2XL3: WDR5

WDR5 in complex with an RBBP5 peptide and histone H3 peptide. Determined by X-ray diffraction at 2.7 Å resolution. Released 4 Aug 2010.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: MUS MUSCULUS
Chains: 6
Atoms: 5,031
Mol. weight: 78.82 kDa
Released: 4 Aug 2010

Explore 2XL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XL3 contains 2 α-helices and 58 β-strands across 2 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: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	1
β-strand	48-53	6	2
β-strand	59-64	6	2
β-strand	69-73	5	2
β-strand	79-83	5	2
β-strand	90-95	6	3
β-strand	101-106	6	3
β-strand	110-115	6	3
β-strand	121-126	6	3
β-strand	132-137	6	4
β-strand	143-148	6	4
β-strand	153-157	5	4
β-strand	163-167	5	4
β-strand	174-179	6	5
β-strand	185-190	6	5
β-strand	195-199	5	5
β-strand	205-209	5	5
α-helix	215-216	2
β-strand	217-222	6	6
β-strand	228-233	6	6
β-strand	237-242	6	6
β-strand	247-252	6	6
β-strand	264-267	4	7
β-strand	273-276	4	7
β-strand	278	1	1
β-strand	283-287	5	7
β-strand	293-297	5	7
β-strand	304-309	6	1
β-strand	315-320	6	1
β-strand	327-331	5	1

Chain B: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	8
β-strand	48-53	6	9
β-strand	59-64	6	9
β-strand	69-73	5	9
β-strand	79-83	5	9
β-strand	90-95	6	10
β-strand	101-106	6	10
β-strand	111-115	5	10
β-strand	121-125	5	10
β-strand	132-137	6	11
β-strand	143-148	6	11
β-strand	153-157	5	11
β-strand	163-167	5	11
β-strand	174-179	6	12
β-strand	185-190	6	12
β-strand	195-199	5	12
β-strand	205-209	5	12
α-helix	215-216	2
β-strand	217-222	6	13
β-strand	228-233	6	13
β-strand	237-242	6	13
β-strand	247-252	6	13
β-strand	264-267	4	14
β-strand	273-276	4	14
β-strand	278	1	8
β-strand	283-287	5	14
β-strand	293-297	5	14
β-strand	304-309	6	8
β-strand	315-320	6	8
β-strand	327-331	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Wd repeat-containing protein 5	A, B	protein	334	MUS MUSCULUS	P61965 (AlphaFold model)
Retinoblastoma-binding protein 5	C, E	protein	14	MUS MUSCULUS	Q8BX09 (AlphaFold model)
Histone H3.1	D, F	protein	9	MUS MUSCULUS	P68433 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2XL3_1 WD REPEAT-CONTAINING PROTEIN 5 (chains A, B)
MATEEKKPETEAARAQPTPSSSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWL
ASSSADKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGK
CLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKL
WDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGH
TDVVISTACHPTENIIASAALENDKTIKLWKSDC

Sequence of entity 2 (C, E), FASTA

>2XL3_2 RETINOBLASTOMA-BINDING PROTEIN 5 (chains C, E)
YAAEDEEVDVTSVD

Sequence of entity 3 (D, F), FASTA

>2XL3_3 HISTONE H3.1 (chains D, F)
ARTKQTARY

Primary citation

Characterisation of a Novel Wdr5 Binding Site that Recruits Rbbp5 Through a Conserved Motif and Enhances Methylation of H3K4 by Mll1. Odho, Z., Southall, S.M., Wilson, J.R. J Biol Chem (2010) 285:32967. DOI 10.1074/JBC.M110.159921 · PubMed

Other PDB entries of the same protein (UniProt P61965 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OK1 1.38 Å, WD repeat containing protein 5 (WDR5)- N225A mutant
9SLO 1.7 Å, WD repeat containing protein 5 (WDR5)- PER1 peptide
8OKF 1.85 Å, WD repeat containing protein 5 (WDR5)- PER2 peptide
2XL2 2.4 Å, WDR5 in complex with an RBBP5 peptide recruited to novel site
8YDD 2.5 Å, Crystal structure of Nanog(R100A) in complex with Wdr5

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