å
Unit-cell length c length_c	87.307 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	29.930 Å
R factor r_factor	0.2460
R_work r_work	0.2310
R_free r_free	0.2630

fit	/app/data/saxs_computation/fu/1fu1/1fu1.fit
pddf	/app/data/pr_computation/fu/1fu1/1fu1.pr.out
profile	/app/data/saxs_computation/fu/1fu1/1fu1.dat