3PKN

Crystal structure of MLLE domain of poly(A) binding protein in complex with PAM2 motif of La-related protein 4 (LARP4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

La-Related Protein 4 Binds Poly(A), Interacts with the Poly(A)-Binding Protein MLLE Domain via a Variant PAM2w Motif, and Can Promote mRNA Stability.

Yang, R.Gaidamakov, S.A.Xie, J.Lee, J.Martino, L.Kozlov, G.Crawford, A.K.Russo, A.N.Conte, M.R.Gehring, K.Maraia, R.J.

(2011) Mol.Cell.Biol. 31: 542-556

  • DOI: 10.1128/MCB.01162-10

  • PubMed Abstract: 
  • The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interac ...

    The conserved RNA binding protein La recognizes UUU-3'OH on its small nuclear RNA ligands and stabilizes them against 3'-end-mediated decay. We report that newly described La-related protein 4 (LARP4) is a factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). Yeast two-hybrid analysis and reciprocal immunoprecipitations (IPs) from HeLa cells revealed that LARP4 interacts with RACK1, a 40S ribosome- and mRNA-associated protein. LARP4 cosediments with 40S ribosome subunits and polyribosomes, and its knockdown decreases translation. Mutagenesis of the RNA binding or PABP interaction motifs decrease LARP4 association with polysomes. Several translation and mRNA metabolism-related proteins use a PAM2 sequence containing a critical invariant phenylalanine to make direct contact with the MLLE domain of PABP, and their competition for the MLLE is thought to regulate mRNA homeostasis. Unlike all ∼150 previously analyzed PAM2 sequences, LARP4 contains a variant PAM2 (PAM2w) with tryptophan in place of the phenylalanine. Binding and nuclear magnetic resonance (NMR) studies have shown that a peptide representing LARP4 PAM2w interacts with the MLLE of PABP within the affinity range measured for other PAM2 motif peptides. A cocrystal of PABC bound to LARP4 PAM2w shows tryptophan in the pocket in PABC-MLLE otherwise occupied by phenylalanine. We present evidence that LARP4 expression stimulates luciferase reporter activity by promoting mRNA stability, as shown by mRNA decay analysis of luciferase and cellular mRNAs. We propose that LARP4 activity is integrated with other PAM2 protein activities by PABP as part of mRNA homeostasis.


    Organizational Affiliation

    31 Center Drive, Bldg. 31, Room 2A25, Bethesda, MD 20892-2426, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyadenylate-binding protein 1
A
88Homo sapiensGene Names: PABPC1 (PAB1, PABP1, PABPC2)
Find proteins for P11940 (Homo sapiens)
Go to Gene View: PABPC1
Go to UniProtKB:  P11940
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
La-related protein 4
B
14Homo sapiensGene Names: LARP4
Find proteins for Q71RC2 (Homo sapiens)
Go to Gene View: LARP4
Go to UniProtKB:  Q71RC2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.225 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 48.910α = 90.00
b = 31.384β = 104.95
c = 52.647γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance