1A1T

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES

• PDB DOI:  https://doi.org/10.2210/pdb1A1T/pdb
• NAKB: 1A1T

• Classification: Viral protein/RNA
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-15 Released: 1998-06-17 
• Deposition Author(s): De Guzman, R.N., Wu, Z.R., Stalling, C.C., Pappalardo, L., Borer, P.N., Summers, M.F.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 800 
• Conformers Submitted: 25 
• Selection Criteria: LEAST TOTAL PENALTY 

Literature

Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.

De Guzman, R.N., Wu, Z.R., Stalling, C.C., Pappalardo, L., Borer, P.N., Summers, M.F.

(1998) Science 279: 384-388

• PubMed: 9430589 
• DOI: https://doi.org/10.1126/science.279.5349.384
• Primary Citation of Related Structures:  
  1A1T


• PubMed Abstract: 
  

The three-dimensional structure of the human immunodeficiency virus-type 1 (HIV-1) nucleocapsid protein (NC) bound to the SL3 stem-loop recognition element of the genomic Psi RNA packaging signal has been determined by heteronuclear magnetic resonance spectroscopy. Tight binding (dissociation constant, approximately 100 nM) is mediated by specific interactions between the amino- and carboxyl-terminal CCHC-type zinc knuckles of the NC protein and the G7 and G9 nucleotide bases, respectively, of the G6-G7-A8-G9 RNA tetraloop. A8 packs against the amino-terminal knuckle and forms a hydrogen bond with conserved Arg32, and residues Lys3 to Arg10 of NC form a 310 helix that binds to the major groove of the RNA stem and also packs against the amino-terminal zinc knuckle. The structure provides insights into the mechanism of viral genome recognition, explains extensive amino acid conservation within NC, and serves as a basis for the development of inhibitors designed to interfere with genome encapsidation.

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Organizational Affiliation: 

Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland-Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13 kDa 
• Atom Count: 873 
• Modelled Residue Count: 75 
• Deposited Residue Count: 75 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEOCAPSID PROTEIN	B [auth A]	55	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: NC, gag
UniProt
Find proteins for Q75677 (Human immunodeficiency virus 1) Explore Q75677  Go to UniProtKB:  Q75677

Entity ID: 1
Molecule	Chains	Length	Organism	Image
SL3 STEM-LOOP RNA	A [auth B]	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 800 
• Conformers Submitted: 25 
• Selection Criteria: LEAST TOTAL PENALTY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-06-17 
Deposition Author(s): De Guzman, R.N., Wu, Z.R., Stalling, C.C., Pappalardo, L., Borer, P.N., Summers, M.F.

Revision History  

• Version 1.0: 1998-06-17
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-16
  Changes: Data collection, Database references, Derived calculations, Other