6MS4 | pdb_00006ms4

Crystal structure of the DENR-MCT-1 complex

• PDB DOI: https://doi.org/10.2210/pdb6MS4/pdb

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


• Deposited: 2018-10-16 Released: 2019-01-02 
• Deposition Author(s): Lomakin, I.B., Steitz, T.A., Dmitriev, S.E.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the DENR-MCT-1 complex revealed zinc-binding site essential for heterodimer formation.

Lomakin, I.B., Dmitriev, S.E., Steitz, T.A.

(2019) Proc Natl Acad Sci U S A 116: 528-533

• PubMed: 30584092 
• DOI: https://doi.org/10.1073/pnas.1809688116
• Primary Citation Related Structures: 
  6MS4


• PubMed Abstract: 
  

  The density-regulated protein (DENR) and the malignant T cell-amplified sequence 1 (MCT-1/MCTS1) oncoprotein support noncanonical translation initiation, promote translation reinitiation on a specific set of mRNAs with short upstream reading frames, and regulate ribosome recycling. DENR and MCT-1 form a heterodimer, which binds to the ribosome. We determined the crystal structure of the heterodimer formed by human MCT-1 and the N-terminal domain of DENR at 2.0-Å resolution. The structure of the heterodimer reveals atomic details of the mechanism of DENR and MCT-1 interaction. Four conserved cysteine residues of DENR (C34, C37, C44, C53) form a classical tetrahedral zinc ion-binding site, which preserves the structure of the DENR's MCT-1-binding interface that is essential for the dimerization. Substitution of all four cysteines by alanine abolished a heterodimer formation. Our findings elucidate further the mechanism of regulation of DENR-MCT-1 activities in unconventional translation initiation, reinitiation, and recycling.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114; [e-mail].
Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia.
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114.
Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114.

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: 26.7 kDa 
• Atom Count: 1,862 
• Modeled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malignant T-cell-amplified sequence 1	A	181	Homo sapiens	Mutation(s): 0  Gene Names: MCTS1, MCT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULC4 (Homo sapiens) Explore Q9ULC4  Go to UniProtKB:  Q9ULC4
PHAROS:  Q9ULC4 GTEx:  ENSG00000232119

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Density-regulated protein	B	46	Homo sapiens	Mutation(s): 1  Gene Names: DENR, DRP1, H14
UniProt & NIH Common Fund Data Resources
Find proteins for O43583 (Homo sapiens) Explore O43583  Go to UniProtKB:  O43583
PHAROS:  O43583 GTEx:  ENSG00000139726

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A], D [auth A], H [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	E [auth A], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.271 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.81	α = 90
b = 67.81	β = 90
c = 124.75	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-02 
Deposition Author(s): Lomakin, I.B., Steitz, T.A., Dmitriev, S.E.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2019-01-09
  Changes: Data collection, Database references
• Version 1.2: 2019-01-23
  Changes: Data collection, Database references
• Version 1.3: 2019-11-20
  Changes: Author supporting evidence
• Version 1.4: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary