2IVZ: TolB

Structure of TolB in complex with a peptide of the colicin E9 T- domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Aug 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: ESCHERICHIA COLI
Chains: 8
Atoms: 13,614
Mol. weight: 195.5 kDa
Ligands: CA
Released: 16 Aug 2006

Explore 2IVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2IVZ contains 39 α-helices and 124 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: 9 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	1
β-strand	39-40	2	2
β-strand	44	1	2
α-helix	55-65	11
β-strand	69-71	3	1
α-helix	72-73	2
α-helix	74-76	3
α-helix	84-86	3
α-helix	89-93	5
β-strand	99-107	9	2
β-strand	113-121	9	2
β-strand	129-137	9	2
α-helix	139-141	3
α-helix	142-158	17
β-strand	167-174	8	3
β-strand	181-187	7	3
β-strand	194-199	6	3
β-strand	203-208	6	4
β-strand	214-219	6	4
β-strand	226-231	6	4
β-strand	237-241	5	4
β-strand	247-252	6	5
β-strand	258-263	6	5
β-strand	270-275	6	5
β-strand	281-283	3	5
β-strand	291-296	6	6
β-strand	302-307	6	6
β-strand	314-319	6	6
β-strand	326-327	2	6
β-strand	334-340	7	7
β-strand	346-353	8	7
β-strand	356-363	8	7
β-strand	369-371	3	7
β-strand	379-383	5	8
β-strand	389-393	5	8
α-helix	396-399	4
β-strand	402-406	5	8
β-strand	412-414	3	8
α-helix	415-417	3
β-strand	420-427	8	3

Chain B: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	9
β-strand	39-40	2	10
α-helix	41-43	3
β-strand	44	1	10
α-helix	55-65	11
β-strand	69-71	3	9
α-helix	72-73	2
α-helix	74-76	3
α-helix	84-86	3
α-helix	89-93	5
β-strand	99-107	9	10
β-strand	113-121	9	10
β-strand	129-137	9	10
α-helix	139-141	3
α-helix	142-158	17
α-helix	161-162	2
β-strand	167-173	7	11
β-strand	181-187	7	11
β-strand	194-199	6	11
β-strand	203-208	6	12
β-strand	214-219	6	12
β-strand	226-231	6	12
β-strand	237-241	5	12
β-strand	247-252	6	13
β-strand	258-263	6	13
β-strand	270-275	6	13
β-strand	281-283	3	13
β-strand	291-296	6	14
β-strand	302-307	6	14
β-strand	314-319	6	14
β-strand	322-327	6	14
β-strand	334-340	7	15
β-strand	346-353	8	15
β-strand	356-363	8	15
β-strand	369-371	3	15
β-strand	379-383	5	16
β-strand	389-396	8	16
β-strand	399-406	8	16
β-strand	412-414	3	16
α-helix	415-417	3
β-strand	421-427	7	11

Chain C: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	17
β-strand	39-40	2	18
α-helix	41-43	3
β-strand	44	1	18
α-helix	55-65	11
β-strand	69-71	3	17
α-helix	72-73	2
α-helix	74-76	3
α-helix	84-86	3
α-helix	89-93	5
β-strand	99-107	9	18
β-strand	113-121	9	18
β-strand	129-137	9	18
α-helix	139-141	3
α-helix	142-158	17
β-strand	167-173	7	19
β-strand	181-187	7	19
β-strand	194-199	6	19
β-strand	203-208	6	20
β-strand	214-219	6	20
β-strand	226-231	6	20
β-strand	237-241	5	20
β-strand	247-252	6	21
β-strand	258-263	6	21
β-strand	270-275	6	21
β-strand	281-283	3	21
β-strand	291-296	6	22
β-strand	302-307	6	22
β-strand	314-319	6	22
β-strand	326-327	2	22
β-strand	334-340	7	23
β-strand	346-352	7	23
β-strand	357-363	7	23
β-strand	369-371	3	23
β-strand	379-383	5	24
β-strand	389-393	5	24
α-helix	396-399	4
β-strand	402-406	5	24
β-strand	412-414	3	24
α-helix	415-417	3
β-strand	421-427	7	19

Chain D: 10 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	36-38	3	25
β-strand	39-40	2	26
α-helix	41-43	3
β-strand	44-45	2	26
α-helix	55-65	11
β-strand	69-71	3	25
α-helix	72-73	2
α-helix	74-76	3
α-helix	84-86	3
α-helix	89-93	5
β-strand	99-107	9	26
β-strand	113-121	9	26
β-strand	129-137	9	26
α-helix	139-141	3
α-helix	142-158	17
β-strand	167-173	7	27
β-strand	181-187	7	27
β-strand	194-199	6	27
β-strand	203-208	6	28
β-strand	214-219	6	28
β-strand	226-231	6	28
β-strand	237-241	5	28
β-strand	247-252	6	29
β-strand	258-263	6	29
β-strand	270-275	6	29
β-strand	281-283	3	29
β-strand	291-296	6	30
β-strand	302-307	6	30
β-strand	314-319	6	30
β-strand	322-327	6	30
β-strand	335-340	6	31
β-strand	346-351	6	31
β-strand	358-363	6	31
β-strand	369-371	3	31
β-strand	379-383	5	32
β-strand	389-393	5	32
α-helix	396-399	4
β-strand	402-406	5	32
β-strand	412-414	3	32
α-helix	415-417	3
β-strand	421-427	7	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein tolb	A, B, C, D	protein	439	ESCHERICHIA COLI	P0A855 (AlphaFold model)
Colicin-E9	E, F, G, H	protein	16	ESCHERICHIA COLI	P09883 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>2IVZ_1 PROTEIN TOLB (chains A, B, C, D)
MMKQALRVAFGFLILWASVLHAEVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVA
ADLRNSGKFNPLDRARLPQQPGSAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLV
DTGGAPGTVLAQNSYKVNKQWLRYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFP
YELRVSDYDGYNQFVVHRSPQPLMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQV
ASFPRHNGAPAFSPDGSKLAFALSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDS
QNLAFTSDQAGRPQVYKVNINGGAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIA
KQDLATGGVQVLSSTFLDETPSLAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDG
QVKFPAWSPYLLEHHHHHH

Sequence of entity 2 (E, F, G, H), FASTA

>2IVZ_2 COLICIN-E9 (chains E, F, G, H)
GASDGSGWSSENNPWG

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7

Primary citation

Competitive Recruitment of the Periplasmic Translocation Portal Tolb by a Natively Disordered Domain of Colicin E9. Loftus, S.R., Walker, D., Mate, M.J. et al. Proc Natl Acad Sci U S A (2006) 103:12353. DOI 10.1073/PNAS.0603433103 · PubMed

Other PDB entries of the same protein (UniProt P0A855 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HQS 1.5 Å, Crystal structure of TolB/Pal complex
2W8B 1.86 Å, Crystal structure of processed TolB in complex with Pal
1CRZ 1.95 Å, Crystal structure of the E. Coli tolb protein
1C5K 2.0 Å, The structure of tolb, an essential component of the tol-dependent translocation system…
4JML 2.0 Å, Crystal structure of the TolB(P201C)-ColicinE9 TBE peptide(A33C) complex.
3IAX 2.6 Å, The crystal structure of the TolB box of Colicin A in complex with TolB reveals…
7NST 3.7 Å, ColicinE9 partial translocation complex
7NSU 4.7 Å, ColicinE9 intact translocation complex
9A2L Model of E. coli TolB by in-cell photo-crosslinking MS and deep learning

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