2RJE | pdb_00002rje

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

• PDB DOI: https://doi.org/10.2210/pdb2RJE/pdb

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


• Deposited: 2007-10-14 Released: 2007-10-30 
• 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: 1.86 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

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 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 116.18 kDa 
• Atom Count: 8,709 
• Modeled Residue Count: 951 
• Deposited Residue Count: 1,015 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lethal(3)malignant brain tumor-like protein	A, B, C	331	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	D [auth P], E [auth Q]	11	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A], G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	D [auth P], E [auth Q]	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.894	α = 90
b = 124.64	β = 90
c = 90.031	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
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: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-25
  Changes: Derived calculations
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description