2VPG: Pygopus homolog 1

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Determined by X-ray diffraction at 1.6 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: HOMO SAPIENS
Chains: 6
Atoms: 1,759
Mol. weight: 24.77 kDa
Ligands: ZN
Released: 17 Jun 2008

Explore 2VPG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VPG contains 8 α-helices and 16 β-strands across 6 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 and C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	342	1	1
β-strand	349	1	1
β-strand	356-358	3	2
β-strand	359	1	3
β-strand	366-368	3	2
α-helix	369-372	4
α-helix	376-384	9
β-strand	388-390	3	3
α-helix	393-397	5

Chains B and D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	178-180	3	3
α-helix	182-193	12

Chains P and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pygopus homolog 1	A, C	protein	63	HOMO SAPIENS	Q9Y3Y4 (AlphaFold model)
B-cell cll/lymphoma 9 protein	B, D	protein	32	HOMO SAPIENS	O00512 (AlphaFold model)
Histone H3 tail	P, R	protein	18	HOMO SAPIENS	P68431 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2VPG_1 PYGOPUS HOMOLOG 1 (chains A, C)
GAMAVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWGCDTC
MAD

Sequence of entity 2 (B, D), FASTA

>2VPG_2 B-CELL CLL/LYMPHOMA 9 PROTEIN (chains B, D)
GAMVYVFSTEMANKAAEAVLKGQVETIVSFHI

Sequence of entity 3 (P, R), FASTA

>2VPG_3 HISTONE H3 TAIL (chains P, R)
ARTKQTARKSTGGKAPRK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Water and common crystallization additives (GOL) are not listed.

Primary citation

Decoding of Methylated Histone H3 Tail by the Pygo- Bcl9 Wnt Signaling Complex. Fiedler, M., Sanchez-Barrena, M.J., Nekrasov, M. et al. Mol Cell (2008) 30:507. DOI 10.1016/J.MOLCEL.2008.03.011 · PubMed

Other PDB entries of the same protein (UniProt Q9Y3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VPB 1.59 Å, Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
2VP7 1.65 Å, Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
2VPE 1.7 Å, Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex
2VPD 2.77 Å, Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex

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