5ELF: Cholera toxin El Tor B-pentamer

Name: PDB 5ELF: Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide
Published: 2016-03-30
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

Cholera toxin El Tor B-pentamer in complex with A-pentasaccharide. Determined by X-ray diffraction at 1.55 Å resolution. Released 30 Mar 2016.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Chains: 10
Atoms: 10,185
Mol. weight: 125.38 kDa
Ligands: CA, BCN, FUC, GLC
Released: 30 Mar 2016

Explore 5ELF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ELF contains 41 α-helices and 60 β-strands across 10 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	1
β-strand	26-30	5	1
β-strand	37-41	5	1
β-strand	47-50	4	1
α-helix	51-53	3
α-helix	61-77	17
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	1
β-strand	26-30	5	1
β-strand	38-41	4	1
β-strand	47-50	4	1
α-helix	51-53	3
α-helix	59-77	19
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain C: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	1
β-strand	26-30	5	1
β-strand	38-41	4	1
β-strand	47-50	4	1
α-helix	51-53	3
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chains D and G: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	1
β-strand	26-30	5	1
β-strand	37-41	5	1
β-strand	47-50	4	1
α-helix	51-53	3
α-helix	59-77	19
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain E: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	1
β-strand	26-30	5	1
β-strand	37-41	5	1
β-strand	47-50	4	1
α-helix	51-53	3
α-helix	59-61	3
α-helix	62-77	16
α-helix	80-81	2
β-strand	82-88	7	1
β-strand	94-102	9	1

Chain F: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-10	6
β-strand	15-22	8	2
β-strand	26-30	5	2
β-strand	37-41	5	2
β-strand	47-50	4	2
α-helix	51-53	3
α-helix	59-78	20
α-helix	80-81	2
β-strand	82-88	7	2
β-strand	94-102	9	2

Chain H: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	2
β-strand	26-30	5	2
β-strand	38-41	4	2
β-strand	47-50	4	2
α-helix	51-52	2
α-helix	59-77	19
α-helix	80-81	2
β-strand	82-88	7	2
β-strand	94-102	9	2

Chain I: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	5-9	5
β-strand	15-22	8	2
β-strand	26-30	5	2
β-strand	37-41	5	2
β-strand	47-50	4	2
α-helix	51-52	2
α-helix	61-77	17
α-helix	80-81	2
β-strand	82-88	7	2
β-strand	94-102	9	2

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cholera enterotoxin subunit B	A, B, C, D, E, F, G, H, I, J	protein	103	Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)	P01556 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>5ELF_1 Cholera enterotoxin subunit B (chains A, B, C, D, E, F, G, H, I, J)
TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDS
QKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	10
BCN	Bicine	C6 H13 N O4	10
FUC	alpha-L-fucopyranose	C6 H12 O5	2
GLC	alpha-D-glucopyranose	C6 H12 O6	2

Water and common crystallization additives (PG4) are not listed.

Primary citation

High-Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence. Heggelund, J.E., Burschowsky, D., Bjrnestad, V.A. et al. PLoS Pathog (2016) 12:e1005567-e1005567. DOI 10.1371/journal.ppat.1005567 · PubMed

Other PDB entries of the same protein (UniProt P01556 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5LZG 1.13 Å, Cholera toxin El Tor B-pentamer in complex with inhibitor PC262
5LZJ 1.2 Å, Cholera toxin El Tor B-pentamer in complex with inhibitor Laura237
3CHB 1.25 Å, Cholera toxin B-pentamer complexed with GM1 pentasaccharide
1JR0 1.3 Å, Cholera toxin B-pentamer with ligand bmsc-0011
1RDP 1.35 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3
1RF2 1.35 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV4
1RD9 1.44 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV2
1MD2 1.45 Å, Cholera toxin B-pentamer with decavalent ligand bmsc-0013
5ELC 1.5 Å, Cholera toxin El Tor B-pentamer in complex with Lewis-y
6HJD 1.54 Å, Cholera toxin classical B-pentamer in complex with Lewis-x
1RCV 1.6 Å, Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV1
5ELE 1.6 Å, Cholera toxin El Tor B-pentamer in complex with A Lewis-y

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