3C3Z | pdb_00003c3z

Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to ribostamycin

PDB DOI: https://doi.org/10.2210/pdb3C3Z/pdb
NAKB: 3C3Z

Classification: RNA
Mutation(s): No

Deposited: 2008-01-29 Released: 2008-05-06
Deposition Author(s): Freisz, S., Lang, K., Micura, R., Dumas, P., Ennifar, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.227 (Depositor), 0.236 (DCC)
R-Value Work:
0.221 (Depositor), 0.234 (DCC)
R-Value Observed:
0.221 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3C3Z

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site.

Freisz, S., Lang, K., Micura, R., Dumas, P., Ennifar, E.

(2008) Angew Chem Int Ed Engl 47: 4110-4113

PubMed: 18435520 Search on PubMed
DOI: https://doi.org/10.1002/anie.200800726
Primary Citation Related Structures:
2QEK, 3C3Z, 3C44, 3C5D, 3C7R

Organizational Affiliation

Architecture et Réactivité de l'ARN, Université Louis Pasteur/CNRS UPR 9002, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg, France.

Macromolecule Content

Total Structure Weight: 15.84 kDa
Atom Count: 1,206
Modeled Residue Count: 46
Deposited Residue Count: 46
Unique hybrid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
HIV-1 subtype F genomic RNA	A, B	23	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIO Query on RIO Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	RIBOSTAMYCIN C₁₇ H₃₄ N₄ O₁₀ NSKGQURZWSPSBC-VVPCINPTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.227 (Depositor), 0.236 (DCC)
R-Value Work: 0.221 (Depositor), 0.234 (DCC)
R-Value Observed: 0.221 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.67	α = 90
b = 30.53	β = 121.31
c = 57.68	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DNA	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-05-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-05-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.