8A8C: T5 phage receptor-binding protein pb5

T5 phage receptor-binding protein pb5 bound to ferrichrome transporter FhuA. Determined by electron microscopy at 3.1 Å resolution. Released 5 Oct 2022.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Escherichia coli K-12, Escherichia phage T5
Chains: 2
Atoms: 9,544
Mol. weight: 150.42 kDa
Ligands: LU9
Released: 5 Oct 2022

Explore 8A8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8A8C contains 27 α-helices and 99 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: 14 helices, 47 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
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
α-helix	70-72	3
β-strand	76-77	2	3
β-strand	91-92	2	3
β-strand	95	1	3
β-strand	104-105	2	2
β-strand	110	1	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	227-238	12	5
β-strand	247	1	6
β-strand	250	1	7
β-strand	254	1	7
α-helix	255-256	2
β-strand	274-291	18	5
β-strand	294-317	24	5
α-helix	327-330	4
β-strand	340-367	28	5
β-strand	370-392	23	5
α-helix	398-399	2
β-strand	400-401	2	5
β-strand	420-442	23	5
β-strand	445-462	18	5
β-strand	468-484	17	5
β-strand	490-499	10	5
β-strand	506	1	8
β-strand	512	1	8
α-helix	513-515	3
β-strand	518-527	10	5
β-strand	534	1	5
β-strand	536-551	16	5
β-strand	559-576	18	5
β-strand	583-597	15	5
α-helix	604-606	3
β-strand	610	1	9
β-strand	612-621	10	5
β-strand	630-639	10	5
β-strand	642-643	2	9
β-strand	651-652	2	9
α-helix	653-654	2
β-strand	655-661	7	5
β-strand	664-665	2	5
β-strand	675-681	7	5
β-strand	689-692	4	6
β-strand	698-700	3	6
α-helix	701-702	2
β-strand	705-712	8	5

Chain B: 13 helices, 52 β-strands

Element	Residues	Length	Sheet
β-strand	42	1	10
β-strand	44-52	9	11
β-strand	54	1	12
β-strand	63-66	4	12
α-helix	67-68	2
α-helix	69-72	4
α-helix	73-77	5
β-strand	81-89	9	11
β-strand	94-96	3	11
β-strand	100-103	4	13
β-strand	104	1	14
β-strand	107-109	3	14
β-strand	112-113	2	14
β-strand	117-126	10	14
β-strand	127-129	3	13
β-strand	135-139	5	12
α-helix	147-150	4
α-helix	151-153	3
β-strand	158-167	10	14
α-helix	174-176	3
α-helix	177-182	6
β-strand	202-203	2	15
α-helix	204-206	3
β-strand	212	1	16
β-strand	219-223	5	12
β-strand	229-231	3	17
α-helix	237-238	2
β-strand	245-246	2	18
β-strand	251-258	8	14
β-strand	267-275	9	14
β-strand	282-283	2	18
α-helix	292-294	3
β-strand	298-300	3	17
β-strand	308-320	13	11
β-strand	325-327	3	11
β-strand	357-360	4	11
β-strand	375-382	8	11
β-strand	383	1	13
α-helix	395-397	3
β-strand	398	1	19
β-strand	401	1	20
β-strand	407	1	20
β-strand	410	1	19
β-strand	418-426	9	11
β-strand	458	1	10
β-strand	459-468	10	21
β-strand	471-474	4	22
β-strand	478-483	6	13
β-strand	486	1	23
β-strand	496-503	8	21
α-helix	508-510	3
β-strand	536-537	2	15
β-strand	543	1	16
β-strand	546-550	5	21
β-strand	553	1	13
β-strand	556-561	6	13
β-strand	564-568	5	14
α-helix	588-590	3
β-strand	593-597	5	14
β-strand	600-605	6	13
β-strand	610	1	23
β-strand	611-617	7	13
β-strand	620	1	14
β-strand	625-628	4	22
β-strand	632-639	8	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ferrichrome outer membrane transporter/phage receptor	A	protein	714	Escherichia coli K-12	P06971 (AlphaFold model)
Receptor-binding protein pb5	B	protein	646	Escherichia phage T5	P23207

