8HIB: Pygo2-LDB1-SSBP2 triple complex

The crystal structure of Pygo2-LDB1-SSBP2 triple complex. Determined by X-ray diffraction at 2.45 Å resolution. Released 22 Nov 2023.

Method: X-ray diffraction
Resolution: 2.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,298
Mol. weight: 51.99 kDa
Released: 22 Nov 2023

Explore 8HIB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8HIB contains 19 α-helices and 9 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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	12-14	3
α-helix	15-32	18
α-helix	36-45	10
α-helix	60-73	14
α-helix	86-92	7

Chain B: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	15-32	18
α-helix	36-45	10
β-strand	52-53	2	2
α-helix	60-74	15

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	62-64	3
β-strand	72-73	2	2

Chain V: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	67-78	12
α-helix	87-97	11
β-strand	98-108	11	1
β-strand	115-120	6	1
α-helix	121-123	3
α-helix	124-133	10
β-strand	136-144	9	1
α-helix	146	1
β-strand	147-150	4	1
β-strand	154-168	15	1
β-strand	175-187	13	1
β-strand	194-207	14	1
α-helix	210-215	6
α-helix	220-223	4
α-helix	237-249	13
α-helix	252-261	10
α-helix	266-279	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
LIM domain-binding protein 1	V	protein	230	Homo sapiens	Q86U70 (AlphaFold model)
Single-stranded DNA-binding protein 2	A, B	protein	94	Homo sapiens	P81877 (AlphaFold model)
Pygopus homolog 2	D	protein	27	Homo sapiens	Q9BRQ0 (AlphaFold model)

Sequence of entity 1 (V), FASTA

>8HIB_1 LIM domain-binding protein 1 (chains V)
GIGRHTPYGNQTDYRIFELNKRLQNWTEECDNLWWDAFTTEFFEDDAMLTITFCLEDGPK
RYTIGRTLIPRYFRSIFEGGATELYYVLKHPKEAFHSNFVSLDCDQGSMVTQHGKPMFTQ
VCVEGRLYLEFMFDDMMRIKTWHFSIRQHRELIPRSILAMHAQDPQMLDQLSKNITRCGL
SNSTLNYLRLCVILEPMQELMSRHKTYSLSPRDCLKTCLFQKWQRMVAPP

Sequence of entity 2 (A, B), FASTA

>8HIB_2 Single-stranded DNA-binding protein 2 (chains A, B)
MYGKGKSNSSAVPSDSQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGF
LHSWWCVFWDLYCAAPERRETCEHSSEAKAFHDY

Sequence of entity 3 (D), FASTA

>8HIB_3 Pygopus homolog 2 (chains D)
YTEFAPPPTPMVDHLVASNPFEDDFGA

Primary citation

Structural basis of the interaction between BCL9-Pygo and LDB-SSBP complexes in assembling the Wnt enhanceosome. Wang, H., Bienz, M., Yan, X.X. et al. Nat Commun (2023) 14:3702-3702. DOI 10.1038/s41467-023-39439-9 · PubMed

Other PDB entries of the same protein (UniProt Q86U70 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7OB5 1.8 Å, Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide
7OB8 1.8 Å, Crystal structure of 14-3-3 sigma in complex with LDB1 phosphopeptide and stabilizer…
9F5B 1.8 Å, Identification of zinc ions in LMO4.
2XJY 2.4 Å, Crystal structure of the LMO2:LDB1-LID complex, P21 crystal form
2XJZ 2.8 Å, Crystal structure of the LMO2:LDB1-LID complex, C2 crystal form
2YPA 2.8 Å, Structure of the SCL:E47:LMO2:LDB1 complex bound to DNA
6TYD 2.8 Å, Structure of human LDB1 in complex with SSBP2
8SSU 2.89 Å, ZnFs 3-11 of CCCTC-binding factor (CTCF) Complexed with 19mer DNA

Browse structure collections

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