6zwk

Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody)

Method: X-RAY DIFFRACTION D_max: 111.3 Å Quality: GOOD

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

Histone H2AX

OrganismNot specified

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 G； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain K； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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
6	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain L； UniProt 134–143	Non-standard monomer：Yes (specific site not provided by mmCIF)	gammaXbody × 1 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

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 6ZWK	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
3SQD Crystal structure of human PTIP BRCT5/6-gamma H2AX complex Deposited 2011-07-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 134–143（10 aa） Fragment：UNP 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 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248
3SQD Crystal structure of human PTIP BRCT5/6-gamma H2AX complex Deposited 2011-07-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 134–143（10 aa） Fragment：UNP 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 6；287 K；18% PEG4000, 100mM Nacacodylate, pH 6.0, vapor diffusion, hanging drop, temperature 287K	Resolution 2.15 Å R-free 0.248
3SZM STRUCTURE OF HUMAN MICROCEPHALIN (MCPH1) TANDEM BRCT DOMAINS IN COMPLEX WITH A GAMMA-H2AX PHOSPHOPEPTIDE Deposited 2011-07-19	Different construct Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
9MLL GammaH2AX containing nucleosomes, Parallel stack Deposited 2024-12-19	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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 33 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 G； PDBConstruct 1–10； UniProt 134–143 Author chain H； PDBConstruct 1–10； UniProt 134–143 Author chain I； PDBConstruct 1–10； UniProt 134–143 Author chain J； PDBConstruct 1–10； UniProt 134–143 Author chain K； PDBConstruct 1–10； UniProt 134–143 Author chain L； 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	6zwk
Deposition date deposition_date	2020-07-28
Structure title title	Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody)
Keywords keywords	NANOBODY, PHOSPHOPEPTIDE-RECOGNITION PROTEIN, GAMMA-H2AX, IMMUNE SYSTEM; IMMUNE SYSTEM
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	33.20 Å
Radius of gyration Rg (electron density) rg_electron	32.50 Å
Forward intensity I(0) i0	140135000.00
Molecular weight molecular_weight	88703.0 kDa
Excluded volume excluded_volume	108640 Å³
Envelope volume envelope_volume	144920 Å³
Hydration-shell volume shell_volume	38331 Å³
Envelope diameter envelope_diameter	117.7 Å
Shell Rg shell_rg	38.22 Å
Envelope Rg envelope_rg	32.05 Å
Shape Rg shape_rg	32.45 Å
Total Rg total_rg	33.08 Å
Total atoms total_atoms	12075
Residues n_residues	726
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	111.3 Å
Rg (real space) rg_real	33.03 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	1.4010e+08
I(0) uncertainty (real space) i0_real_error	2.3460e+06
Rg (reciprocal space) rg_reciprocal	33.11 Å
I(0) (reciprocal space) i0_reciprocal	140100000.0000
Solution quality estimate total_estimate	0.8679
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.4 Å
Skewness Skewness skewness	0.140
Kurtosis Kurtosis kurtosis	-0.301
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14270000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.777; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	gammaXbody
Molecular weight formula_weight	16577.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	14070

TEVQLVESGGGLVQAGDSLRLSCAASGLTFSRYAMGWFRQAPGNEREFVAVITASGRTTLYADSVKGRFTISRDNAKNTVALQMQSLKPEDTAVYYCAADYGTSRYTRRQSEYEYWGQGTQVTVSSAAATSMFQDPQERPRASAHHHHHH

来源 Source

来源生物 organism	Vicugna pacos
通用名 common_name	alpaca
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Histone H2AX
Molecular weight formula_weight	1209.2 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I,J,K,L

CKATQASQEY

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	980

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	6zwkA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zwkB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zwkC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zwkD01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zwkE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zwkF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	87.412 Å
Unit-cell length b length_b	87.412 Å
Unit-cell length c length_c	105.409 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	18

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	61.490 Å
R factor r_factor	0.1508
R_work r_work	0.1491
R_free r_free	0.1844

fit	/app/data/saxs_computation/zw/6zwk/6zwk.fit
pddf	/app/data/pr_computation/zw/6zwk/6zwk.pr.out
profile	/app/data/saxs_computation/zw/6zwk/6zwk.dat

Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody)

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

Histone H2AX

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)