PDB 4rzd structure summary ‹ Protein Data Bank in Europe (PDBe)

X-ray diffraction

2.75Å resolution

Crystal Structure of a PreQ1 Riboswitch

Released: 01 Jul 2015

DOI: 10.2210/pdb4rzd/pdb

Source organism: Faecalibacterium prausnitzii

Primary publication:
Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.

Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE

Proc Natl Acad Sci U S A 112 E3485-94 (2015)

PMID: 26106162

Function and Biology Details

Biochemical function:

not assigned

Biological process:

not assigned

Cellular component:

not assigned

Sequence domain:

PreQ1-III riboswitch

Structure analysis Details

Assembly composition:

monomeric (preferred)

Assembly name:

PreQ1-III riboswitch (preferred)

PDBe Complex ID:

PDB-CPX-195940 (preferred)

Entry contents:

1 distinct RNA molecule

Macromolecule:

PreQ1-III Riboswitch (Class 3) Chain: A

Molecule details ›

Chain: A
Length: 101 nucleotides
Theoretical weight: 32.64 KDa
Source organism: Faecalibacterium prausnitzii
Sequence domains: PreQ1-III riboswitch

Ligands and Environments

1 bound ligand:

1 modified residue:

Experiments and Validation Details

X-ray source: SSRL BEAMLINE BL11-1

Spacegroup: P6₅22

Unit cell:

a: 84.083Å b: 84.083Å c: 278.365Å

α: 90° β: 90° γ: 120°

R-values:

R R_work R_free

0.214 0.212 0.228

Quick links

View

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
Assembly composition XML
FASTA (Entry)
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)

4rzd @ RCSB
4rzd @ PDBj
4rzd @ PDBSum
4rzd @ Proteopedia

Downloads

Archive mmCIF file
Updated mmCIF file
PDB file
PDB header
PDB file (gz)
PDBML
PDBML (ATOM lines)
PDBML (no atoms)
Structure Factors
EDS map
EDS difference map
Assembly composition XML
Assembly 1 (mmCIF; gz)
Assembly 1 (atom only; mmCIF)
FASTA (Entry)
Summary report (PDF)
Full report (PDF)
Percentile plot (PNG)
Percentile plot (SVG)
Validation data (XML)

3D Visualisation

Citations

7 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Šponer et al. (2018)

6 more

9 mentions without citation

Long-Range Interactions in Riboswitch Control of Gene Expression.

Jones et al. (2017)

8 more

PDBe › 4rzd