5MKI

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode.

Lekontseva, N.Mikhailina, A.Fando, M.Kravchenko, O.Balobanov, V.Tishchenko, S.Nikulin, A.

(2020) Biochimie 175: 1-12

  • DOI: https://doi.org/10.1016/j.biochi.2020.05.001
  • Primary Citation of Related Structures:  
    5MKI, 5MKL

  • PubMed Abstract: 

    Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.


  • Organizational Affiliation

    Institute of Protein Research Russian Academy of Sciences, Institutskaya 4, Moscow Region, Pushchino, 142290, Russia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Like-Sm ribonucleoprotein core
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
72Methanococcus vannielii SBMutation(s): 0 
Gene Names: Mevan_0470
UniProt
Find proteins for A6UPF5 (Methanococcus vannielii (strain ATCC 35089 / DSM 1224 / JCM 13029 / OCM 148 / SB))
Explore A6UPF5 
Go to UniProtKB:  A6UPF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6UPF5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
Y [auth M]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
O [auth C]
P [auth D]
Q [auth E]
R [auth F]
S [auth G]
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth I],
U [auth J],
V [auth K],
W [auth L],
X [auth M]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.671α = 90
b = 114.221β = 113.7
c = 71.993γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Scientific FoundationRussian Federation14-14-00496

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2021-03-03
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description