6XBO | pdb_00006xbo

X-ray crystal structure of the mouse CMP-Sialic acid transporter in complex with 5-methyl CMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Inhibition of CMP-sialic acid transport by endogenous 5-methyl CMP.

Ahuja, S.Cahill, J.Hartfield, K.Whorton, M.R.

(2021) PLoS One 16: e0249905-e0249905

  • DOI: https://doi.org/10.1371/journal.pone.0249905
  • Primary Citation Related Structures: 
    6XBO

  • PubMed Abstract: 

    Nucleotide-sugar transporters (NSTs) transport nucleotide-sugar conjugates into the Golgi lumen where they are then used in the synthesis of glycans. We previously reported crystal structures of a mammalian NST, the CMP-sialic acid transporter (CST) (Ahuja and Whorton 2019). These structures elucidated many aspects of substrate recognition, selectivity, and transport; however, one fundamental unaddressed question is how the transport activity of NSTs might be physiologically regulated as a means to produce the vast diversity of observed glycan structures. Here, we describe the discovery that an endogenous methylated form of cytidine monophosphate (m5CMP) binds and inhibits CST. The presence of m5CMP in cells results from the degradation of RNA that has had its cytosine bases post-transcriptionally methylated through epigenetic processes. Therefore, this work not only demonstrates that m5CMP represents a novel physiological regulator of CST, but it also establishes a link between epigenetic control of gene expression and regulation of glycosylation.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health & Science University, Portland, Oregon, United States of America.

Macromolecule Content 

  • Total Structure Weight: 41.65 kDa 
  • Atom Count: 2,841 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 330 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CMP-sialic acid transporter330Mus musculusMutation(s): 0 
Gene Names: Slc35a1
Membrane Entity: Yes 
UniProt
Find proteins for Q61420 (Mus musculus)
Explore Q61420 
Go to UniProtKB:  Q61420
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ61420
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2PE

Query on 2PE



Download:Ideal Coordinates CCD File
P [auth A],
Q [auth A]
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
5MC
(Subject of Investigation/LOI)

Query on 5MC



Download:Ideal Coordinates CCD File
B [auth A]5-METHYLCYTIDINE-5'-MONOPHOSPHATE
C10 H16 N3 O8 P
NJQONZSFUKNYOY-JXOAFFINSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.198 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.184 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.26α = 90
b = 49.4β = 107.62
c = 49.83γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM130909

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-07-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description