6U7F: HCoV-229E RBD Class IV

HCoV-229E RBD Class IV in complex with human APN. Determined by X-ray diffraction at 2.75 Å resolution. Released 13 Nov 2019.

Method: X-ray diffraction
Resolution: 2.75 Å
Organisms: Homo sapiens, Human coronavirus 229E
Chains: 4
Atoms: 16,575
Mol. weight: 243.67 kDa
Ligands: NAG, ZN
Released: 13 Nov 2019

Explore 6U7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U7F contains 101 α-helices and 103 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: 50 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-92	13	1
β-strand	102-113	12	1
β-strand	119-123	5	2
β-strand	128-129	2	1
α-helix	130-131	2
β-strand	132	1	3
β-strand	135	1	3
β-strand	137-141	5	1
α-helix	147-149	3
β-strand	150-156	7	2
β-strand	161-166	6	2
β-strand	175-185	11	1
β-strand	192-200	9	4
β-strand	203-211	9	4
α-helix	217-219	3
β-strand	223	1	2
β-strand	231	1	5
β-strand	232-240	9	1
β-strand	244-247	4	4
α-helix	250	1
β-strand	251	1	6
β-strand	256-257	2	1
β-strand	264-268	5	1
β-strand	269	1	6
α-helix	270-273	4
β-strand	275	1	5
α-helix	277-279	3
β-strand	282-285	4	4
β-strand	288-293	6	7
β-strand	299-304	6	7
α-helix	306-311	6
α-helix	315-331	17
β-strand	340-346	7	7
β-strand	353-354	2	7
β-strand	359-363	5	7
α-helix	364-367	4
α-helix	376-392	17
β-strand	395	1	8
β-strand	399	1	8
β-strand	400-401	2	9
α-helix	404-406	3
α-helix	408-425	18
α-helix	431-434	4
α-helix	435	1
α-helix	436-441	6
α-helix	442-447	6
α-helix	457-458	2
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-490	11
α-helix	493-506	14
β-strand	511-512	2	9
α-helix	514-527	14
α-helix	536-544	9
β-strand	550-555	6	10
β-strand	560-565	6	10
β-strand	586-588	3	11
β-strand	590-592	3	12
β-strand	595-596	2	12
β-strand	600-602	3	11
β-strand	606-608	3	10
α-helix	610-612	3
β-strand	620-622	3	12
α-helix	624-626	3
β-strand	631-634	4	10
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-847	10
α-helix	856-858	3
α-helix	859-868	10
α-helix	873-888	16
α-helix	898-906	9
α-helix	912-925	14
α-helix	931-933	3
α-helix	934-965	32

Chain B: 49 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	70-72	3
α-helix	76-77	2
β-strand	80-92	13	13
β-strand	102-113	12	13
β-strand	119-123	5	14
β-strand	128-129	2	13
α-helix	130-131	2
β-strand	132	1	15
β-strand	135	1	15
β-strand	137-141	5	13
α-helix	147-149	3
β-strand	150-156	7	14
β-strand	161-166	6	14
β-strand	175-185	11	13
β-strand	192-200	9	16
β-strand	203-211	9	16
α-helix	217-220	4
β-strand	223	1	14
β-strand	231	1	17
β-strand	232-240	9	13
β-strand	244-247	4	16
α-helix	250	1
β-strand	251	1	18
β-strand	256-258	3	13
β-strand	261-268	8	13
β-strand	269	1	18
α-helix	270-273	4
β-strand	275	1	17
α-helix	277-279	3
β-strand	282-285	4	16
β-strand	288-293	6	19
β-strand	299-304	6	19
α-helix	306-311	6
α-helix	315-332	18
β-strand	340-346	7	19
β-strand	353-354	2	19
β-strand	359-363	5	19
α-helix	364-366	3
α-helix	376-392	17
β-strand	395	1	20
β-strand	399	1	20
β-strand	400-401	2	21
α-helix	404-406	3
α-helix	407-425	19
α-helix	431-434	4
α-helix	435	1
α-helix	436-440	5
α-helix	441-447	7
α-helix	459-461	3
α-helix	465-470	6
α-helix	474	1
α-helix	475-479	5
α-helix	480-490	11
α-helix	493-507	15
β-strand	511-512	2	21
α-helix	514-528	15
α-helix	536-544	9
β-strand	550-555	6	22
β-strand	560-565	6	22
β-strand	586-588	3	23
β-strand	590-592	3	24
β-strand	595-596	2	24
β-strand	600-602	3	23
β-strand	606-608	3	22
α-helix	610-612	3
β-strand	620-622	3	24
α-helix	624-626	3
β-strand	631-634	4	22
α-helix	636-649	14
α-helix	650-652	3
α-helix	655-670	16
α-helix	676-681	6
α-helix	684-688	5
α-helix	692-709	18
α-helix	715-736	22
α-helix	747-762	16
α-helix	766-781	16
α-helix	790-803	14
α-helix	806-817	12
α-helix	822-831	10
α-helix	832-834	3
α-helix	838-847	10
α-helix	856-858	3
α-helix	859-868	10
α-helix	870-888	19
α-helix	898-906	9
α-helix	912-924	13
α-helix	931-933	3
α-helix	934-965	32

