8B14: T5 Receptor Binding Protein pb5

T5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA. Determined by electron microscopy at 2.6 Å resolution. Released 8 Feb 2023.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Escherichia coli, Escherichia phage T5
Chains: 2
Atoms: 9,698
Mol. weight: 150.86 kDa
Ligands: LU9, DDQ
Released: 8 Feb 2023

Explore 8B14 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8B14 contains 29 α-helices and 93 β-strands across 2 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: 16 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	22-27	6
α-helix	29-31	3
β-strand	32-33	2	1
β-strand	41-42	2	1
α-helix	43-45	3
β-strand	50-54	5	2
α-helix	55-61	7
α-helix	66-69	4
β-strand	76-77	2	3
β-strand	91-92	2	3
β-strand	95	1	3
α-helix	98-100	3
β-strand	104-106	3	2
β-strand	109-110	2	2
β-strand	114	1	4
β-strand	117	1	4
α-helix	123-125	3
β-strand	126-133	8	2
α-helix	137-140	4
β-strand	147-153	7	2
β-strand	161-169	9	5
β-strand	173-183	11	5
β-strand	190-202	13	5
β-strand	209-221	13	5
β-strand	228-241	14	5
β-strand	247	1	6
β-strand	250	1	7
β-strand	254	1	7
β-strand	274-289	16	5
β-strand	294-317	24	5
α-helix	321-323	3
β-strand	326	1	8
α-helix	327-330	4
α-helix	336-339	4
β-strand	340-367	28	5
β-strand	370-392	23	5
β-strand	397-401	5	5
β-strand	429-451	23	5
β-strand	454-463	10	5
β-strand	466-471	6	5
β-strand	476-481	6	5
β-strand	484-493	10	5
β-strand	499-510	12	5
β-strand	515	1	9
α-helix	520	1
β-strand	521	1	9
α-helix	522-524	3
β-strand	525-536	12	5
β-strand	543-560	18	5
β-strand	568-585	18	5
β-strand	591-606	16	5
α-helix	613-615	3
β-strand	621-630	10	5
β-strand	639-648	10	5
β-strand	651-652	2	10
β-strand	660-661	2	10
α-helix	662-663	2
β-strand	664-674	11	5
β-strand	684-690	7	5
β-strand	698-701	4	6
β-strand	707-709	3	6
α-helix	710-711	2
β-strand	714-722	9	5

Chain B: 13 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	44-52	9	11
β-strand	54	1	12
β-strand	63-66	4	12
α-helix	67-68	2
α-helix	69-77	9
β-strand	81-89	9	11
β-strand	94-96	3	11
β-strand	100-109	10	11
β-strand	112-113	2	11
β-strand	117-129	13	11
β-strand	135-139	5	12
α-helix	147-150	4
α-helix	151-153	3
β-strand	158-168	11	11
α-helix	177-182	6
β-strand	183-184	2	13
β-strand	192	1	8
α-helix	196-198	3
β-strand	202	1	14
α-helix	204-206	3
β-strand	212	1	15
β-strand	219-223	5	12
β-strand	225	1	16
β-strand	229-231	3	17
β-strand	245-247	3	18
β-strand	250-258	9	11
β-strand	267-275	9	11
β-strand	281-283	3	18
α-helix	287-289	3
β-strand	298-300	3	17
β-strand	303	1	16
β-strand	308-320	13	11
β-strand	325-327	3	11
β-strand	357-360	4	11
β-strand	375-383	9	11
α-helix	396-397	2
β-strand	398-401	4	11
β-strand	407-410	4	11
β-strand	417-425	9	11
β-strand	459	1	19
β-strand	464-468	5	15
β-strand	471-474	4	20
β-strand	478-485	8	11
β-strand	496-503	8	15
α-helix	507-510	4
α-helix	519-522	4
β-strand	533-534	2	13
β-strand	536	1	14
β-strand	543-550	8	15
β-strand	553	1	11
β-strand	556-568	13	11
β-strand	578	1	11
α-helix	579-580	2
β-strand	593-605	13	11
β-strand	611-620	10	11
β-strand	625-628	4	20
α-helix	629	1
β-strand	632-638	7	15
β-strand	639	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
FhuA iron-ferrichrome transporter	A	protein	723	Escherichia coli	P06971 (AlphaFold model)
pb5 bacteriophage T5 receptor binding protein	B	protein	640	Escherichia phage T5	P23207

