8YDD: Nanog(R100A)

Crystal structure of Nanog(R100A) in complex with Wdr5. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Mus musculus
Chains: 5
Atoms: 8,454
Mol. weight: 118.06 kDa
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

8YDD contains 8 α-helices and 84 β-strands across 5 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, 28 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	120-126	7	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	229-233	5	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	282-287	6	7
β-strand	293-298	6	7
β-strand	304-309	6	1
β-strand	315-320	6	1
β-strand	327-331	5	1

Chain B: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	1
β-strand	48-53	6	8
β-strand	59-64	6	8
β-strand	69-73	5	8
β-strand	79-83	5	8
β-strand	90-95	6	9
β-strand	101-106	6	9
β-strand	110-115	6	9
β-strand	121-126	6	9
β-strand	132-137	6	10
β-strand	143-148	6	10
β-strand	153-157	5	10
β-strand	163-167	5	10
β-strand	174-179	6	11
β-strand	185-190	6	11
β-strand	194-199	6	11
β-strand	205-210	6	11
β-strand	217-222	6	12
β-strand	229-233	5	12
β-strand	237-242	6	12
β-strand	247-252	6	12
β-strand	264-267	4	13
β-strand	273-277	5	13
β-strand	283-287	5	13
β-strand	293-297	5	13
β-strand	304-309	6	1
β-strand	315-320	6	1
β-strand	326-331	6	1

Chain C: 0 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	14
β-strand	48-53	6	15
β-strand	59-64	6	15
β-strand	69-73	5	15
β-strand	79-83	5	15
β-strand	90-95	6	16
β-strand	101-106	6	16
β-strand	110-115	6	16
β-strand	121-126	6	16
β-strand	132-137	6	17
β-strand	143-148	6	17
β-strand	153-157	5	17
β-strand	163-167	5	17
β-strand	174-179	6	18
β-strand	185-190	6	18
β-strand	195-199	5	18
β-strand	205-209	5	18
β-strand	217-222	6	19
β-strand	228-233	6	19
β-strand	237-242	6	19
β-strand	247-252	6	19
β-strand	264-267	4	20
β-strand	273-277	5	20
β-strand	283-287	5	20
β-strand	293-297	5	20
β-strand	304-309	6	14
β-strand	315-320	6	14
β-strand	327-331	5	14

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	105-117	13
α-helix	123-132	10
α-helix	137-147	11

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	99-101	3
α-helix	105-117	13
α-helix	123-133	11
α-helix	137-148	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 5	A, B, C	protein	313	Mus musculus	P61965 (AlphaFold model)
Homeobox protein NANOG	D, E	protein	61	Mus musculus	Q80Z64 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8YDD_1 WD repeat-containing protein 5 (chains A, B, C)
SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEK
TISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQS
NLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTA
SGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYC
IFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAAL
ENDKTIKLWKSDC

Sequence of entity 2 (D, E), FASTA

>8YDD_2 Homeobox protein NANOG (chains D, E)
SKQKMATVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW
Q

Primary citation

WDR5 remodels NANOG condensates to drive transcriptional programs and sustain stem cell identity. Wang, D., Shi, X., Xie, J. et al. Nat Commun (2026). DOI 10.1038/s41467-026-68623-w · 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
2XL3 2.7 Å, WDR5 in complex with an RBBP5 peptide and histone H3 peptide

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