Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.11 kDa 
• Atom Count: 536 
• Modelled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

1NEM

Saccharide-RNA recognition in the neomycin B / RNA aptamer complex

• PDB DOI: 10.2210/pdb1NEM/pdb
• NDB: 1NEM

• Classification: RNA
• Mutation(s): No 


• Deposited: 1999-03-15 Released: 1999-08-31 
• Deposition Author(s): Jiang, L., Majumdar, A., Hu, W., Jaishree, T.J., Xu, W., Patel, D.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 9 
• Selection Criteria: LEAST RESTRAINT VIOLATION 

Literature

Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer

Jiang, L., Majumdar, A., Hu, W., Jaishree, T.J., Xu, W., Patel, D.J.

(1999) Structure 7: 817-827

• PubMed: 10425683 
• DOI: 10.1016/s0969-2126(99)80105-1
• Primary Citation of Related Structures:  
  1NEM


• PubMed Abstract: 
  

Aminoglycoside antibiotics can target RNA folds with micromolar affinity and inhibit biological processes ranging from protein biosynthesis to ribozyme action and viral replication. Specific features of aminoglycoside antibiotic-RNA recognition have been probed using chemical, biochemical, spectroscopic and computational approaches on both natural RNA targets and RNA aptamers identified through in vitro selection. Our previous studies on tobramycin-RNA aptamer complexes are extended to neomycin B bound to its selected RNA aptamer with 100 nM affinity.

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Organizational Affiliation: 

Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*AP*CP*UP*GP*GP*GP*CP*GP*AP*GP*AP*AP*GP*UP*UP*UP*AP*GP*UP*CP*C)-3'	A	23	N/A

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2,6-diamino-2,6-dideoxy-beta-L-idopyranose-(1-3)-beta-D-ribofuranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G38023GV GlyCosmos:  G38023GV

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BDG	C [auth A]	2,6-diamino-2,6-dideoxy-alpha-D-glucopyranose C6 H14 N2 O4 SQTHUUHOUPJYLK-UKFBFLRUSA-N
NEB	D [auth A]	2-DEOXY-D-STREPTAMINE C6 H15 N2 O3 DTFAJAKTSMLKAT-JDCCYXBGSA-O

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 9 
• Selection Criteria: LEAST RESTRAINT VIOLATION 
• OLDERADO: 1NEM Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-03-15 
• Released Date: 1999-08-31 
Deposition Author(s): Jiang, L., Majumdar, A., Hu, W., Jaishree, T.J., Xu, W., Patel, D.J.

Revision History  

• Version 1.0: 1999-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary