2VPD: Pygopus homolog 1

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Determined by X-ray diffraction at 2.77 Å resolution. Released 17 Jun 2008.

Method: X-ray diffraction
Resolution: 2.77 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 1,473
Mol. weight: 22.24 kDa
Ligands: ZN
Released: 17 Jun 2008

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

Secondary structure: helices and β-sheets

2VPD contains 9 α-helices and 14 β-strands across 4 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.

Chain A: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	342	1	1
β-strand	349	1	1
β-strand	356-358	3	2
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

Chain B: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	173-180	8	3
α-helix	182-193	12

Chain C: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	338-340	3
β-strand	341-342	2	4
β-strand	343	1	5
β-strand	349-350	2	4
β-strand	356-358	3	5
β-strand	359	1	3
β-strand	366-368	3	5
α-helix	369-372	4
α-helix	376-384	9
β-strand	388-390	3	3
α-helix	393-396	4

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	172-180	9	3
α-helix	182-193	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pygopus homolog 1	A, C	protein	67	HOMO SAPIENS	Q9Y3Y4 (AlphaFold model)
B-cell cll/lymphoma 9 protein	B, D	protein	35	HOMO SAPIENS	O00512 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2VPD_1 PYGOPUS HOMOLOG 1 (chains A, C)
MGHSSSDPVYPCGICTNEVNDDQDAILCEASCQKWFHRICTGMTETAYGLLTAEASAVWG
CDTCMAD

Sequence of entity 2 (B, D), FASTA

>2VPD_2 B-CELL CLL/LYMPHOMA 9 PROTEIN (chains B, D)
AMAAKVVYVFSTEMANKAAEAVLKGQVETIVSFHI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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
2VPG 1.6 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

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