6CK5 | pdb_00006ck5

PRPP riboswitch from T. mathranii bound to PRPP

PDB DOI: https://doi.org/10.2210/pdb6CK5/pdb
NAKB: 6CK5

Classification: RNA
Organism(s): Thermoanaerobacter mathranii
Mutation(s): No

Deposited: 2018-02-27 Released: 2018-06-20
Deposition Author(s): Knappenberger, A.J., Reiss, C.W., Strobel, S.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.

Knappenberger, A.J., Reiss, C.W., Strobel, S.A.

(2018) Elife 7

PubMed: 29877798 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.36381
Primary Citation Related Structures:
6CK4, 6CK5

PubMed Abstract:
Two classes of riboswitches related to the ykkC guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the ykkC RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. ykkC aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the ykkC aptamer acquires new specificity represents a striking case of evolvability in RNA.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.

Macromolecule Content

Total Structure Weight: 79.23 kDa
Atom Count: 4,545
Modeled Residue Count: 208
Deposited Residue Count: 234
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
PRPP riboswitch	A, B	117	Thermoanaerobacter mathranii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRP Query on PRP Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain IA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain IA [auth B]	IA [auth B], S [auth A]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain IA [auth B] Focus chain S [auth A] Interactions & Density Focus chain IA [auth B] Focus chain S [auth A]
BA Query on BA Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain X [auth B] SDF format, chain U [auth B] SDF format, chain N [auth A] SDF format, chain K [auth A] SDF format, chain I [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth B] MOL2 format, chain U [auth B] MOL2 format, chain N [auth A] MOL2 format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth B] mmCIF format, chain U [auth B] mmCIF format, chain N [auth A] mmCIF format, chain K [auth A] mmCIF format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	AA [auth B] C [auth A] D [auth A] E [auth A] F [auth A] AA [auth B], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain HA [auth B] SDF format, chain GA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B]	GA [auth B], HA [auth B], R [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain R [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain R [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], O [auth A], P [auth A], Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.252 (Depositor), 0.250 (DCC)
R-Value Work: 0.214 (Depositor), 0.214 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.977	α = 90
b = 89.575	β = 96.9
c = 136.367	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
SCALEPACK	data scaling
Coot	model building
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-20

Deposition Author(s):

Knappenberger, A.J.

Reiss, C.W.

Strobel, S.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History (Full details and data files)

Version 1.0: 2018-06-20
Type: Initial release
Version 1.1: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary