2W8B: Processed TolB

Crystal structure of processed TolB in complex with Pal. Determined by X-ray diffraction at 1.86 Å resolution. Released 17 Feb 2009.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: ESCHERICHIA COLI
Chains: 8
Atoms: 17,488
Mol. weight: 230.27 kDa
Released: 17 Feb 2009

Explore 2W8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W8B contains 52 α-helices and 148 β-strands across 8 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: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	1
β-strand	35-37	3	2
β-strand	38-39	2	3
α-helix	40-42	3
β-strand	43-44	2	3
α-helix	54-64	11
β-strand	68-70	3	2
α-helix	71-72	2
α-helix	73-75	3
α-helix	88-92	5
β-strand	98-106	9	3
β-strand	112-120	9	3
β-strand	128-136	9	3
α-helix	138-140	3
α-helix	141-157	17
β-strand	166-172	7	4
β-strand	180-186	7	4
β-strand	193-198	6	4
β-strand	202-207	6	5
β-strand	213-218	6	5
β-strand	225-230	6	5
β-strand	236-240	5	5
β-strand	246-251	6	6
β-strand	257-262	6	6
β-strand	269-274	6	6
β-strand	280-282	3	6
β-strand	290-295	6	7
β-strand	301-306	6	7
β-strand	313-318	6	7
β-strand	325-326	2	7
β-strand	333-339	7	8
β-strand	345-352	8	8
β-strand	355-362	8	8
β-strand	368-370	3	8
β-strand	378-382	5	1
β-strand	388-395	8	1
β-strand	398-405	8	1
β-strand	411-413	3	1
β-strand	420-426	7	4

Chain B: 7 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	26-29	4	9
β-strand	35-37	3	10
β-strand	38-39	2	11
α-helix	40-42	3
β-strand	43-44	2	11
α-helix	54-64	11
β-strand	68-70	3	10
α-helix	73-75	3
α-helix	88-92	5
β-strand	98-106	9	11
β-strand	112-120	9	11
β-strand	128-136	9	11
α-helix	138-140	3
α-helix	141-157	17
α-helix	160-161	2
β-strand	166-172	7	12
β-strand	180-186	7	12
β-strand	193-198	6	12
β-strand	202-207	6	13
β-strand	213-218	6	13
β-strand	225-230	6	13
β-strand	236-240	5	13
β-strand	246-251	6	14
β-strand	257-262	6	14
β-strand	269-274	6	14
β-strand	280-282	3	14
β-strand	290-295	6	15
β-strand	301-306	6	15
β-strand	313-318	6	15
β-strand	325-326	2	15
β-strand	333-339	7	16
β-strand	345-352	8	16
β-strand	355-362	8	16
β-strand	368-370	3	16
β-strand	378-382	5	9
β-strand	388-395	8	9
β-strand	398-405	8	9
β-strand	411-413	3	9
β-strand	420-426	7	12

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	70-72	3	17
α-helix	82-94	13
β-strand	103-107	5	17
α-helix	115-135	21
α-helix	140-142	3
β-strand	143-147	5	17
α-helix	160-163	4
β-strand	168-172	5	17

Chain D: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	18
β-strand	26-29	4	19
α-helix	31-33	3
β-strand	35-37	3	20
β-strand	38-39	2	21
α-helix	40-42	3
β-strand	43-44	2	21
α-helix	54-64	11
β-strand	68-70	3	20
α-helix	71-72	2
α-helix	73-75	3
α-helix	83-85	3
α-helix	88-92	5
β-strand	98-106	9	21
β-strand	112-120	9	21
β-strand	128-136	9	21
α-helix	138-140	3
α-helix	141-157	17
β-strand	166-172	7	22
β-strand	180-186	7	22
β-strand	193-198	6	22
β-strand	202-207	6	23
β-strand	213-218	6	23
β-strand	225-230	6	23
β-strand	236-240	5	23
β-strand	246-251	6	24
β-strand	257-262	6	24
β-strand	269-274	6	24
β-strand	280-282	3	24
β-strand	290-295	6	25
β-strand	301-306	6	25
β-strand	313-318	6	25
β-strand	325-326	2	25
β-strand	334-339	6	26
β-strand	345-352	8	26
β-strand	355-362	8	26
β-strand	368-370	3	26
β-strand	378-382	5	19
β-strand	388-395	8	19
β-strand	398-405	8	19
β-strand	411-413	3	19
β-strand	416	1	18
β-strand	420-426	7	22

