8Y8A: Transmembrane protease serine 2

Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2. Determined by electron microscopy at 3.19 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 3.19 Å
Organisms: Homo sapiens, Human coronavirus HKU1 (isolate N5)
Chains: 6
Atoms: 33,387
Mol. weight: 555.63 kDa
Ligands: NAG
Released: 17 Jul 2024

Explore 8Y8A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Y8A contains 133 α-helices and 335 β-strands across 6 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: 35 helices, 99 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	9
α-helix	32-34	3
β-strand	35	1	10
α-helix	36	1
β-strand	46	1	11
β-strand	48	1	11
β-strand	49	1	12
β-strand	60-67	8	13
α-helix	68-69	2
β-strand	75	1	10
β-strand	80-81	2	14
β-strand	85-86	2	9
α-helix	87-90	4
β-strand	96-97	2	15
β-strand	101-107	7	16
β-strand	109-112	4	17
β-strand	117-120	4	17
β-strand	123-127	5	15
β-strand	136-142	7	15
β-strand	145-151	7	15
β-strand	155	1	18
β-strand	161-162	2	14
β-strand	175	1	18
β-strand	183-190	8	15
β-strand	197-205	9	16
β-strand	208-214	7	16
β-strand	220	1	12
β-strand	221-227	7	16
β-strand	234-238	5	15
β-strand	240-241	2	14
β-strand	256	1	16
β-strand	259	1	16
β-strand	262-270	9	13
β-strand	276-281	6	13
α-helix	286-294	9
β-strand	302-305	4	19
β-strand	316-319	4	20
β-strand	326	1	21
α-helix	329-333	5
β-strand	337-339	3	22
β-strand	346-350	5	23
β-strand	353	1	21
β-strand	354	1	24
α-helix	356-362	7
β-strand	365-371	7	23
β-strand	383-392	10	23
α-helix	398-401	4
α-helix	408-412	5
β-strand	415	1	25
α-helix	416-417	2
β-strand	422-430	9	23
β-strand	435-437	3	22
α-helix	446-448	3
β-strand	459-463	5	26
β-strand	467-468	2	27
α-helix	479-482	4
β-strand	487	1	28
β-strand	494	1	29
α-helix	495-496	2
β-strand	504-506	3	30
β-strand	515	1	28
β-strand	516-518	3	30
β-strand	522	1	31
β-strand	527	1	31
β-strand	536-537	2	27
β-strand	542	1	25
β-strand	548	1	27
β-strand	550-551	2	32
α-helix	553-555	3
β-strand	564	1	29
α-helix	569-571	3
β-strand	572-573	2	32
β-strand	575-579	5	26
β-strand	581-582	2	23
β-strand	585-597	13	23
β-strand	602	1	23
β-strand	604	1	24
β-strand	620-624	5	20
β-strand	627-631	5	20
β-strand	632	1	33
β-strand	635-636	2	34
β-strand	647-649	3	34
β-strand	655-659	5	34
β-strand	666-667	2	34
β-strand	670	1	33
α-helix	671-673	3
β-strand	678-681	4	19
β-strand	689-691	3	19
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-713	2	19
β-strand	720-721	2	19
β-strand	724-725	2	35
β-strand	737-739	3	35
β-strand	742-746	5	35
β-strand	762-766	5	35
α-helix	772	1
β-strand	773-775	3	36
β-strand	782	1	37
β-strand	785	1	37
β-strand	786-791	6	38
β-strand	794-804	11	39
β-strand	809-812	4	40
α-helix	814-818	5
α-helix	823-829	7
α-helix	830-832	3
α-helix	833-861	29
β-strand	866-868	3	41
β-strand	878	1	42
β-strand	883	1	42
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-940	7
β-strand	943-946	4	40
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1062	5
α-helix	1067-1069	3
α-helix	1071-1113	43
β-strand	1131-1137	7	39
β-strand	1140-1150	11	39
β-strand	1153-1158	6	38
β-strand	1159	1	43
β-strand	1162-1163	2	44
β-strand	1169-1172	4	45
β-strand	1175-1179	5	43
β-strand	1184-1188	5	43
β-strand	1195	1	43
β-strand	1202-1205	4	45
β-strand	1213-1214	2	44

