7S0Z: TcdB

Structures of TcdB in complex with R-Ras. Determined by X-ray diffraction at 2.34 Å resolution. Released 8 Sept 2021.

Method: X-ray diffraction
Resolution: 2.34 Å
Organisms: Clostridioides difficile, Homo sapiens
Chains: 4
Atoms: 12,426
Mol. weight: 169.42 kDa
Ligands: MG, GLC, MN, UDP
Released: 8 Sept 2021

Explore 7S0Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S0Z contains 85 α-helices and 42 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 33 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	22-34	13
α-helix	42-62	21
α-helix	69-89	21
β-strand	92-93	2	5
α-helix	94-95	2
β-strand	97-101	5	6
α-helix	109-121	13
β-strand	126-131	6	6
α-helix	138-155	18
α-helix	168-196	29
α-helix	202-214	13
α-helix	218-233	16
β-strand	237-239	3	6
α-helix	240-242	3
α-helix	244-247	4
α-helix	252-256	5
α-helix	257-262	6
α-helix	265-279	15
β-strand	282-285	4	6
β-strand	290	1	7
α-helix	291-292	2
β-strand	293	1	8
α-helix	294	1
α-helix	302-304	3
α-helix	310-325	16
α-helix	336-338	3
α-helix	341-352	12
α-helix	357-359	3
β-strand	361	1	8
α-helix	362-363	2
β-strand	368-369	2	5
β-strand	375-379	5	6
β-strand	382-390	9	6
α-helix	395-419	25
α-helix	425-439	15
α-helix	445-451	7
α-helix	454-456	3
α-helix	465-469	5
α-helix	472-484	13
α-helix	496-499	4
α-helix	500-502	3
β-strand	503	1	6
α-helix	506-508	3
β-strand	510	1	7
α-helix	525-539	15

Chain B: 36 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	22-34	13
α-helix	42-62	21
α-helix	69-89	21
β-strand	92-93	2	1
α-helix	94-95	2
β-strand	97-101	5	2
α-helix	106-108	3
α-helix	109-121	13
β-strand	126-131	6	2
α-helix	138-155	18
α-helix	168-196	29
α-helix	202-214	13
α-helix	218-233	16
β-strand	237-239	3	2
α-helix	240-242	3
α-helix	244-247	4
α-helix	252-256	5
α-helix	257-261	5
α-helix	265-279	15
β-strand	282-285	4	2
β-strand	290	1	3
α-helix	291-292	2
β-strand	293	1	4
α-helix	294	1
α-helix	302-304	3
α-helix	310-325	16
α-helix	336-338	3
α-helix	341-352	12
α-helix	357-359	3
β-strand	361	1	4
α-helix	362-363	2
β-strand	368-369	2	1
β-strand	375-379	5	2
β-strand	382-390	9	2
α-helix	395-419	25
α-helix	425-439	15
α-helix	445-450	6
α-helix	454-456	3
α-helix	465-469	5
α-helix	472-483	12
α-helix	496-499	4
α-helix	500-502	3
β-strand	503	1	2
α-helix	504-505	2
α-helix	506-508	3
β-strand	510	1	3
α-helix	515-517	3
α-helix	525-540	16

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-35	8	9
α-helix	42-51	10
β-strand	66-72	7	9
β-strand	75-83	9	9
α-helix	91-99	9
β-strand	103-109	7	9
α-helix	113-130	18
β-strand	137-142	6	9
α-helix	147-149	3
α-helix	154-163	10
β-strand	168-170	3	9
β-strand	172	1	10
β-strand	177	1	10
α-helix	179-196	18
α-helix	200	1

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-35	8	11
α-helix	42-51	10
β-strand	67-72	6	11
β-strand	75-83	9	11
α-helix	91-99	9
β-strand	103-109	7	11
α-helix	113-130	18
β-strand	137-142	6	11
α-helix	144-149	6
α-helix	154-163	10
β-strand	168-170	3	11
β-strand	172	1	12
β-strand	177	1	12
α-helix	179-196	18
α-helix	200	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Toxin B	A, B	protein	541	Clostridioides difficile	Q9EXR0 (AlphaFold model)
Ras-related protein R-Ras	C, D	protein	179	Homo sapiens	P10301 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7S0Z_1 Toxin B (chains A, B)
MSLVNRKQLEKMANVRFRVQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDTYI
DTYKKSGRNKALKKFKEYLVIEILELKNSNLTPVEKNLHFIWIGGQINDTAINYINQWKD
VNSDYNVNVFYDSNAFLINTLKKTIIESASNDTLESFRENLNDPEFNHTAFFRKRMQIIY
DKQQNFINYYKAQKEENPDLIIDDIVKTYLSNEYSKDIDELNAYIEESLNKVTENSGNDV
RNFEEFKTGEVFNLYEQELVERWNLAGASDILRVAILKNIGGVYLDVDMLPGIHPDLFKD
INKPDSVKTAVDWEEMQLEAIMKHKEYIPEYTSKHFDTLDEEVQSSFESVLASKSDKSEI
FLPLGDIEVSPLEVKIAFAKGSIINQALISAKDSYCSDLLIKQIQNRYKILNDTLGPIIS
QGNDFNTTMNNFGESLGAIANEENISFIAKIGSYLRVGFYPEANTTITLSGPTIYAGAYK
DLLTFKEMSIDTSILSSELRNFEFPKVNISQATEQEKNSLWQFNEERAKIQFEEYKKNYF
E

Sequence of entity 2 (C, D), FASTA

>7S0Z_2 Ras-related protein R-Ras (chains C, D)
DPPPSETHKLVVVGGGGVGKSALTIQFIQSYFVSDYDPNIEDSYTKICSVDGIPARLDIL
DTAGQEEFGAMREQYMRAGHGFLLVFAINDRQSFNEVGKLFTQILRVKDRDDFPVVLVGN
KADLESQRQVPRSEASAFGASHHVAYFEASAKLRLNVDEAFEQLVRAVRKYQEQELPPS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5
GLC	alpha-D-glucopyranose	C6 H12 O6	2
MN	Manganese (II) ion	Mn	2
UDP	Uridine-5'-diphosphate	C9 H14 N2 O12 P2	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (PEG, ACT, EDO, NH4) are not listed.

Primary citation

Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B. Liu, Z., Zhang, S., Chen, P. et al. Sci Adv (2021) 7:eabi4582-eabi4582. DOI 10.1126/sciadv.abi4582 · PubMed

Other PDB entries of the same protein (UniProt Q9EXR0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OQ7 2.39 Å, Structure of the GTD domain of Clostridium difficile toxin B in complex with VHH E3
8Y9C 3.0 Å, De novo design mini-binder in complex with TcdB4
7V1N 3.2 Å, Structure of the Clade 2 C. difficile TcdB in complex with its receptor TFPI

Browse structure collections

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