8DGW: HCoV-HKU1 spike stem helix peptide

Crystal structure of HCoV-HKU1 spike stem helix peptide in complex with Fab of broadly neutralizing antibody CC95.108 isolated from a vaccinated COVID-19 convalescent. Determined by X-ray diffraction at 2.81 Å resolution. Released 25 Jan 2023.

Method: X-ray diffraction
Resolution: 2.81 Å
Organisms: Homo sapiens, Human coronavirus HKU1 (isolate N1)
Chains: 12
Atoms: 13,052
Mol. weight: 196.94 kDa
Released: 25 Jan 2023

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

Secondary structure: helices and β-sheets

8DGW contains 62 α-helices and 194 β-strands across 12 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: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	10-12	3	15
β-strand	18-25	8	14
α-helix	29-31	3
β-strand	34-39	6	15
β-strand	45-51	7	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	67-72	6	14
β-strand	77-82	6	14
α-helix	84-86	3
β-strand	88-95	8	15
β-strand	99-103	5	15
β-strand	107-111	5	15
α-helix	115-116	2
β-strand	117	1	16
β-strand	120-124	5	17
β-strand	130	1	17
β-strand	135-145	11	17
β-strand	146	1	16
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
β-strand	194-200	7	18
α-helix	201-203	3
β-strand	205-211	7	18

Chain B: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
β-strand	5	1	20
β-strand	9-13	4	21
β-strand	18-24	7	20
β-strand	31	1	22
β-strand	33-38	6	21
β-strand	45-48	4	21
β-strand	49	1	23
β-strand	53	1	23
β-strand	62-67	6	20
β-strand	70-76	7	20
α-helix	80-82	3
β-strand	85-92	8	21
β-strand	95B-98	4	21
β-strand	99	1	19
β-strand	102-106	5	21
β-strand	112	1	24
β-strand	115-119	5	25
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	25
β-strand	141	1	24
β-strand	146-151	6	26
β-strand	154	1	26
β-strand	160-162	3	25
α-helix	163-165	3
β-strand	166-167	2	25
β-strand	173-181	9	25
α-helix	183-187	5
β-strand	192-198	7	26
β-strand	201-207	7	26

Chain C: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	10-12	3	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	28
β-strand	45-51	7	28
β-strand	57-59	3	28
β-strand	67-72	6	27
β-strand	77-82	6	27
α-helix	84-86	3
β-strand	88-95	8	28
β-strand	99-103	5	28
β-strand	107-111	5	28
α-helix	115-116	2
β-strand	117	1	29
β-strand	120-124	5	30
β-strand	135-145	11	30
β-strand	146	1	29
β-strand	151-154	4	31
α-helix	155-157	3
β-strand	163-165	3	30
α-helix	166-168	3
β-strand	169-170	2	30
β-strand	176-185	10	30
α-helix	186-189	4
β-strand	195-200	6	31
α-helix	201-203	3
β-strand	205-210	6	31

Chain D: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	32
β-strand	5	1	33
β-strand	9-13	4	34
β-strand	19-24	6	33
α-helix	27-29	5
β-strand	31	1	35
β-strand	33-38	6	34
β-strand	45-48	4	34
β-strand	49	1	36
β-strand	53	1	36
β-strand	62-67	6	33
β-strand	70-75	6	33
α-helix	80-82	3
β-strand	85-92	8	34
β-strand	95B-98	4	34
β-strand	99	1	32
β-strand	102-106	5	34
β-strand	112	1	37
β-strand	115-119	5	38
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	38
β-strand	141	1	37
β-strand	146-151	6	39
β-strand	154-156	3	39
β-strand	160-162	3	38
α-helix	163-165	3
β-strand	166-167	2	38
β-strand	173-181	9	38
α-helix	183-188	6
β-strand	192-198	7	39
β-strand	201-207	7	39

Chain E: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	40
β-strand	10-12	3	41
β-strand	18-25	8	40
α-helix	29-31	3
β-strand	34-39	6	41
β-strand	45-51	7	41
β-strand	57-59	3	41
β-strand	67-72	6	40
β-strand	77-82	6	40
α-helix	84-86	3
β-strand	88-95	8	41
β-strand	99-103	5	41
β-strand	104	1	40
β-strand	107-111	5	41
α-helix	115-116	2
β-strand	117	1	42
β-strand	120-124	5	43
β-strand	137-145	9	43
β-strand	146	1	42
β-strand	151-154	4	44
α-helix	155-157	3
β-strand	163-165	3	43
α-helix	166-168	3
β-strand	169-170	2	43
β-strand	176-183	8	43
α-helix	186-188	3
β-strand	194-200	7	44
α-helix	201-203	3
β-strand	205-211	7	44

Chain F: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	45
β-strand	5	1	46
β-strand	9-13	4	47
β-strand	19-24	6	46
α-helix	27-29	5
β-strand	31	1	48
β-strand	33-38	6	47
β-strand	45-48	4	47
β-strand	49	1	49
β-strand	53	1	49
β-strand	62-67	6	46
β-strand	70-75	6	46
α-helix	80-82	3
β-strand	85-92	8	47
β-strand	95B-98	4	47
β-strand	99	1	45
β-strand	102-106	5	47
β-strand	112	1	50
β-strand	115-119	5	51
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	51
β-strand	141	1	50
β-strand	146-151	6	52
β-strand	154-155	2	52
α-helix	156	1
β-strand	160-162	3	51
α-helix	163-165	3
β-strand	166-167	2	51
β-strand	173-181	9	51
α-helix	183-187	5
β-strand	192-198	7	52
β-strand	201-207	7	52

Chains G and J: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	1228-1230	3
α-helix	1234-1241	8
β-strand	1243	1	9

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	57-59	3	2
α-helix	61-64	4
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
β-strand	99-103	5	2
β-strand	107-111	5	2
α-helix	115-116	2
β-strand	117	1	3
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-170	2	4
β-strand	176-185	10	4
α-helix	186-188	3
β-strand	194-200	7	5
α-helix	201-203	3
β-strand	205-211	7	5

3 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antibody CC95.108 Fab heavy chain	A, C, E, H	protein	220	Homo sapiens
Antibody CC95.108 Fab light chain	B, D, F, L	protein	216	Homo sapiens
Spike protein S2'	G, I, J, K	protein	25	Human coronavirus HKU1 (isolate N1)	Q5MQD0 (AlphaFold model)

Sequence of entity 1 (A, C, E, H), FASTA

>8DGW_1 Antibody CC95.108 Fab heavy chain (chains A, C, E, H)
QVQLVQSGTEVRQPGASVRVSCKASGYTFTDSYIHWVRQAPGQGLEWMGIIKPSGGNTRY
AQRFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDSRGPGIFWGQGTLVTVSSAST
KGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLY
SLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 2 (B, D, F, L), FASTA

>8DGW_2 Antibody CC95.108 Fab light chain (chains B, D, F, L)
QSVLTQPPSVSAAPERKVTISCSGSSSNIGTNFVSWYQQLPGTAPKLLIYENNKRPSGIP
DRFSGSKSGTSATLGITGLQTGDEADYYCGAWDSTPGTWVFGGGTRLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (G, I, J, K), FASTA

>8DGW_3 Spike protein S2' (chains G, I, J, K)
HSVPKLSDFESELSHWFKNQTSIAP

Primary citation

Broadly neutralizing anti-S2 antibodies protect against all three human betacoronaviruses that cause deadly disease. Zhou, P., Song, G., Liu, H. et al. Immunity (2023) 56:669-686.e7. DOI 10.1016/j.immuni.2023.02.005 · 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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