Chain B: 39 helices, 84 β-strands

Element	Residues	Length	Sheet
β-strand	25	1	82
β-strand	34	1	83
β-strand	54-55	2	71
β-strand	59-67	9	84
α-helix	68-69	2
β-strand	75-76	2	83
β-strand	85	1	82
α-helix	88-90	3
β-strand	97	1	85
β-strand	101-107	7	83
β-strand	109-112	4	86
β-strand	117-120	4	86
β-strand	123-127	5	85
β-strand	136-141	6	85
β-strand	145-151	7	85
β-strand	155	1	87
β-strand	161-162	2	88
β-strand	175	1	87
β-strand	183-190	8	85
β-strand	197-205	9	83
β-strand	208-214	7	83
β-strand	221-227	7	83
β-strand	234-238	5	85
β-strand	240-241	2	88
β-strand	256-260	5	83
β-strand	262-270	9	84
β-strand	276-281	6	84
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-305	4	89
α-helix	307-309	3
β-strand	317-319	3	90
α-helix	329-332	4
β-strand	337-339	3	91
α-helix	340	1
β-strand	346-349	4	92
β-strand	353-354	2	93
α-helix	356-362	7
β-strand	364-371	8	92
β-strand	382-383	2	93
β-strand	385-392	8	92
α-helix	399-401	3
α-helix	408-412	5
β-strand	422-430	9	92
β-strand	435-437	3	91
α-helix	446-448	3
β-strand	459-463	5	94
β-strand	467-468	2	95
α-helix	482-484	3
β-strand	487	1	96
β-strand	494	1	97
α-helix	495-496	2
β-strand	504-506	3	98
β-strand	515	1	96
β-strand	516-518	3	98
β-strand	522	1	99
β-strand	527	1	99
β-strand	536-537	2	95
β-strand	550-551	2	100
α-helix	553-555	3
β-strand	564	1	97
α-helix	569-571	3
β-strand	572-573	2	100
β-strand	575-579	5	94
β-strand	581-582	2	92
β-strand	585-595	11	92
β-strand	602-604	3	93
β-strand	619-624	6	90
β-strand	627-632	6	90
β-strand	635-636	2	101
β-strand	647-649	3	101
β-strand	655-660	6	101
β-strand	665-668	4	101
β-strand	670	1	90
α-helix	671-673	3
β-strand	678-681	4	89
α-helix	688	1
β-strand	689-693	5	89
α-helix	697-699	3
α-helix	700-704	5
β-strand	712-714	3	89
β-strand	718-721	4	89
β-strand	724-731	8	102
β-strand	737	1	102
β-strand	742-746	5	102
β-strand	762-767	6	102
β-strand	773-775	3	41
β-strand	782	1	103
β-strand	785	1	103
β-strand	786-804	19	104
β-strand	809-811	3	105
α-helix	815-818	4
α-helix	826-829	4
α-helix	830-832	3
α-helix	835-861	27
β-strand	866-868	3	74
α-helix	885-887	3
α-helix	902-908	7
α-helix	915-922	8
α-helix	924-927	4
α-helix	934-939	6
β-strand	944-946	3	105
α-helix	947-948	2
α-helix	952-963	12
α-helix	964-967	4
α-helix	979-988	10
α-helix	994-997	4
α-helix	1001-1017	17
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1058-1064	7
α-helix	1067-1109	43
α-helix	1110-1114	5
β-strand	1129-1137	9	104
β-strand	1140-1158	19	104
β-strand	1159	1	106
β-strand	1162-1163	2	107
β-strand	1169-1172	4	107
β-strand	1175-1179	5	106
β-strand	1184-1188	5	106
β-strand	1195	1	106
β-strand	1202-1205	4	107
β-strand	1213-1214	2	107

