6OD9 | pdb_00006od9

Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser

PDB DOI: https://doi.org/10.2210/pdb6OD9/pdb
NAKB: 6OD9

Classification: RNA
Organism(s): Fusobacterium ulcerans
Mutation(s): No

Deposited: 2019-03-26 Released: 2019-07-17
Deposition Author(s): Jones, C.P., Tran, B., Ferre-D'Amare, A.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.10 Å
R-Value Free:
0.308 (Depositor), 0.304 (DCC)
R-Value Work:
0.258 (Depositor), 0.253 (DCC)
R-Value Observed:
0.260 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser.

Jones, C., Tran, B., Conrad, C., Stagno, J., Trachman 3rd, R., Fischer, P., Meents, A., Ferre-D'Amare, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 496-500

PubMed: 31282869 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2053230X19008549
Primary Citation Related Structures:
6OD9

PubMed Abstract:
Riboswitches are conformationally dynamic RNAs that regulate gene expression by binding specific small molecules. ZTP riboswitches bind the purine-biosynthetic intermediate 5-aminoimidazole-4-carboxamide riboside 5'-monophosphate (ZMP) and its triphosphorylated form (ZTP). Ligand binding to this riboswitch ultimately upregulates genes involved in folate and purine metabolism. Using an X-ray free-electron laser (XFEL), the room-temperature structure of the Fusobacterium ulcerans ZTP riboswitch bound to ZMP has now been determined at 4.1 Å resolution. This model, which was refined against a data set from ∼750 diffraction images (each from a single crystal), was found to be consistent with that previously obtained from data collected at 100 K using conventional synchrotron X-radiation. These experiments demonstrate the feasibility of time-resolved XFEL experiments to understand how the ZTP riboswitch accommodates cognate ligand binding.

Organizational Affiliation

Biochemistry and Biophysics Center, National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892, USA.

Macromolecule Content

Total Structure Weight: 49.58 kDa
Atom Count: 2,710
Modeled Residue Count: 124
Deposited Residue Count: 150
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA (75-MER)	A, B	75	Fusobacterium ulcerans
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMZ (Subject of Investigation/LOI) Query on AMZ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE C₉ H₁₅ N₄ O₈ P NOTGFIUVDGNKRI-UUOKFMHZSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CS Query on CS Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B]	G [auth A], M [auth B]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain F [auth A]	E [auth A], F [auth A], J [auth B], K [auth B], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.10 Å
R-Value Free: 0.308 (Depositor), 0.304 (DCC)
R-Value Work: 0.258 (Depositor), 0.253 (DCC)
R-Value Observed: 0.260 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.74	α = 90
b = 92.74	β = 90
c = 120.48	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-07-17

Deposition Author(s):

Jones, C.P.

Tran, B.

Ferre-D'Amare, A.R.

Revision History (Full details and data files)

Version 1.0: 2019-07-17
Type: Initial release
Version 1.1: 2019-07-24
Changes: Data collection, Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description