Sequence of entity 1 (A), FASTA

>8B14_1 FhuA iron-ferrichrome transporter (chains A)
AVEPKEDTITVTAAPAPQESAWGPAATIAARQSATGTKTDTPIQKVPQSISVVTAEEMAL
HQPKSVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAV
IDPYMLERAEIMRGPVSVLYGKSSPGGLLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDF
SDSLDDDGVYSYRLTGLARSANAQQKGSEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPE
TGYYGWLPKEGTVEPLPNGKRLPTDFNEGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNL
RFAENKTSQNSVYGYGVCSDPANAYSKQCAALAPADKGHYLARKYVVDDEKLQNFSVDTQ
LQSKFATGDIDHTLLTGVDFMRMRNDINAWFGYDDSVPLLNLYNPSHHHHHHGSVNTDFD
FNAKDPANSGPYRILNKQKQTGVYVQDQAQWDKVLVTLGGRYDWADQESLNRVAGTTDKR
DDKQFTWRGGVNYLFDNGVTPYFSYSESFEPSSQVGKDGNIFAPSKGKQYEVGVKYVPED
RPIVVTGAVYNLTKTNNLMADPEGSFFSVEGGEIRARGVEIEAKAALSASVNVVGSYTYT
DAEYTTDTTYKGNTPAQVPKHMASLWADYTFFDGPLSGLTLGTGGRYTGSSYGDPANSFK
VGSYTVVDALVRYDLARVGMAGSNVALHVNNLFDREYVASCFNTYGCFWGAERQVVATAT
FRF

Sequence of entity 2 (B), FASTA

>8B14_2 pb5 bacteriophage T5 receptor binding protein (chains B)
MSFFAGKLNNKSILSLRRGSGGDTNQHINPDSQTIFHSDMSHVIITETHSTGLRLDQGAG
DYYWSEMPSRVTQLHNNDPNRVVLTEIEFSDGSRHMLSGMSMGVGAKAYGIINPQIMSQG
GLKTQITASADLSLDVGYFNTGTSGTIPQKLRDGTGCQHMFGAFSGRRGFASSAMYLGGA
ALYKSAWSGSGYVVADAGTLTIPSDYVRHPGARNFGFNAIYVRGRSCNRVLYGMEGPNYT
TGGAVQGASSSGALNFTYNPSNPESPKYSVGFARADPTNYAYWESMGDPNDSANGPIGIY
SEHLGIYPSKITWYVTNLVYNGSGYNIDGGLFNGNDIKLSPREFIIKGVNVNNTSWKFIN
FIEKNFNVGNRADFRDVGCNLSKDSPSTGISGIATFGLPTTESNNAPSIKGGNVGGLHAN
VVSIYNFLPSASWYVSSNPPKIGNNYGDVWSENLLPLRLLGGSGSTILSGNIVFQGNGSV
HVGTVGLDLNSSRNGAIVCTMEFIDDTWLSAGGIGCFNPTEMLSQGAEYGDSRFRIGGNT
INKKLHQILSLPAGEYVPFFTIKGTVVNACKLQAAAYNPTPYWVSGLPGSVGQTGYYTLT
YYMRNDGNNNISIWLDSSMSNIIGMKACLPNIKLIIQRLT

Ligands and cofactors

ID	Name	Formula	Copies
LU9	[(2R,3S,4R,5R,6R)-2-[[(2R,4R,5R,6R)-6-[(1R)-1,2-bis(oxidanyl)ethyl]-4-[(2R,4R,5…	C93 H164 N2 O39 P2	1
DDQ	Decylamine-n,n-dimethyl-N-oxide	C12 H27 N O	1

Primary citation

Deciphering Bacteriophage T5 Host Recognition Mechanism and Infection Trigger. Degroux, S., Effantin, G., Linares, R. et al. J Virol (2023) 97:e0158422-e0158422. DOI 10.1128/jvi.01584-22 · PubMed

Other PDB entries of the same protein (UniProt P06971 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4CU4 2.3 Å, FhuA from E. coli in complex with the lasso peptide microcin J25 (MccJ25)
1QFG 2.5 Å, E. Coli ferric hydroxamate receptor (FHUA)
2FCP 2.5 Å, Ferric hydroxamate uptake receptor (FHUA) from e.coli
1BY5 2.6 Å, Fhua from E. Coli, with its ligand ferrichrome
1FCP 2.7 Å, Ferric hydroxamate uptake receptor (FHUA) from e.coli in complex with bound…
1QFF 2.7 Å, E. Coli ferric hydroxamate uptake receptor (FHUA) in complex with bound ferrichrome-iron
1BY3 2.74 Å, Fhua from E. Coli
1FI1 2.9 Å, FhuA in complex with lipopolysaccharide and rifamycin CGP4832
1QJQ 2.95 Å, Ferric hydroxamate receptor from escherichia coli (FHUA)
1QKC 3.1 Å, Escherichia coli ferric hydroxamate uptake receptor (FHUA) in complex delta two-albomycin
8A8C 3.1 Å, T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA
2GRX 3.3 Å, Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for…

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