WDR5 and RBBP5: the second arm of the WRAD hub, RBBP5 V375-D376-V377 into the same propeller face, co-crystallised with the MLL1 WIN peptide in one structure
also called RBBP5 VDV motif · WDR5-RbBP5 interface · 3P4F
WDR5 holds two things at once: the KMT2A enzyme on one side and a partner called RBBP5 on the other, and a single crystal shows both grips together. The fusion protein is not in that picture at all.
The same thing, for a scientist
PDB 3P4F (2.35 A) is a ternary crystal of WDR5 with an RBBP5 peptide and an MLL1 WIN peptide. The deposited RBBP5 entity is EDEEVDVTSVY, which aligns uniquely to Q15291 residues 371-381 against the fetched UniProt sequence, placing the hydrophobic V-D-V triad at V375-D376-V377; the deposited MLL1 entity HGAARAEVHL aligns to Q03164 3761-3770 and carries an S3763A substitution. The structure is the assembly logic of WRAD in one picture: WDR5 is a two-sided adaptor, bridging the MLL1 WIN motif to RBBP5, and RBBP5 in turn reaches ASH2L. Every contact in this chain lies C-terminal to the KMT2A breakpoint cluster region or on a subunit the fusion never touches, so the whole module is wild-type-allele biology in a KMT2A-rearranged cell.
Residues, checked not recalled
RBBP5 (Q15291): deposited peptide EDEEVDVTSVY = residues 371-381, with the buried V-D-V at V375, D376, V377. This alignment was computed in this cycle against the UniProt Q15291 sequence fetched the same day 3.
WDR5 (P61964): the same beta-propeller that receives the MLL1 WIN arginine on its other face. 3P4F contains all three chains, so it is the only deposit in which the MLL1 and RBBP5 grips on WDR5 can be compared side by side 3.
KMT2A (Q03164): WIN peptide 3761-3770 with S3763A - a substituted peptide, which matters if anyone models this interface.
What this contributes that the graph did not have
The graph holds subunit-level entries for WDR5 and RBBP5 and an entry for the WIN motif's loss, but no entry states where on RBBP5 the contact sits. It does now: 371-381, V375/D376/V377. The unresolved half is affinity - the primary paper is not open access and no Kd for the WDR5-RBBP5 pair was recoverable from any of the four routes this cycle, so this interface is recorded with structure and no number.
And in the assembled complex
Three independent cryo-EM reconstructions of the MLL1 core complex on a nucleosome - 6KIU/6KIZ, 6PWV and 7UD5 - contain WDR5, RBBP5, ASH2L, DPY30 and an MLL1 fragment together 456. The MLL1 entity in 6PWV is a 209-residue C-terminal fragment and in 7UD5 a 226-residue fragment annotated to a KMT2A cDNA clone. None of these structures contains any part of KMT2A N-terminal to the breakpoint cluster region, which is the whole of what a der(11) fusion retains. The best structural biology in this field is entirely about the half of the protein the fusion throws away.
| partner a | gene-wdr5 |
|---|---|
| partner b | gene-rbbp5 |
| motif b | RBBP5 371-381, hydrophobic V-D-V triad at V375-D376-V377 |
| motif a | WDR5 WD40 beta-propeller, the face opposite the MLL1 WIN channel |
| kd status | no dissociation constant recovered; the primary structural paper (PMID 21220120) has no PMCID and was unreadable by all four routes in this cycle |
| fate in fusion | contextually lost - RBBP5 and WDR5 are intact proteins in the cell, but the KMT2A element that recruits them (the WIN motif) is absent from every der(11) fusion, so the module is wild-type-allele biology |
| druggability | a shallow peptide-in-groove contact with no reported chemical matter; the tractable member of this module is the WDR5 WIN channel, which is a different surface |
| resolution note | all PDB metadata and entity sequences fetched from data.rcsb.org 2026-09-20; RBBP5 and KMT2A residue spans derived by alignment to UniProt Q15291 and Q03164 fetched the same day |
| minimal activating unit | a minimised RBBP5-ASH2L heterodimer, which activates all MLL-family methyltransferases (PMID 26886794); the crystallised MLL1 SET constructs carry activating N3861I/Q3867L substitutions |
interface residues b
[ "RBBP5 V375", "RBBP5 D376", "RBBP5 V377" ]
kd measurements
[]
structures
[ "3P4F", "6PWV", "6KIU", "6KIZ", "7UD5", "6W5I" ]
structure details — the numbers behind the chart
[
{
"pdb": "3P4F",
