8VGT: HKU1 RBD

Structure of the HKU1 RBD bound to the human TMPRSS2 receptor. Determined by electron microscopy at 2.9 Å resolution. Released 6 Mar 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Human coronavirus HKU1 (isolate N1), Homo sapiens
Chains: 2
Atoms: 4,714
Mol. weight: 84.64 kDa
Ligands: NAG
Released: 6 Mar 2024

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

Secondary structure: helices and β-sheets

8VGT contains 24 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: 13 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	329-333	5
β-strand	337-339	3	1
α-helix	341-343	3
β-strand	345-349	5	2
α-helix	356-359	4
β-strand	364-371	8	2
α-helix	375-377	3
β-strand	382-383	2	3
β-strand	385-392	8	2
α-helix	395-401	7
α-helix	409-413	5
α-helix	415-417	3
β-strand	422-430	9	2
β-strand	435-437	3	1
α-helix	443-447	5
β-strand	459-463	5	4
β-strand	466-468	3	5
β-strand	477	1	6
α-helix	478	1
α-helix	479-482	4
β-strand	487	1	7
α-helix	489-490	2
β-strand	491-492	2	6
β-strand	494	1	8
α-helix	501-503	3
β-strand	504-507	4	7
β-strand	515-518	4	7
β-strand	536-538	3	5
β-strand	550-551	2	9
β-strand	556	1	10
β-strand	558-559	2	6
β-strand	566	1	8
β-strand	569	1	10
α-helix	571-573	3
β-strand	574-575	2	9
β-strand	577-581	5	4
β-strand	584	1	2
β-strand	587-597	11	2
β-strand	604-605	2	3

Chain B: 11 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	149-152	4	11
β-strand	157-162	6	11
β-strand	167-170	4	11
β-strand	171	1	12
β-strand	172	1	11
α-helix	178-185	8
α-helix	186-190	5
β-strand	196-200	5	11
β-strand	209-212	4	12
α-helix	221-224	4
β-strand	225-228	4	12
β-strand	236-240	5	11
β-strand	257	1	13
β-strand	260-261	2	14
α-helix	262-263	2
β-strand	270-275	6	15
β-strand	278-287	10	15
β-strand	290-293	4	15
α-helix	296-298	3
α-helix	305-307	3
β-strand	308-312	5	15
β-strand	316	1	16
α-helix	317-319	3
β-strand	326-333	8	15
β-strand	338	1	17
β-strand	343	1	17
β-strand	347-351	5	15
α-helix	354-357	4
β-strand	365	1	14
α-helix	366-368	3
β-strand	378-383	6	14
β-strand	396	1	16
β-strand	398-405	8	14
α-helix	407-410	4
β-strand	424-427	4	14
β-strand	435	1	13
β-strand	444-449	6	14
β-strand	452-461	10	14
β-strand	467	1	18
β-strand	470	1	18
β-strand	472-476	5	14
α-helix	477-489	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Spike protein S1	A	protein	338	Human coronavirus HKU1 (isolate N1)	Q5MQD0 (AlphaFold model)
Transmembrane protease serine 2	B	protein	416	Homo sapiens	O15393 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VGT_1 Spike protein S1 (chains A)
MGILPSPGMPALLSLVSLLSVLLMGCVAETGTRIPDLPDCDIDKWLNNFNVPSPLNWERK
IFSNCNFNLSTLLRLVHTDSFSCNNFDESKIYGSCFKSIVLDKFAIPNSRRSDLQLGSSG
FLQSSNYKIDTTSSSCQLYYSLPAINVTINNYNPSSWNRRYGFNNFNLSSHSVVYSRYCF
SVNNTFCPCAKPSFASSCKSHKPPSASCPIGTNYRSCESTTVLDHTDWCRCSCLPDPITA
YDPRSCSQKKSLVGVGEHCAGFGVDEEKCGVLDGSYNVSCLCSTDAFLGWSYDTCVSNNR
CNIFSNFILNGINSGTTCSNDLLQPNTGGSHHHHHHHH

Sequence of entity 2 (B), FASTA

>8VGT_2 Transmembrane protease serine 2 (chains B)
MKWVTFISLLFLFSSAYSMGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVR
LYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFM
KLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQV
SLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKV
ISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKG
KTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDAGGPLVCSKNN
IWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGDDDDKSGHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. McCallum, M., Park, Y.J., Stewart, C. et al. Cell (2024) 187:4231. DOI 10.1016/j.cell.2024.06.006 · PubMed

Other PDB entries of the same protein (UniProt Q5MQD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9JCY 1.8 Å, Crystal structure of the HCoV-HKU1 RBD in complex with Fab
5KWB 1.91 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BT2 1.93 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein D1 (Down State, locally refined)
9BSW 2.06 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDA state)
7EJN 2.11 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-HKU1) spike protein
9BT9 2.11 Å, Cryo-EM Structure of HKU1 spike D1 Domain (Active state, locally refined)
9BT1 2.22 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BT0 2.23 Å, Cryo-EM structure of HCoV-HKU1 Spike glycoprotein (DDD state)
5GNB 2.3 Å, Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human…
9BTB 2.33 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…
9BSX 2.37 Å, Cryo-EM structure of HCoV-HKU1 glycoprotein in complex with 9O-acetyl GD3 sialoglycan…
9BTA 2.39 Å, Cryo-EM density map of HKU1 spike glycoprotein D1 domain in complex with 9O-acetyl GD3…

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