3sqd

Crystal structure of human PTIP BRCT5/6-gamma H2AX complex

Method: X-RAY DIFFRACTION D_max: 82.7 Å Quality: EXCELLENT

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

PAX-interacting protein 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 860–1069	Fragment：BRCT 5-BRCT 6 domains	Histone H2A.x × 1 （P16104）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 860–1069	Fragment：BRCT 5-BRCT 6 domains	Histone H2A.x × 1 （P16104）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	PAXI1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–219； UniProt 860–1069 Author chain B； PDBConstruct 10–219； UniProt 860–1069

Histone H2A.x

OrganismNot specified

UniProt P16104

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 134–143	Fragment：UNP residues 134-143 Non-standard monomer：Yes (specific site not provided by mmCIF)	PAX-interacting protein 1 × 1 （Q6ZW49）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 134–143	Fragment：UNP residues 134-143 Non-standard monomer：Yes (specific site not provided by mmCIF)	PAX-interacting protein 1 × 1 （Q6ZW49）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3SQD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D31 Crystal structure of disulfide-linked HLA-G dimer Deposited 2005-09-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 78–86（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；293 K；CAPS, PEG8000, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.298
2D31 Crystal structure of disulfide-linked HLA-G dimer Deposited 2005-09-23	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 78–86（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；293 K；CAPS, PEG8000, NaCl, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.298
2DYP Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G Deposited 2006-09-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 78–86（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris-HCl pH8.0, 45% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.278
3SHV Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex Deposited 2011-06-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 134–143（10 aa） Fragment：residues in UNP 134-143	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 7.5；293 K；0.2M Sodium acetate trihydrate, 100mM TRIS hydrochloride(pH 8.5), 30%(w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.242
3SHV Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex Deposited 2011-06-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 134–143（10 aa） Fragment：residues in UNP 134-143	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 7.5；293 K；0.2M Sodium acetate trihydrate, 100mM TRIS hydrochloride(pH 8.5), 30%(w/v) PEG4000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.242
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain O 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 134–143（10 aa） Fragment：C-TERMINAL FRAGMENT, RESIDUES 134-143	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 4.8；20% PEG 4000, 0.1M (NH4)H2PO4, 0.1M BIS-TRIS-PROPANE , PH 4.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 2.63 Å R-free 0.252
6K1I Human nucleosome core particle with gammaH2A.X variant Deposited 2019-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 23 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate	Resolution 2.75 Å R-free 0.277
6K1J Human nucleosome core particle with H2A.X variant Deposited 2019-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；Potassium Chloride, Manganese Chloride, Potassium Cacodylate	Resolution 2.85 Å R-free 0.319
6K1K Human nucleosome core particle with H2A.X S139E variant Deposited 2019-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Mutation：S139E variant Mutation：S139E variant	CL CHLORIDE ION × 2 MN MANGANESE (II) ION × 33 K POTASSIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291.15 K；potassium chloride, manganese chloride, potassium cacodylate	Resolution 2.20 Å R-free 0.275
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
6ZWK Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody) Deposited 2020-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 134–143（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG 3350, 0.2M Sodium acetate	Resolution 1.55 Å R-free 0.184
9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain N 1–143（143 aa） Chain R 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9MLN GammaH2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9MLR GammaH2AX containing nucleosome, Half-wrapped (Class 2) Deposited 2024-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9MLS GammaH2AX containing nucleosome, Extended (Class 3) Deposited 2024-12-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9MMK H2AX containing nucleosome, Canonical (Class 1) Deposited 2024-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9MMM H2AX containing nucleosomes, Parallel stack Deposited 2024-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain N 1–143（143 aa） Chain R 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9MMN H2AX containing nucleosomes, Left offset stack Deposited 2024-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain N 1–143（143 aa） Chain R 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9MMO H2AX containing nucleosomes, Right offset stack Deposited 2024-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain N 1–143（143 aa） Chain R 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9MMT H2AX containing nucleosome, Unwrapped (Class 2) Deposited 2024-12-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain c 1–143（143 aa） Chain g 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.38 Å
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric	Chain C 1–143（143 aa） Chain G 1–143（143 aa） Chain c 1–143（143 aa） Chain g 1–143（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.00 Å

23 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H2AX_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 134–143 Author chain D； PDBConstruct 1–10； UniProt 134–143

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	3sqd
Deposition date deposition_date	2011-07-05
Structure title title	Crystal structure of human PTIP BRCT5/6-gamma H2AX complex
Keywords keywords	tandem brct domains, H2AX, CELL CYCLE; CELL CYCLE
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	27.58 Å
Radius of gyration Rg (electron density) rg_electron	26.57 Å
Forward intensity I(0) i0	37410000.00
Molecular weight molecular_weight	49306.0 kDa
Excluded volume excluded_volume	62580 Å³
Envelope volume envelope_volume	81746 Å³
Hydration-shell volume shell_volume	25749 Å³
Envelope diameter envelope_diameter	85.8 Å
Shell Rg shell_rg	33.77 Å
Envelope Rg envelope_rg	26.13 Å
Shape Rg shape_rg	26.56 Å
Total Rg total_rg	27.45 Å
Total atoms total_atoms	3468
Residues n_residues	428
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	82.7 Å
Rg (real space) rg_real	27.47 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	3.7410e+07
I(0) uncertainty (real space) i0_real_error	5.2720e+05
Rg (reciprocal space) rg_reciprocal	27.51 Å
I(0) (reciprocal space) i0_reciprocal	37410000.0000
Solution quality estimate total_estimate	0.9122
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	41.4 Å
Skewness Skewness skewness	0.083
Kurtosis Kurtosis kurtosis	-0.771
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11580000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.959

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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	PAX-interacting protein 1
Molecular weight formula_weight	25147.2 kDa
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	3741

MGHHHHHHMKLTPELTPFVLFTGFEPVQVQQYIKKLYILGGEVAESAQKCTHLIASKVTRTVKFLTAISVVKHIVTPEWLEECFRCQKFIDEQNYILRDAEAEVLFSFSLEESLKRAHVSPLFKAKYFYITPGICPSLSTMKAIVECAGGKVLSKQPSFRKLMEHKQNSSLSEIILISCENDLHLCREYFARGIDVHNAEFVLTGVLTQTLDYESYKFN

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 polymer

Description description	Histone H2A.x
Molecular weight formula_weight	1235.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

KKATQASQEY

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	273

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3sqdA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	3sqdA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	3sqdB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

Domain ID domain_id	3sqdB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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8. Citations (1)

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Unit-cell length a length_a	84.973 Å
Unit-cell length b length_b	101.812 Å
Unit-cell length c length_c	61.815 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.153 Å
Low-resolution limit resolution_low	24.994 Å
R factor r_factor	0.1997
R_work r_work	0.1972
R_free r_free	0.2480

fit	/app/data/saxs_computation/sq/3sqd/3sqd.fit
pddf	/app/data/pr_computation/sq/3sqd/3sqd.pr.out
profile	/app/data/saxs_computation/sq/3sqd/3sqd.dat

Crystal structure of human PTIP BRCT5/6-gamma H2AX complex

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

PAX-interacting protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Histone H2A.x

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)