"title_fetched": "Structural and biochemical insights into MLL1 core complex assembly and regulation.",
"method": "X-ray",
"resolution_A": 2.35,
"contents": "WDR5 317-mer + RBBP5 11-mer (Q15291 371-381) + MLL1 10-mer (Q03164 3761-3770, S3763A)",
"fetched": "2026-09-20"
},
{
"pdb": "6PWV",
"title_fetched": "Cryo-EM structure of MLL1 core complex bound to the nucleosome",
"method": "EM",
"resolution_A": 6.2,
"contents": "RBBP5 + WDR5 + ASH2L + DPY30 + KMT2A 209-mer + histone octamer + 147-bp DNA",
"fetched": "2026-09-20"
},
{
"pdb": "7UD5",
"title_fetched": "Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome",
"method": "EM",
"resolution_A": 4.25,
"contents": "MLL1 fragment annotated to cDNA clone B4DIJ7, WDR5, ASH2L, RBBP5, DPY30, ubiquitin, nucleosome",
"fetched": "2026-09-20"
},
{
"pdb": "6KIZ",
"title_fetched": "Cryo-EM structure of human MLL1-NCP complex, binding mode2",
"method": "EM",
"resolution_A": 4.5,
"fetched": "2026-09-20"
},
{
"pdb": "5F6L",
"title_fetched": "The crystal structure of MLL1 (N3861I/Q3867L) in complex with RbBP5 and Ash2L",
"method": "X-ray",
"resolution_A": null,
"contents": "MLL1 SET-domain construct carrying activating mutations, with RBBP5 and ASH2L",
"fetched": "2026-09-20"
}
]- Target mismatch: the module is assembled on a KMT2A element the fusion does not contain, so disrupting it is a wild-type-allele intervention.
- Essential function: WDR5, RBBP5 and ASH2L are shared across all six SET1-family complexes, so a disruptor of this assembly removes H3K4 methylation broadly, not selectively.
- Delivery: the contact is a short peptide in a shallow groove with no chemical matter reported, which is the least tractable class of protein-protein interface.
- Modelling error: 3P4F's MLL1 peptide carries an S3763A substitution and 7UD5's MLL1 chain is annotated to a cDNA clone rather than Q03164, so residue indices taken straight off these deposits will be wrong.
- What is the WDR5-RBBP5 dissociation constant? The primary paper is closed and no number is recoverable; this is a one-experiment gap.
- Do WIN-site inhibitors displace RBBP5 from WDR5 as well as MLL1, given that both grips are on the same propeller?
- Does any cryo-EM reconstruction exist that contains both the KMT2A N-terminal fragment and the WRAD module? As of this cycle none does, in any deposit.
- E1strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
MLL1 core complex assembly proceeds through WDR5 as a two-sided adaptor bridging the MLL1 WIN motif and RBBP5.
Structural and biochemical insights into MLL1 core complex assembly. · Avdic V, Zhang P, Lanouette S, et al. · Structure 2011What this evidence cannot show
The primary paper has no PMCID and was not retrievable by any of the four routes in this cycle (EPMC core returns no pmcid), so this claim is supported by the deposited structure and the abstract-level title rather than by a read of the full text. No affinity is recorded here for that reason.
Evidence that argues against this (1)
- The later cryo-EM reconstructions show the complex adopts multiple states on the nucleosome, so a single crystal of isolated peptides describes connectivity rather than the working geometry. Rahman S et al. 2022
- E2strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
RBBP5 contacts ASH2L through a D/E box carrying Ser350, and phosphorylation of S350 raises RbBP5 344-357 affinity for the ASH2L SPRY domain 15-fold by ITC; S350A abolishes ASH2L co-immunoprecipitation.
A phosphorylation switch on RbBP5 regulates histone H3 Lys4 methylation. · Zhang P, Chaturvedi CP, Tremblay V, et al. · Genes Dev 2015What this evidence cannot show
The 15-fold figure is a fold-change reported from ITC without an absolute Kd in the accessible text; the co-IP is from ectopically expressed Flag-RbBP5.
Evidence that argues against this (1)
- The authors themselves note S350 makes no significant direct contact with ASH2L in the structure, so the effect is attributed to the added phosphate rather than to the serine, and the unphosphorylated interface is correspondingly weak. Zhang P et al. 2015
- E3established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.database
PDB 3P4F is a 2.35 A ternary crystal containing WDR5, an RBBP5 peptide mapping to Q15291 371-381 and an MLL1 WIN peptide mapping to Q03164 3761-3770.