Chain C: 41 helices, 100 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	46
β-strand	35	1	47
β-strand	49	1	48
β-strand	54-55	2	34
β-strand	60-67	8	49
α-helix	68-69	2
α-helix	72-74	3
β-strand	75-76	2	47
β-strand	80-81	2	50
β-strand	85-86	2	46
α-helix	87-90	4
β-strand	96-97	2	51
β-strand	101-107	7	47
β-strand	109-111	3	52
β-strand	118-120	3	52
β-strand	124-127	4	51
β-strand	136-141	6	51
β-strand	145-151	7	51
β-strand	155	1	53
β-strand	161-162	2	50
β-strand	175	1	53
α-helix	180-182	3
β-strand	183-190	8	51
β-strand	197-205	9	47
β-strand	208-214	7	47
β-strand	220	1	48
β-strand	221-227	7	47
β-strand	234-237	4	51
β-strand	240-241	2	50
β-strand	246	1	54
β-strand	250	1	54
β-strand	256-260	5	47
β-strand	262-270	9	49
β-strand	276-281	6	49
α-helix	286-294	9
α-helix	299-300	2
β-strand	302-307	6	55
β-strand	316-319	4	56
β-strand	326	1	57
α-helix	329-333	5
β-strand	337-339	3	58
α-helix	340	1
β-strand	346-349	4	59
β-strand	353	1	57
β-strand	354	1	60
α-helix	356-362	7
β-strand	364-371	8	59
α-helix	375-378	4
β-strand	382-383	2	61
β-strand	385-392	8	59
α-helix	398-401	4
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	59
β-strand	435-437	3	58
α-helix	444-447	4
β-strand	459-463	5	62
β-strand	466	1	63
β-strand	467-468	2	64
α-helix	479-482	4
β-strand	487	1	65
β-strand	494	1	66
α-helix	495-496	2
β-strand	504-506	3	67
β-strand	515	1	65
β-strand	516-518	3	67
β-strand	522	1	68
β-strand	527	1	68
β-strand	536-537	2	64
β-strand	549	1	63
β-strand	550-551	2	69
α-helix	553-555	3
β-strand	564	1	66
α-helix	569-571	3
β-strand	572-573	2	69
β-strand	575-579	5	62
β-strand	581-582	2	59
β-strand	585-595	11	59
β-strand	602-603	2	61
β-strand	604	1	60
α-helix	612-614	3
β-strand	620-624	5	56
β-strand	628-631	4	56
β-strand	632	1	70
β-strand	635	1	71
β-strand	647-648	2	71
β-strand	657-659	3	71
β-strand	666-667	2	71
β-strand	670	1	70
α-helix	671-673	3
β-strand	676-681	6	55
β-strand	689	1	55
β-strand	691	1	72
α-helix	697-703	7
β-strand	712-713	2	72
α-helix	719	1
β-strand	720-721	2	72
β-strand	724-731	8	73
β-strand	737-739	3	73
β-strand	742-746	5	73
β-strand	762-767	6	73
β-strand	773-775	3	74
β-strand	782	1	75
β-strand	785	1	75
β-strand	788-791	4	76
β-strand	794-804	11	77
β-strand	809-811	3	78
α-helix	814-817	4
α-helix	823-829	7
α-helix	830-832	3
α-helix	839-861	23
β-strand	866-868	3	36
β-strand	878	1	79
β-strand	883	1	79
α-helix	902-908	7
α-helix	915-923	9
α-helix	934-941	8
β-strand	944-946	3	78
α-helix	947-948	2
α-helix	952-964	13
α-helix	979-988	10
α-helix	994-999	6
α-helix	1002-1017	16
α-helix	1018-1020	3
α-helix	1024-1044	21
α-helix	1045-1048	4
α-helix	1059-1062	4
α-helix	1067-1069	3
α-helix	1071-1113	43
β-strand	1129-1137	9	77
β-strand	1140-1150	11	77
β-strand	1153-1156	4	76
β-strand	1159	1	80
β-strand	1162-1164	3	81
β-strand	1168-1172	5	81
β-strand	1175-1179	5	80
β-strand	1184-1188	5	80
β-strand	1195	1	80
α-helix	1199-1201	3
β-strand	1202-1205	4	81
β-strand	1213-1214	2	81

Chain G: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	108
α-helix	262-263	2
β-strand	271-275	5	109
β-strand	278-283	6	109
β-strand	284	1	110
β-strand	291-293	3	110
α-helix	300-302	3
β-strand	309-310	2	109
β-strand	326-327	2	109
β-strand	328-333	6	110
β-strand	338	1	111
β-strand	343	1	111
β-strand	347-351	5	110
α-helix	365-368	4
β-strand	378-383	6	108
β-strand	398-405	8	108
α-helix	407-410	4
β-strand	424-427	4	108
β-strand	442-449	8	108
β-strand	452-462	11	108
β-strand	472-475	4	108
α-helix	481-491	11

Chain H: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	5
α-helix	262-263	2
β-strand	271-275	5	6
β-strand	278-283	6	6
β-strand	284	1	7
β-strand	291-293	3	7
α-helix	300-302	3
β-strand	309-311	3	6
β-strand	326-327	2	6
β-strand	328-333	6	7
β-strand	338	1	8
β-strand	343	1	8
β-strand	347-351	5	7
β-strand	365	1	5
α-helix	366-368	3
β-strand	378-383	6	5
α-helix	392-394	3
β-strand	398-404	7	5
α-helix	405-406	2
α-helix	407-410	4
β-strand	424-427	4	5
β-strand	442-449	8	5
β-strand	452-461	10	5
β-strand	472-475	4	5
α-helix	481-491	11

Chain T: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	260-261	2	1
α-helix	262-263	2
β-strand	271-275	5	2
β-strand	278-283	6	2
β-strand	284	1	3
β-strand	291-293	3	3
α-helix	300-302	3
β-strand	309-311	3	2
β-strand	326-327	2	2
β-strand	328-333	6	3
β-strand	338	1	4
β-strand	343	1	4
β-strand	347-351	5	3
α-helix	365-368	4
β-strand	378-383	6	1
β-strand	398-404	7	1
α-helix	405-406	2
α-helix	407-410	4
β-strand	424-427	4	1
β-strand	442-449	8	1
β-strand	452-461	10	1
β-strand	472-475	4	1
α-helix	481-491	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2	G, H, T	protein	383	Homo sapiens	O15393 (AlphaFold model)
Spike glycoprotein	A, B, C	protein	1263	Human coronavirus HKU1 (isolate N5)	Q0ZME7

