Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.06 kDa 
• Atom Count: 2208 
• Modelled Residue Count: 246 
• Deposited Residue Count: 246 
• Unique protein chains: 1

4EMR

Crystal Structure determination of type1 ribosome inactivating protein complexed with 7-methylguanosine-triphosphate at 1.75A

• DOI: 10.2210/pdb4EMR/pdb

• Classification: HYDROLASE
• Organism(s): Momordica balsamina
• Mutation(s): No 


• Deposited: 2012-04-12 Released: 2012-05-02 
• Deposition Author(s): Kumar, M., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 

Literature

First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina.

Kushwaha, G.S., Yamini, S., Kumar, M., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

(2013) Proteins 81: 896-905

• PubMed: 23280611 
• DOI: 10.1002/prot.24248
• Primary Citation of Related Structures:  
  4I47, 4EMR, 4EMF


• PubMed Abstract: 
  

This is the first structural evidence of recognition of mRNA cap structures by a ribosome inactivating protein. It is well known that a unique cap structure is formed at the 5' end of mRNA for carrying out various processes including mRNA maturation, translation initiation, and RNA turnover. The binding studies and crystal structure determinations of type 1 ribosome inactivating protein (RIP-1) from Momordica balsamina (MbRIP-1) were carried out with mRNA cap structures including (i) N7-methyl guanine (m7G), (ii) N7-methyl guanosine diphosphate (m7GDP), and (iii) N7-methyl guanosine triphosphate (m7GTP). These compounds showed affinities to MbRIP-1 at nanomolar concentrations. The structure determinations of the complexes of MbRIP-1 with m7G, m7GDP, and m7GTP at 2.65, 1.77, and 1.75 Å resolutions revealed that all the three compounds bound to MbRIP-1 in the substrate binding site at the positions which are slightly shifted towards Glu85 as compared to those of rRNA substrates. In this position, Glu85 forms several hydrogen bonds with guanine moiety while N-7 methyl group forms van der Waals contacts. However, the guanine rings are poorly stacked in these complexes. Thus, the mode of binding by MbRIP-1 to mRNA cap structures is different which results in the inhibition of depurination. Since some viruses are known to exploit the capping property of the host, this action of MbRIP-1 may have implications for the antiviral activity of this protein in vivo. The understanding of the mode of binding of MbRIP-1 to cap structures may also assist in the design of anti-viral agents.

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Organizational Affiliation: 

Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
rRNA N-glycosidase	A	246	Momordica balsamina	Mutation(s): 0  Gene Names: RIP EC: 3.2.2.22
Find proteins for D9J2T9 (Momordica balsamina) Explore D9J2T9  Go to UniProtKB:  D9J2T9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGP	A	7-METHYL-GUANOSINE-5'-TRIPHOSPHATE C11 H19 N5 O14 P3 DKVRNHPCAOHRSI-KQYNXXCUSA-O

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MGP	Kd :  32.099998474121094   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.251 
• R-Value Work: 0.205 
• R-Value Observed: 0.208 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.065	α = 90
b = 130.065	β = 90
c = 40.277	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-12 
• Released Date: 2012-05-02 
Deposition Author(s): Kumar, M., Kushwaha, G.S., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2013-05-15
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary