7S0Z | pdb_00007s0z

Structures of TcdB in complex with R-Ras

PDB DOI: https://doi.org/10.2210/pdb7S0Z/pdb

Classification: Hydrolase/Transferase
Organism(s): Clostridioides difficile, Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-08-31 Released: 2021-09-08
Deposition Author(s): Zheng, L., Rongsheng, J., Peng, C.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.241 (Depositor), 0.240 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Models: 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

Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B.

Liu, Z., Zhang, S., Chen, P., Tian, S., Zeng, J., Perry, K., Dong, M., Jin, R.

(2021) Sci Adv 7: eabi4582-eabi4582

PubMed: 34678063 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/sciadv.abi4582
Primary Citation Related Structures:
7S0Y, 7S0Z

PubMed Abstract:
Toxin B (TcdB) is a primary cause of Clostridioides difficile infection (CDI). This toxin acts by glucosylating small GTPases in the Rho/Ras families, but the structural basis for TcdB recognition and selectivity of specific GTPase substrates remain unsolved. Here, we report the cocrystal structures of the glucosyltransferase domain (GTD) of two distinct TcdB variants in complex with human Cdc42 and R-Ras, respectively. These structures reveal a common structural mechanism by which TcdB recognizes Rho and R-Ras. Furthermore, we find selective clustering of adaptive residue changes in GTDs that determine their substrate preferences, which helps partition all known TcdB variants into two groups that display distinct specificities toward Rho or R-Ras. Mutations that selectively disrupt GTPases binding reduce the glucosyltransferase activity of the GTD and the toxicity of TcdB holotoxin. These findings establish the structural basis for TcdB recognition of small GTPases and reveal strategies for therapeutic interventions for CDI.

Organizational Affiliation

Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.

Macromolecule Content

Total Structure Weight: 169.42 kDa
Atom Count: 12,426
Modeled Residue Count: 1,440
Deposited Residue Count: 1,440
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin B	A [auth B], B [auth A]	541	Clostridioides difficile	Mutation(s): 0 Gene Names: tcdB, SAMEA708418_03270 EC: 2.4.1 (PDB Primary Data), 3.4.22 (UniProt)
UniProt
Find proteins for Q9EXR0 (Clostridioides difficile) Explore Q9EXR0 Go to UniProtKB: Q9EXR0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9EXR0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein R-Ras	C, D	179	Homo sapiens	Mutation(s): 0 Gene Names: RRAS EC: 3.6.5 (PDB Primary Data), 3.6.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P10301 (Homo sapiens) Explore P10301 Go to UniProtKB: P10301
PHAROS: P10301 GTEx: ENSG00000126458
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10301
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain BB [auth D] SDF format, chain ZA [auth C] MOL2 format, chain BB [auth D] MOL2 format, chain ZA [auth C] mmCIF format, chain BB [auth D] mmCIF format, chain ZA [auth C]	BB [auth D], ZA [auth C]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain BB [auth D] Focus chain ZA [auth C] Interactions & Density Focus chain BB [auth D] Focus chain ZA [auth C]
UDP Query on UDP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain W [auth A] MOL2 format, chain E [auth B] MOL2 format, chain W [auth A] mmCIF format, chain E [auth B] mmCIF format, chain W [auth A]	E [auth B], W [auth A]	URIDINE-5'-DIPHOSPHATE C₉ H₁₄ N₂ O₁₂ P₂ XCCTYIAWTASOJW-XVFCMESISA-N		Interactions Focus chain E [auth B] Focus chain W [auth A] Interactions & Density Focus chain E [auth B] Focus chain W [auth A]
GLC Query on GLC Download:Ideal Coordinates CCD File SDF format, chain SA [auth A] SDF format, chain T [auth B] MOL2 format, chain SA [auth A] MOL2 format, chain T [auth B] mmCIF format, chain SA [auth A] mmCIF format, chain T [auth B]	SA [auth A], T [auth B]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain SA [auth A] Focus chain T [auth B] Interactions & Density Focus chain SA [auth A] Focus chain T [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain UA [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain WA [auth C] SDF format, chain VA [auth C] SDF format, chain U [auth B] SDF format, chain O [auth B] SDF format, chain M [auth B] SDF format, chain J [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain CA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain CA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain VA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain CA [auth A]	AA [auth A] CA [auth A] G [auth B] H [auth B] J [auth B] AA [auth A], CA [auth A], G [auth B], H [auth B], J [auth B], M [auth B], O [auth B], U [auth B], UA [auth A], VA [auth C], WA [auth C], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain CA [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain U [auth B] Focus chain UA [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain CA [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain U [auth B] Focus chain UA [auth A] Focus chain VA [auth C] Focus chain WA [auth C] Focus chain Y [auth A] Focus chain Z [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain IA [auth A] SDF format, chain JA [auth A] SDF format, chain K [auth B] SDF format, chain KA [auth A] SDF format, chain YA [auth C] SDF format, chain V [auth B] SDF format, chain RA [auth A] SDF format, chain N [auth B] SDF format, chain LA [auth A] SDF format, chain L [auth B] SDF format, chain GA [auth A] SDF format, chain FA [auth A] SDF format, chain DA [auth A] SDF format, chain BA [auth A] MOL2 format, chain AB [auth D] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain RA [auth A] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth A] MOL2 format, chain L [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain AB [auth D] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain RA [auth A] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth A] mmCIF format, chain L [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain BA [auth A]	AB [auth D] BA [auth A] DA [auth A] FA [auth A] GA [auth A] AB [auth D], BA [auth A], DA [auth A], FA [auth A], GA [auth A], IA [auth A], JA [auth A], K [auth B], KA [auth A], L [auth B], LA [auth A], N [auth B], RA [auth A], V [auth B], YA [auth C]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AB [auth D] Focus chain BA [auth A] Focus chain DA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain N [auth B] Focus chain RA [auth A] Focus chain V [auth B] Focus chain YA [auth C] Interactions & Density Focus chain AB [auth D] Focus chain BA [auth A] Focus chain DA [auth A] Focus chain FA [auth A] Focus chain GA [auth A] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain K [auth B] Focus chain KA [auth A] Focus chain L [auth B] Focus chain LA [auth A] Focus chain N [auth B] Focus chain RA [auth A] Focus chain V [auth B] Focus chain YA [auth C]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain NA [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain NA [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain NA [auth A]	NA [auth A], Q [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain NA [auth A] Focus chain Q [auth B] Interactions & Density Focus chain NA [auth A] Focus chain Q [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain PA [auth A] SDF format, chain TA [auth A] SDF format, chain QA [auth A] SDF format, chain OA [auth A] SDF format, chain CB [auth D] MOL2 format, chain PA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain CB [auth D] mmCIF format, chain PA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain CB [auth D]	CB [auth D], OA [auth A], PA [auth A], QA [auth A], TA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain TA [auth A] Interactions & Density Focus chain CB [auth D] Focus chain OA [auth A] Focus chain PA [auth A] Focus chain QA [auth A] Focus chain TA [auth A]
NH4 Query on NH4 Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain HA [auth A] SDF format, chain MA [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain XA [auth C] SDF format, chain X [auth A] SDF format, chain I [auth B] SDF format, chain F [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain XA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain I [auth B] MOL2 format, chain F [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain XA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain I [auth B] mmCIF format, chain F [auth B]	EA [auth A] F [auth B] HA [auth A] I [auth B] MA [auth A] EA [auth A], F [auth B], HA [auth A], I [auth B], MA [auth A], R [auth B], S [auth B], X [auth A], XA [auth C]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Interactions Focus chain EA [auth A] Focus chain F [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain MA [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth A] Focus chain XA [auth C] Interactions & Density Focus chain EA [auth A] Focus chain F [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain MA [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain X [auth A] Focus chain XA [auth C]