PDB 3P4F: Structural and biochemical insights into MLL1 core complex assembly and regulation. · Avdic V, Zhang P, Lanouette S, et al. · RCSB Protein Data Bank 2011What this evidence cannot show
Entry title, method, resolution and all three polymer entity sequences fetched from data.rcsb.org on 2026-09-20; residue spans derived by aligning those sequences to UniProt sequences fetched the same day. The MLL1 peptide is not wild-type: it carries S3763A.
Evidence that argues against this (1)
- Peptide co-crystals of an assembly hub can capture a contact that is transient in the intact complex; the cryo-EM structures place RBBP5 and WDR5 in a larger arrangement that a three-peptide crystal cannot report. Park SH et al. 2019
- E4established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
Cryo-EM structures of the human MLL1 core complex bound to the nucleosome contain WDR5, RBBP5, ASH2L, DPY30 and only a C-terminal MLL1 fragment.
Cryo-EM structure of the human MLL1 core complex bound to the nucleosome. · Park SH, Ayoub A, Lee YT, et al. · Nat Commun 2019What this evidence cannot show
6.2 A for 6PWV; the MLL1 entity is a 209-residue fragment, so nothing can be said from it about the N-terminal 3,700 residues.
Evidence that argues against this (1)
- The Xue et al. reconstructions of the same assembly reach 4.5 A in one binding mode and describe two distinct nucleosome-binding modes, so a single reconstruction is not the geometry. Xue H et al. 2019
- E5established confidence 5 of 5: Multiple independent lines of evidence; treated as settled in the field.paper
An independent cryo-EM study resolves MLL1-WRAD on the nucleosome in multiple states, at 4.25 A for the H2B-ubiquitinated complex.
Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. · Rahman S, Hoffmann NA, Worden EJ, et al. · Proc Natl Acad Sci U S A 2022What this evidence cannot show
Fetched resolution 4.25 A for PDB 7UD5; the MLL1 entity is annotated to the cDNA clone B4DIJ7 rather than to Q03164, which is a numbering trap for anyone reading residue indices straight off the deposit.
Evidence that argues against this (1)
- The DPY30 and ASH2L intrinsically disordered regions modulate activity on chromatin and are largely invisible in these reconstructions, so the resolved density is a lower bound on the functional interface. Lee YT et al. 2021
- E6strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
MLL methyltransferase complexes engage the nucleosome in more than one binding mode.
Structural basis of nucleosome recognition and modification by MLL methyltransferases. · Xue H, Yao T, Cao M, et al. · Nature 2019What this evidence cannot show
Cryo-EM at 4.5 A for the mode-2 reconstruction (6KIZ); mode assignment is a modelling conclusion.
Evidence that argues against this (1)
- None of these structures includes the KMT2A N-terminal fragment, so multistate behaviour of the WRAD module has no demonstrated bearing on a fusion protein that lacks the module entirely. Park SH et al. 2019
- E7strong confidence 4 of 5: Replicated in peer-reviewed work by more than one group.paper
A minimised RBBP5-ASH2L heterodimer is the structural unit that interacts with and activates all MLL-family histone methyltransferases, shown by crystal structures of MLL1 SET-domain constructs with RBBP5 and ASH2L.
Structural basis for activity regulation of MLL family methyltransferases. · Li Y, Han J, Zhang Y, et al. · Nature 2016What this evidence cannot show
The crystallised MLL1 constructs carry activating substitutions (N3861I/Q3867L) introduced to make the complex tractable, so the structures are of an engineered, hyperactive SET domain rather than wild type. The claim is explicitly family-level, i.e. it is not MLL1-specific.
Evidence that argues against this (1)
- Because the RBBP5-ASH2L unit activates ALL MLL-family methyltransferases, disrupting it is a pan-SET1-family intervention with no route to MLL1 selectivity - which is the same objection that applies to the WDR5 WIN site. Li Y et al. 2016
RBBP5 V375-D376-V377 on the WDR5 propeller
RBBP5 371-381
the two grips share one propeller and are co-crystallised in 3P4F
structural coordinates for the wild-type side of that distinction
no deposit contains both the KMT2A N-terminal fragment and WRAD
the other end of RBBP5; together they chain WDR5 to ASH2L