Chain C: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	303-309	7	25
β-strand	317	1	7
α-helix	321-322	2
β-strand	324-329	6	25
β-strand	333	1	26
β-strand	337	1	26
β-strand	349-352	4	25
β-strand	354-355	2	27
β-strand	358-362	5	27
β-strand	386	1	27
β-strand	395-402	8	27
β-strand	406-414	9	27

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	303-309	7	28
β-strand	317	1	19
α-helix	321-322	2
β-strand	324-329	6	28
β-strand	333	1	29
β-strand	337	1	29
β-strand	339	1	30
β-strand	349-352	4	28
β-strand	354-355	2	30
β-strand	358-362	5	30
β-strand	384-386	3	30
β-strand	394-402	9	30
β-strand	407-416	10	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aminopeptidase N	A, B	protein	906	Homo sapiens	P15144 (AlphaFold model)
Spike glycoprotein	C, D	protein	145	Human coronavirus 229E	Q1HVL3

Sequence of entity 1 (A, B), FASTA

>6U7F_1 Aminopeptidase N (chains A, B)
GGRPDQSKAWNRYRLPNTLKPDSYRVTLRPYLTPNDRGLYVFKGSSTVRFTCKEATDVII
IHSKKLNYTLSQGHRVVLRGVGGSQPPDIDKTELVEPTEYLVVHLKGSLVKDSQYEMDSE
FEGELADDLAGFYRSEYMEGNVRKVVATTQMQAADARKSFPCFDEPAMKAEFNITLIHPK
DLTALSNMLPKGPSTPLPEDPNWNVTEFHTTPKMSTYLLAFIVSEFDYVEKQASNGVLIR
IWARPSAIAAGHGDYALNVTGPILNFFAGHYDTPYPLPKSDQIGLPDFNAGAMENWGLVT
YRENSLLFDPLSSSSSNKERVVTVIAHELAHQWFGNLVTIEWWNDLWLNEGFASYVEYLG
ADYAEPTWNLKDLMVLNDVYRVMAVDALASSHPLSTPASEINTPAQISELFDAISYSKGA
SVLRMLSSFLSEDVFKQGLASYLHTFAYQNTIYLNLWDHLQEAVNNRSIQLPTTVRDIMN
RWTLQMGFPVITVDTSTGTLSQEHFLLDPDSNVTRPSEFNYVWIVPITSIRDGRQQQDYW
LIDVRAQNDLFSTSGNEWVLLNLNVTGYYRVNYDEENWRKIQTQLQRDHSAIPVINRAQI
INDAFNLASAHKVPVTLALNNTLFLIEERQYMPWEAALSSLSYFKLMFDRSEVYGPMKNY
LKKQVTPLFIHFRNNTNNWREIPENLMDQYSEVNAISTACSNGVPECEEMVSGLFKQWME
NPNNNPIHPNLRSTVYCNAIAQGGEEEWDFAWEQFRNATLVNEADKLRAALACSKELWIL
NRYLSYTLNPDLIRKQDATSTIISITNNVIGQGLVWDFVQSNWKKLFNDYGGGSFSFSNL
IQAVTRRFSTEYELQQLEQFKKDNEETGFGSGTRALEQALEKTKANIKWVKENKEVVLQW
FTENSK

Sequence of entity 2 (C, D), FASTA

>6U7F_2 Spike glycoprotein (chains C, D)
GGRPLPVYHKHMFIVLYVNFKLRSGVGRCYNCRPAVVNITLANFNETKGPLCVDTSHFTT
QFVGAKFDRWSASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIMANLANLNSH
TIGTLYVSWSDGDGITGVPQPVEGV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15
ZN	Zinc ion	Zn	2

Primary citation

The human coronavirus HCoV-229E S-protein structure and receptor binding. Li, Z., Tomlinson, A.C.A., Wong, A.H.M. et al. Elife (2019) 8. DOI 10.7554/eLife.51230 · PubMed

Other PDB entries of the same protein (UniProt P15144 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7AEW 1.2 Å, 14-3-3 sigma bound to bis-phosphorylated aminopeptidase N (APN, CD13) via canonical and…
6XWD 1.6 Å, 14-3-3 sigma bound to canonical mono-phosphorylated aminopeptidase N (APN, CD13) binding…
4FYT 1.85 Å, Human aminopeptidase N (CD13) in complex with amastatin
4FYQ 1.9 Å, Human aminopeptidase N (CD13)
4FYR 1.91 Å, Human aminopeptidase N (CD13) in complex with bestatin
4FYS 2.01 Å, Human aminopeptidase N (CD13) in complex with angiotensin IV
6U7G 2.35 Å, HCoV-229E RBD Class V in complex with human APN
5LHD 2.6 Å, Structure of glycosylated human aminopeptidase N
9CAM 2.96 Å, Aminopeptidase N close state
6U7E 3.0 Å, HCoV-229E RBD Class III in complex with human APN
7VPQ 3.1 Å, Structures of a deltacoronavirus spike protein bound to porcine and human receptors…
9CAO 3.14 Å, Aminopeptidase N open state

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