Sequence of entity 1 (G, H, T), FASTA

>8Y8A_1 Transmembrane protease serine 2 (chains G, H, T)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPE
WIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALM
KLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQR
CNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAY
RPGVYGNVMVFTDWIYRQMRADG

Sequence of entity 2 (A, B, C), FASTA

>8Y8A_2 Spike glycoprotein (chains A, B, C)
VIGDFNCTNSFINDYNKTIPRISEDVVDVSLGLGTYYVLNRVYLNTTLLFTGYFPKSGAN
FRDLALKGSIYLSTLWYKPPFLSDFNNGIFSKVKNTKLYVNNTLYSEFSTIVIGSVFVNT
SYTIVVQPHNGILEITACQYTMCEYPHTVCKSKGSIRNESWHIDSSEPLCLFKKNFTYNV
SADWLYFHFYQERGVFYAYYADVGMPTTFLFSLYLGTILSHYYVMPLTCNAISSNTDNET
LEYWVTPLSRRQYLLNFDEHGVITNAVDCSSSFLSEIQCKTQSFAPNTGVYDLSGFTVKP
VATVYRRIPNLPDCDIDNWLNNVSVPSPLNWERRIFSNCNFNLSTLLRLVHVDSFSCNNL
DKSKIFGSCFNSITVDKFAIPNRRRDDLQLGSSGFLQSSNYKIDISSSSCQLYYSLPLVN
VTINNFNPSSWNRRYGFGSFNLSSYDVVYSDHCFSVNSDFCPCADPSVVNSCAKSKPPSA
ICPAGTKYRHCDLDTTLYVKNWCRCSCLPDPISTYSPNTCPQKKVVVGIGEHCPGLGINE
EKCGTQLNHSSCFCSPDAFLGWSFDSCISNNRCNIFSNFIFNGINSGTTCSNDLLYSNTE
ISTGVCVNYDLYGITGQGIFKEVSAAYYNNWQNLLYDSNGNIIGFKDFLTNKTYTILPCY
SGRVSAAFYQNSSSPALLYRNLKCSYVLNNISFISQPFYFDSYLGCVLNAVNLTSYSVSS
CDLRMGSGFCIDYALPSSGGSGSGISSPYRFVTFEPFNVSFVNDSVETVGGLFEIQIPTN
FTIAGHEEFIQTSSPKVTIDCSAFVCSNYAACHDLLSEYGTFCDNINSILNEVNDLLDIT
QLQVANALMQGVTLSSNLNTNLHSDVDNIDFKSLLGCLGSQCGSSSRSPLEDLLFNKVKL
SDVGFVEAYNNCTGGSEIRDLLCVQSFNGIKVLPPILSETQISGYTTAATVAAMFPPWSA
AAGVPFPLNVQYRINGLGVTMDVLNKNQKLIANAFNKALLSIQNGFTATPSALAKIQSVV
NANAQALNSLLQQLFNKFGAISSSLQEILSRLDPPEAQVQIDRLINGRLTALNAYVSQQL
SDITLIKAGASRAIEKVNECVKSQSPRINFCGNGNHILSLVQNAPYGLLFIHFSYKPTSF
KTVLVSPGLCLSGDRGIAPKQGYFIKQNDSWMFTGSSYYYPEPISDKNVVFMNSCSVNFT
KAPFIYLNNSIPNLSDFEAELSLWFKNHTSIAPNLTFNSHINATFLDLYYEMNVIQESIK
SLN

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

TMPRSS2 and glycan receptors synergistically facilitate coronavirus entry. Wang, H., Liu, X., Zhang, X. et al. Cell (2024) 187:4261. DOI 10.1016/j.cell.2024.06.016 · PubMed

Other PDB entries of the same protein (UniProt O15393 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V04 1.58 Å, High resolution TMPRSS2 structure following acylation by nafamostat
8S0L 1.8 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
9JD1 1.9 Å, Crystal structure of TMPRSS2 in complex with Fab
7MEQ 1.95 Å, Crystal structure of human TMPRSS2 in complex with Nafamostat
9JD0 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody
9U8G 2.0 Å, Crystal structure of TMPRSS2 in complex with nanobody77_10
9E83 2.07 Å, TMPRSS2 crystal structure following acylation by UCSF_157
8V1F 2.19 Å, TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol
8S0N 2.3 Å, Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07
7Y0E 2.39 Å, Crystal structure of TMPRSS2 in complex with Camostat
8HD8 2.4 Å, Crystal structure of TMPRSS2 in complex with 212-148
9IZN 2.4 Å, Crystal structure of HKU1A RBD bound to TMPRSS2

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