6CK4 | pdb_00006ck4

G96A mutant of the PRPP riboswitch from T. mathranii bound to ppGpp

PDB DOI: https://doi.org/10.2210/pdb6CK4/pdb
NAKB: 6CK4

Classification: RNA
Organism(s): Thermoanaerobacter mathranii
Mutation(s): Yes

Deposited: 2018-02-27 Released: 2018-06-20
Deposition Author(s): Reiss, C.W., Knappenberger, A.J., 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: 3.10 Å
R-Value Free:
0.304 (Depositor), 0.302 (DCC)
R-Value Work:
0.248 (Depositor), 0.248 (DCC)
R-Value Observed:
0.251 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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: 155.11 kDa
Atom Count: 9,041
Modeled Residue Count: 418
Deposited Residue Count: 468
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G4P (Subject of Investigation/LOI) Query on G4P Download:Ideal Coordinates CCD File SDF format, chain KA [auth C] SDF format, chain R [auth A] SDF format, chain WA [auth D] SDF format, chain Z [auth B] MOL2 format, chain KA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain WA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain KA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain WA [auth D] mmCIF format, chain Z [auth B]	KA [auth C], R [auth A], WA [auth D], Z [auth B]	GUANOSINE-5',3'-TETRAPHOSPHATE C₁₀ H₁₇ N₅ O₁₇ P₄ BUFLLCUFNHESEH-UUOKFMHZSA-N		Interactions Focus chain KA [auth C] Focus chain R [auth A] Focus chain WA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain KA [auth C] Focus chain R [auth A] Focus chain WA [auth D] Focus chain Z [auth B]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain LA [auth C] MOL2 format, chain LA [auth C] mmCIF format, chain LA [auth C]	LA [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain LA [auth C] Interactions & Density Focus chain LA [auth C]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain V [auth B] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B]	EA [auth C] FA [auth C] GA [auth C] HA [auth C] I [auth A] EA [auth C], FA [auth C], GA [auth C], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], OA [auth D], P [auth A], PA [auth D], Q [auth A], QA [auth D], RA [auth D], SA [auth D], TA [auth D], UA [auth D], V [auth B], VA [auth D], W [auth B], X [auth B], Y [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Interactions & Density Focus chain EA [auth C] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain UA [auth D] Focus chain V [auth B] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] F [auth A] AA [auth C], BA [auth C], CA [auth C], DA [auth C], F [auth A], G [auth A], H [auth A], MA [auth D], NA [auth D], S [auth B], T [auth B], U [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.304 (Depositor), 0.302 (DCC)
R-Value Work: 0.248 (Depositor), 0.248 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.252	α = 91.18
b = 62.147	β = 89.61
c = 125.909	γ = 101.94

Software Package:

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

Reiss, C.W.

Knappenberger, A.J.

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: Advisory, Author supporting evidence, Data collection, Derived calculations
Version 1.2: 2020-01-01
Changes: Author supporting evidence
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations, Structure summary