7VN9: C04 Fab heavy chain

Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab. Determined by X-ray diffraction at 4.49 Å resolution. Released 26 Oct 2022.

Method: X-ray diffraction
Resolution: 4.49 Å
Organisms: Homo sapiens, Human coronavirus 229E
Chains: 6
Atoms: 8,541
Mol. weight: 129.5 kDa
Ligands: NAG
Released: 26 Oct 2022

Explore 7VN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VN9 contains 22 α-helices and 115 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: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	17
β-strand	11-12	2	18
β-strand	18-24	7	17
α-helix	29-31	3
β-strand	34-39	6	19
β-strand	45-52	8	19
β-strand	57-60	4	19
α-helix	62-64	3
β-strand	69-73	5	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-98	7	19
β-strand	100	1	20
β-strand	109	1	20
β-strand	113	1	19
β-strand	117-119	3	19
β-strand	120-121	2	18
α-helix	125-126	2
β-strand	127	1	21
β-strand	130-134	5	22
α-helix	135	1
β-strand	146-155	10	22
β-strand	156	1	21
β-strand	160-163	4	23
β-strand	173-175	3	22
α-helix	176-178	3
β-strand	179-180	2	22
β-strand	186-194	9	22
β-strand	207-210	4	23
β-strand	215-217	3	23

Chain B: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	19-25	7	24
β-strand	33-38	6	25
β-strand	45-49	5	25
β-strand	53-54	2	25
β-strand	62-67	6	24
β-strand	70-75	6	24
α-helix	80-82	3
β-strand	85-90	6	25
β-strand	97-98	2	25
β-strand	102-106	5	25
β-strand	111	1	26
β-strand	116	1	27
α-helix	119-121	3
α-helix	122-127	6
β-strand	132-139	8	27
β-strand	140	1	26
α-helix	151-153	3
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-179	7	27

Chain C: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	299	1	28
β-strand	302-306	5	29
β-strand	308-309	2	30
β-strand	324-325	2	30
β-strand	328-329	2	29
β-strand	333	1	31
β-strand	337	1	31
β-strand	339-340	2	28
β-strand	345-346	2	28
β-strand	348-352	5	29
β-strand	360-364	5	28
β-strand	381-388	8	28
β-strand	395-404	10	28
β-strand	408-427	20	28

Chain E: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	299-306	8	13
β-strand	308-309	2	14
β-strand	324-325	2	14
β-strand	328-329	2	13
β-strand	333	1	15
β-strand	337	1	15
β-strand	339-340	2	16
β-strand	345-352	8	13
β-strand	361-364	4	16
α-helix	372	1
β-strand	382-388	7	16
β-strand	396-404	9	16
β-strand	408-425	18	16
β-strand	426-427	2	13

Chain H: 4 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	45-52	8	3
β-strand	57-60	4	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	100	1	4
β-strand	109	1	4
β-strand	113	1	3
β-strand	114	1	1
β-strand	117-119	3	3
β-strand	120-121	2	2
α-helix	125-126	2
β-strand	127	1	5
β-strand	130-134	5	6
β-strand	147-155	9	6
β-strand	156	1	5
β-strand	161-164	4	7
β-strand	173-175	3	6
α-helix	176-178	3
β-strand	179-180	2	6
β-strand	186-193	8	6
β-strand	204-210	7	7
β-strand	215-221	7	7

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-13	4	9
β-strand	19-26	8	8
β-strand	33-38	6	9
β-strand	44-49	6	9
β-strand	53-54	2	9
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	97-98	2	9
β-strand	102-106	5	9
β-strand	111	1	10
α-helix	112-113	2
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	125-127	3
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
β-strand	159-163	5	11
α-helix	164-167	4
β-strand	173-182	10	11
α-helix	183-188	6
β-strand	191-197	7	12
β-strand	205-206	2	12
β-strand	209-210	2	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C04 Fab heavy chain	A, H	protein	231	Homo sapiens
C04 Fab light chain	B, L	protein	215	Homo sapiens
Spike glycoprotein S1	C, E	protein	148	Human coronavirus 229E	P15423 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>7VN9_1 C04 Fab heavy chain (chains A, H)
EVQLVESGGGLVQPGGSLRLSCAASGFNISSSYIHWVRQAPGKGLEWVASIYSSYGYTYY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARWWASVGGAGGGLDYWGQGTLVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHT

Sequence of entity 2 (B, L), FASTA

>7VN9_2 C04 Fab light chain (chains B, L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQGYGWLITFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECG

Sequence of entity 3 (C, E), FASTA

>7VN9_3 Spike glycoprotein S1 (chains C, E)
PVYHKHTFIVLYVDFKPQSGGGKCFNCYPAGVNITLANFNETKGPLCVDTSHFTTKYVAV
YANVGRWSASINTGNCPFSFGKVNNFVKFGSVCFSLKDIPGGCAMPIVANWAYSKYYTIG
SLYVSWSDGDGITGVPQPVEGVENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Antigenic mapping reveals sites of vulnerability on alpha-HCoV spike protein. Xiang, J., Su, J., Lan, Q. et al. Commun Biol (2022) 5:1179-1179. DOI 10.1038/s42003-022-04160-8 · PubMed

Other PDB entries of the same protein (UniProt P15423 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7EJM 1.71 Å, Complex Structure of HLA-A*2402 with the Peptide from HCoV(CoV-229E) spike protein
5YL9 1.86 Å, 1.86 Angstrom crystal structure of human Coronavirus 229E fusion core
5ZUV 2.21 Å, Crystal Structure of the Human Coronavirus 229E HR1 motif in complex with pan-CoVs…
7YI6 2.28 Å, bnAb 3D1 in complex with 6-mer HR1 peptide from HCoV-229E S protein
5ZHY 2.44 Å, Structural characterization of the HCoV-229E fusion core
6U7H 3.1 Å, Cryo-EM structure of the HCoV-229E spike glycoprotein
7CYC 3.21 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
6ATK 3.5 Å, Crystal structure of the human coronavirus 229E spike protein receptor binding domain in…
7CYD 3.55 Å, Cryo-EM structures of Alphacoronavirus spike glycoprotein
8WDE 3.6 Å, CryoEM structure of the spike protein of human CoV 229E in complex with receptor hAPN…
7VNG 3.8 Å, Crystal structure of human coronavirus 229E spike protein receptor-binding domain in…

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