Sequence of entity 1 (A), FASTA

>8A8C_1 Ferrichrome outer membrane transporter/phage receptor (chains A)
AVEPKEDTITVTAAPAPQESAWGPAATIAARQSATGTKTDTPIQKVPQSISVVTAEEMAL
HQPKSVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAV
IDPYMLERAEIMRGPVSVLYGKSSPGGLLNMVSKRPTTEPLKEVQFKAGTDSLFQTGFDF
SDSLDDDGVYSYRLTGLARSANAQQKGSEEQRYAIAPAFTWRPDDKTNFTFLSYFQNEPE
TGYYGWLPKEGTVEPLPNGKRLPTDFNEGAKNNTYSRNEKMVGYSFDHEFNDTFTVRQNL
RFAENKTSQNSVYGYGVCSDPANAYSKQCAALAPADKGHYLARKYVVDDEKLQNFSVDTQ
LQSKFATGDIDHTLLTGVDFMRMRNDINAWFGYDDSVPLLNLYNPVNTDFDFNAKDPANS
GPYRILNKQKQTGVYVQDQAQWDKVLVTLGGRYDWADQESLNRVAGTTDKRDDKQFTWRG
GVNYLFDNGVTPYFSYSESFEPSSQVGKDGNIFAPSKGKQYEVGVKYVPEDRPIVVTGAV
YNLTKTNNLMADPEGSFFSVEGGEIRARGVEIEAKAALSASVNVVGSYTYTDAEYTTDTT
YKGNTPAQVPKHMASLWADYTFFDGPLSGLTLGTGGRYTGSSYGDPANSFKVGSYTVVDA
LVRYDLARVGMAGSNVALHVNNLFDREYVASCFNTYGCFWGAERQVVATATFRF

Sequence of entity 2 (B), FASTA

>8A8C_2 Receptor-binding protein pb5 (chains B)
MSFFAGKLNNKSILSLRRGSGGDTNQHINPDSQTIFHSDMSHVIITETHSTGLRLDQGAG
DYYWSEMPSRVTQLHNNDPNRVVLTEIEFSDGSRHMLSGMSMGVGAKAYGIINPQIMSQG
GLKTQITASADLSLDVGYFNTGTSGTIPQKLRDGTGCQHMFGAFSGRRGFASSAMYLGGA
ALYKSAWSGSGYVVADAGTLTIPSDYVRHPGARNFGFNAIYVRGRSCNRVLYGMEGPNYT
TGGAVQGASSSGALNFTYNPSNPESPKYSVGFARADPTNYAYWESMGDPNDSANGPIGIY
SEHLGIYPSKITWYVTNLVYNGSGYNIDGGLFNGNDIKLSPREFIIKGVNVNNTSWKFIN
FIEKNFNVGNRADFRDVGCNLSKDSPSTGISGIATFGLPTTESNNAPSIKGGNVGGLHAN
VVSIYNFLPSASWYVSSNPPKIGNNYGDVWSENLLPLRLLGGSGSTILSGNIVFQGNGSV
HVGTVGLDLNSSRNGAIVCTMEFIDDTWLSAGGIGCFNPTEMLSQGAEYGDSRFRIGGNT
INKKLHQILSLPAGEYVPFFTIKGTVVNACKLQAAAYNPTPYWVSGLPGSVGQTGYYTLT
YYMRNDGNNNISIWLDSSMSNIIGMKACLPNIKLIIQRLTHHHHHH

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

Primary citation

Structural basis for host recognition and superinfection exclusion by bacteriophage T5. van den Berg, B., Silale, A., Basle, A. et al. Proc Natl Acad Sci U S A (2022) 119:e2211672119-e2211672119. DOI 10.1073/pnas.2211672119 · 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
8B14 2.6 Å, T5 Receptor Binding Protein pb5 in complex with its E. coli receptor FhuA
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
2GRX 3.3 Å, Crystal structure of TonB in complex with FhuA, E. coli outer membrane receptor for…

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