9G4A | pdb_00009g4a

Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide

• PDB DOI: https://doi.org/10.2210/pdb9G4A/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-07-15 Released: 2025-07-30 
• Deposition Author(s): Mechaly, A.E., Michail, C., Haouz, A., Rodrigues-Lima, F.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.241 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide

Mechaly, A.E., Michail, C., Haouz, A., Rodrigues-Lima, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2,357 
• Modeled Residue Count: 263 
• Deposited Residue Count: 310 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-lysine N-methyltransferase SETD2	A	295	Homo sapiens	Mutation(s): 1  Gene Names: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069 EC: 2.1.1.359 (PDB Primary Data), 2.1.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYW2 (Homo sapiens) Explore Q9BYW2  Go to UniProtKB:  Q9BYW2
PHAROS:  Q9BYW2 GTEx:  ENSG00000181555

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	B	15	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	F [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.241 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.835	α = 90
b = 76.633	β = 90
c = 77.055	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data reduction
XDS	data reduction
autoPROC	data scaling
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Mechaly, A.E., Michail, C., Haouz, A., Rodrigues-Lima, F.

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Funding Organization	Location	Grant Number
Other government	France	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release