Chain E: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	70-72	3	27
α-helix	82-84	3
α-helix	85-97	13
β-strand	103-108	6	27
α-helix	115-135	21
α-helix	140-142	3
β-strand	143-149	7	27
α-helix	160-166	7
β-strand	168-172	5	27

Chain F: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	28
β-strand	26-29	4	29
α-helix	31-33	3
β-strand	35-37	3	30
β-strand	38-39	2	31
α-helix	40-42	3
β-strand	43-44	2	31
α-helix	54-64	11
β-strand	68-70	3	30
α-helix	71-72	2
α-helix	73-75	3
α-helix	83-85	3
α-helix	88-92	5
β-strand	98-106	9	31
β-strand	112-120	9	31
β-strand	128-136	9	31
α-helix	138-140	3
α-helix	141-157	17
β-strand	166-172	7	32
β-strand	180-186	7	32
β-strand	193-198	6	32
β-strand	202-207	6	33
β-strand	213-218	6	33
β-strand	225-230	6	33
β-strand	236-240	5	33
β-strand	246-251	6	34
β-strand	257-262	6	34
β-strand	269-274	6	34
β-strand	280-282	3	34
β-strand	290-295	6	35
β-strand	301-306	6	35
β-strand	313-318	6	35
β-strand	325-326	2	35
β-strand	333-339	7	36
β-strand	345-352	8	36
β-strand	355-362	8	36
β-strand	368-370	3	36
β-strand	378-382	5	29
β-strand	388-395	8	29
β-strand	398-405	8	29
β-strand	411-413	3	29
β-strand	416	1	28
β-strand	420-426	7	32
α-helix	427-429	3

Chain G: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	70-72	3	37
α-helix	82-84	3
α-helix	85-97	13
β-strand	103-107	5	37
α-helix	115-135	21
α-helix	140-142	3
β-strand	143-147	5	37
α-helix	160-166	7
β-strand	168-172	5	37

Chain H: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	70-72	3	38
α-helix	80-81	2
α-helix	82-97	16
β-strand	103-107	5	38
α-helix	115-135	21
α-helix	140-142	3
β-strand	143-147	5	38
α-helix	160-166	7
β-strand	168-173	6	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein tolb	A	protein	409	ESCHERICHIA COLI	P0A855 (AlphaFold model)
Protein tolb	B, D, F	protein	409	ESCHERICHIA COLI	P0A855 (AlphaFold model)
Peptidoglycan-associated lipoprotein	C, E, G, H	protein	118	ESCHERICHIA COLI	P0A912 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2W8B_1 PROTEIN TOLB (chains A)
EVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPG
SAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWL
RYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQP
LMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFA
LSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNING
GAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPS
LAPNGTMVLYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL

Sequence of entity 2 (B, D, F), FASTA

>2W8B_2 PROTEIN TOLB (chains B, D, F)
EVRIVIDSGVDSGRPIGVVPFQWAGPGAAPEDIGGIVAADLRNSGKFNPLDRARLPQQPG
SAQEVQPAAWSALGIDAVVVGQVTPNPDGSYNVAYQLVDTGGAPGTVLAQNSYKVNKQWL
RYAGHTASDEVFEKLTGIKGAFRTRIAYVVQTNGGQFPYELRVSDYDGYNQFVVHRSPQP
LMSPAWSPDGSKLAYVTFESGRSALVIQTLANGAVRQVASFPRHNGAPAFSPDGSKLAFA
LSKTGSLNLYVMDLASGQIRQVTDGRSNNTEPTWFPDSQNLAFTSDQAGRPQVYKVNING
GAPQRITWEGSQNQDADVSSDGKFMVMVSSNGGQQHIAKQDLATGGVQVLSSTFLDETPS
LAPNGTMVIYSSSQGMGSVLNLVSTDGRFKARLPATDGQVKFPAWSPYL

Sequence of entity 3 (C, E, G, H), FASTA

>2W8B_3 PEPTIDOGLYCAN-ASSOCIATED LIPOPROTEIN (chains C, E, G, H)
MLQQNNIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGE
RRANAVKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYLEHHHHHH

Primary citation

Allosteric Beta-Propeller Signalling in Tolb and its Manipulation by Translocating Colicins. Bonsor, D.A., Hecht, O., Vankemmelbeke, M. et al. EMBO J (2009) 28:2846. DOI 10.1038/EMBOJ.2009.224 · 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
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…
2IVZ 2.0 Å, Structure of TolB in complex with a peptide of the colicin E9 T- domain
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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