9IZN: HKU1A RBD

Crystal structure of HKU1A RBD bound to TMPRSS2. Determined by X-ray diffraction at 2.4 Å resolution. Released 23 Oct 2024.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Human coronavirus HKU1 (isolate N1)
Chains: 2
Atoms: 5,771
Mol. weight: 86.45 kDa
Ligands: NAG
Released: 23 Oct 2024

Explore 9IZN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IZN contains 34 α-helices and 57 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: 22 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	312-315	4
β-strand	317-319	3	6
α-helix	320-321	2
α-helix	324-325	2
β-strand	326	1	7
α-helix	329-333	5
β-strand	337-339	3	8
α-helix	340	1
α-helix	341-343	3
β-strand	345-349	5	9
β-strand	353-354	2	7
α-helix	356-362	7
β-strand	364-371	8	9
α-helix	375-377	3
β-strand	382-383	2	7
β-strand	385-392	8	9
α-helix	395-401	7
α-helix	408-412	5
α-helix	415-417	3
β-strand	422-430	9	9
α-helix	431-433	3
β-strand	435-437	3	8
α-helix	443-447	5
β-strand	459-463	5	10
β-strand	467-468	2	11
β-strand	477	1	12
α-helix	479-482	4
β-strand	487	1	13
α-helix	489-491	3
β-strand	492	1	12
β-strand	494	1	14
α-helix	495-496	2
α-helix	499-503	5
β-strand	504-509	6	13
β-strand	512-518	7	13
α-helix	530-532	3
β-strand	536-537	2	11
β-strand	550-551	2	15
α-helix	553-555	3
β-strand	556	1	16
β-strand	558	1	12
β-strand	566	1	14
β-strand	569	1	16
α-helix	571-573	3
β-strand	574-575	2	15
β-strand	577-581	5	10
β-strand	583	1	9
β-strand	587-597	11	9
β-strand	604-606	3	7
α-helix	610-612	3
β-strand	621-626	6	6
β-strand	629-638	10	6
α-helix	640-642	3
β-strand	649-652	4	6
β-strand	656-661	6	6
β-strand	668-672	5	6

Chain B: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	149-152	4	1
α-helix	153-155	3
β-strand	157-162	6	1
β-strand	167-170	4	1
β-strand	172	1	1
α-helix	178-188	11
β-strand	196-200	5	1
α-helix	232-234	3
β-strand	236-240	5	1
α-helix	261-263	3
β-strand	270-275	6	2
β-strand	278-287	10	2
β-strand	290-293	4	2
α-helix	295-298	4
α-helix	305-307	3
β-strand	309-312	4	2
β-strand	316	1	3
α-helix	317-319	3
β-strand	326-333	8	2
β-strand	338	1	4
β-strand	343	1	4
β-strand	347-351	5	2
β-strand	365	1	5
α-helix	366-368	3
β-strand	378-383	6	5
α-helix	392-394	3
β-strand	396	1	3
β-strand	398-405	8	5
α-helix	407-410	4
β-strand	424-428	5	5
β-strand	444-449	6	5
β-strand	452-461	10	5
β-strand	472-476	5	5
α-helix	477-480	4
α-helix	481-489	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protease serine 2	B	protein	392	Homo sapiens	O15393 (AlphaFold model)
Spike protein S1	A	protein	379	Human coronavirus HKU1 (isolate N1)	Q5MQD0 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9IZN_1 Transmembrane protease serine 2 (chains B)
MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSW
HPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHS
DACSSKAVVSLRCIACGVNLNSSRQSQIVGGESALPGAWPWQVSLHVQNVHVCGGSIITP
EWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIAL
MKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQ
RCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKA
YRPGVYGNVMVFTDWIYRQMRADGHHHHHHHH

Sequence of entity 2 (A), FASTA

>9IZN_2 Spike protein S1 (chains A)
SGFTVKPVATVHRRIPDLPDCDIDKWLNNFNVPSPLNWERKIFSNCNFNLSTLLRLVHTD
SFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSGFLQSSNYKIDTTSSSCQLY
YSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCFSVNNTFCPCAKPSFASSCK
SHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITAYDPRSCSQKKSLVGVGEHC
AGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNRCNIFSNFILNGINSGTTCS
NDLLQPNTEVFTDVCVDYDLYGITGQGIFKEVSAVYYNSWQNLLYDSNGNIIGFKDFVTN
KTYNIFPCYAGHHHHHHHH

Ligands and cofactors

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

Primary citation

High-resolution crystal structure of human coronavirus HKU1 receptor binding domain bound to TMPRSS2 receptor. Wang, W., Guan, J., Ren, M. et al. Hlife (2024). DOI 10.1016/j.hlife.2024.09.005

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
7XYD 2.58 Å, Crystal structure of TMPRSS2 in complex with Nafamostat

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