6ZWK: Phosphorylated C-terminal tail of histone H2AX

Crystal structure of the phosphorylated C-terminal tail of histone H2AX in complex with a specific nanobody (C6 gammaXbody). Determined by X-ray diffraction at 1.55 Å resolution. Released 21 Jul 2021.

Method: X-ray diffraction
Resolution: 1.55 Å
Organisms: Vicugna pacos, Homo sapiens
Chains: 12
Atoms: 7,621
Mol. weight: 106.91 kDa
Released: 21 Jul 2021

Explore 6ZWK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZWK contains 18 α-helices and 80 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, B, D and E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-13	4	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	2
β-strand	46-51	6	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-96	9	2
β-strand	100-100A	2	3
α-helix	100E-100G	3
β-strand	102-103	2	2
β-strand	107-112	6	2

Chains C and F: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	11-13	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	32-39	8	9
β-strand	46-51	6	9
β-strand	57-59	3	9
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	100-100A	2	10
α-helix	100E-100G	3
β-strand	102-103	2	9
β-strand	107-109	3	9
β-strand	110-112	3	8

Chains G, H, I, J, K and L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	140-141	2	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
gammaXbody	A, B, C, D, E, F	protein	150	Vicugna pacos
Histone H2AX	G, H, I, J, K, L	protein	10	Homo sapiens	P16104 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6ZWK_1 gammaXbody (chains A, B, C, D, E, F)
TEVQLVESGGGLVQAGDSLRLSCAASGLTFSRYAMGWFRQAPGNEREFVAVITASGRTTL
YADSVKGRFTISRDNAKNTVALQMQSLKPEDTAVYYCAADYGTSRYTRRQSEYEYWGQGT
QVTVSSAAATSMFQDPQERPRASAHHHHHH

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>6ZWK_2 Histone H2AX (chains G, H, I, J, K, L)
CKATQASQEY

Primary citation

A Novel Nanobody Precisely Visualizes Phosphorylated Histone H2AX in Living Cancer Cells under Drug-Induced Replication Stress. Moeglin, E., Desplancq, D., Stoessel, A. et al. Cancers (Basel) (2021) 13. DOI 10.3390/cancers13133317 · PubMed

Other PDB entries of the same protein (UniProt P16104 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3U3Z 1.5 Å, Structure of human microcephalin (MCPH1) tandem BRCT domains in complex with an H2A.X…
1YDP 1.9 Å, 1.9A crystal structure of HLA-G
3SHV 2.1 Å, Crystal structure of human MCPH1 tandem BRCT domains-gamma H2AX complex
3SQD 2.15 Å, Crystal structure of human PTIP BRCT5/6-gamma H2AX complex
6K1K 2.2 Å, Human nucleosome core particle with H2A.X S139E variant
2AZM 2.41 Å, Crystal structure of the MDC1 brct repeat in complex with the histone tail of gamma-H2AX
2DYP 2.5 Å, Crystal Structure of LILRB2(LIR2/ILT4/CD85d) complexed with HLA-G
3SZM 2.63 Å, Structure of human microcephalin (MCPH1) tandem brct domains in complex with a…
6K1I 2.75 Å, Human nucleosome core particle with gammaH2A.X variant
6K1J 2.85 Å, Human nucleosome core particle with H2A.X variant
9Q8X 2.94 Å, Ku70/80 bound to a 153 bp H2AX nucleosome
9MLR 3.1 Å, GammaH2AX containing nucleosome, Half-wrapped (Class 2)

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