2PQW

Crystal structure of L3MBTL1 in complex with H4K20Me2 (residues 17-25), trigonal form

• PDB DOI: https://doi.org/10.2210/pdb2PQW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-02 Released: 2007-07-31 
• Deposition Author(s): Allali-Hassani, A., Liu, Y., Herzanych, N., Ouyang, H., Mackenzie, F., Crombet, L., Loppnau, P., Kozieradzki, I., Vedadi, M., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J.R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

L3MBTL1 recognition of mono- and dimethylated histones.

Min, J., Allali-Hassani, A., Nady, N., Qi, C., Ouyang, H., Liu, Y., MacKenzie, F., Vedadi, M., Arrowsmith, C.H.

(2007) Nat Struct Mol Biol 14: 1229-1230

• PubMed: 18026117 
• DOI: https://doi.org/10.1038/nsmb1340
• Primary Citation of Related Structures:  
  2PQW, 2RJC, 2RJD, 2RJE, 2RJF


• PubMed Abstract: 
  

  Crystal structures of the L3MBTL1 MBT repeats in complex with histone H4 peptides dimethylated on Lys20 (H4K20me2) show that only the second of the three MBT repeats can bind mono- and dimethylated histone peptides. Its binding pocket has similarities to that of 53BP1 and is able to recognize the degree of histone lysine methylation. An unexpected mode of peptide-mediated dimerization suggests a possible mechanism for chromatin compaction by L3MBTL1.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, 100 College Street, Toronto, Ontario, M5G 1L5, Canada.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 38.51 kDa 
• Atom Count: 2,938 
• Modelled Residue Count: 324 
• Deposited Residue Count: 332 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal(3)malignant brain tumor-like protein	A	323	Homo sapiens	Mutation(s): 0  Gene Names: L3MBTL, KIAA0681, L3MBT
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y468 (Homo sapiens) Explore Q9Y468  Go to UniProtKB:  Q9Y468
PHAROS:  Q9Y468 GTEx:  ENSG00000185513

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	9	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.013	α = 90
b = 117.013	β = 90
c = 90.38	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-31 
Deposition Author(s): Allali-Hassani, A., Liu, Y., Herzanych, N., Ouyang, H., Mackenzie, F., Crombet, L., Loppnau, P., Kozieradzki, I., Vedadi, M., Weigelt, J., Sundstrom, M., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J.R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description