3K1V

Cocrystal structure of a mutant class-I preQ1 riboswitch

PDB DOI: https://doi.org/10.2210/pdb3K1V/pdb
Entry: 3K1V supersedes: 3FU4
NAKB: 3K1V

Classification: RNA
Mutation(s): No

Deposited: 2009-09-28 Released: 2009-10-06
Deposition Author(s): Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.269
R-Value Work: 0.230
R-Value Observed: 0.230

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Ligand Structure Quality Assessment

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

Literature

Cocrystal Structure of a Class I Preq1 Riboswitch Reveals a Pseudoknot Recognizing an Essential Hypermodified Nucleobase

Klein, D.J., Edwards, T.E., Ferre-D'Amare, A.R.

(2009) Nat Struct Mol Biol 16: 343

PubMed: 19234468 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb.1563
Primary Citation of Related Structures:
3FU2, 3K1V

PubMed Abstract:
Riboswitches are mRNA domains that bind metabolites and modulate gene expression in cis. We report cocrystal structures of a remarkably compact riboswitch (34 nucleotides suffice for ligand recognition) from Bacillus subtilis that is selective for the essential nucleobase preQ(1) (7-aminomethyl-7-deazaguanine). The structures reveal a previously unrecognized pseudoknot fold and suggest a conserved gene-regulatory mechanism whereby ligand binding promotes sequestration of an RNA segment that otherwise assembles into a transcriptional antiterminator.

Organizational Affiliation

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109-1024, USA.

Macromolecule Content

Total Structure Weight: 11.18 kDa
Atom Count: 693
Modelled Residue Count: 30
Deposited Residue Count: 34
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
PreQ1 riboswitch	A	34	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRF Query on PRF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	7-DEAZA-7-AMINOMETHYL-GUANINE C₇ H₉ N₅ O MEYMBLGOKYDGLZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.269
R-Value Work: 0.230
R-Value Observed: 0.230
Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.81	α = 90
b = 76.81	β = 90
c = 85.9	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Klein, D.J.

Edwards, T.E.

Ferre-D'Amare, A.R.

This entry supersedes: 3FU4

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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