8DG9: RSV prefusion F trimer

Cryo-EM Structure of RSV prefusion F trimer in complex with three MxR Fabs. Determined by electron microscopy at 2.24 Å resolution. Released 22 Feb 2023.

Method: Electron microscopy
Resolution: 2.24 Å
Organisms: Respiratory syncytial virus A2, Homo sapiens
Chains: 9
Atoms: 15,450
Mol. weight: 265.59 kDa
Ligands: NAG
Released: 22 Feb 2023

Explore 8DG9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DG9 contains 65 α-helices and 165 β-strands across 9 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: 16 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	1
β-strand	38-60	23	1
α-helix	74-96	23
α-helix	139-141	3
β-strand	144	1	2
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	1
β-strand	186-194	9	1
α-helix	195-198	4
α-helix	199-203	5
α-helix	218-238	21
β-strand	243-244	2	1
α-helix	254-263	10
α-helix	268-275	8
α-helix	278-283	6
β-strand	286-292	7	1
β-strand	296-318	23	1
β-strand	321-322	2	3
β-strand	333-336	4	3
β-strand	340-345	6	1
β-strand	348-352	5	1
β-strand	358-361	4	1
β-strand	364-368	5	1
α-helix	369-371	3
β-strand	373-376	4	1
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	3
β-strand	404-407	4	4
β-strand	411-416	6	4
β-strand	422-426	5	5
β-strand	430-434	5	5
β-strand	438-443	6	4
β-strand	449-452	4	5
β-strand	455-458	4	5
α-helix	459-460	2
β-strand	465-469	5	1
α-helix	474-477	4
β-strand	487-491	5	3
α-helix	492-512	21

Chain B: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	14
β-strand	38-60	23	14
α-helix	74-96	23
α-helix	139-141	3
β-strand	144	1	4
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	14
β-strand	186-194	9	14
α-helix	195-197	3
α-helix	198-203	6
α-helix	218-238	21
β-strand	243-244	2	14
α-helix	247-248	2
α-helix	254-262	9
α-helix	268-275	8
α-helix	278-283	6
β-strand	286-293	8	14
β-strand	296-318	23	14
β-strand	321-322	2	15
β-strand	333-336	4	15
β-strand	340-345	6	14
β-strand	348-352	5	14
β-strand	358-361	4	14
β-strand	364-368	5	14
α-helix	369-371	3
β-strand	373-375	3	14
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	15
β-strand	404-407	4	16
β-strand	411-416	6	16
β-strand	422-426	5	17
β-strand	430-434	5	17
β-strand	438-443	6	16
β-strand	449-452	4	17
β-strand	455-458	4	17
α-helix	459-460	2
β-strand	465-469	5	14
α-helix	474-477	4
β-strand	490-491	2	15
α-helix	492-512	21

Chain C: 17 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	26
β-strand	38-60	23	26
α-helix	74-96	23
α-helix	139-141	3
β-strand	144	1	16
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	26
β-strand	186-194	9	26
α-helix	195-201	7
α-helix	218-238	21
β-strand	243-244	2	26
α-helix	247-248	2
α-helix	254-262	9
α-helix	268-275	8
α-helix	278-283	6
β-strand	286-292	7	26
β-strand	296-318	23	26
β-strand	321-322	2	27
β-strand	333-336	4	27
β-strand	340-345	6	26
β-strand	348-352	5	26
β-strand	358-361	4	26
β-strand	364-368	5	26
α-helix	369-371	3
β-strand	373-375	3	26
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	27
β-strand	404-407	4	2
β-strand	411-416	6	2
β-strand	422-426	5	28
β-strand	430-434	5	28
α-helix	435-436	2
β-strand	438-443	6	2
β-strand	449-452	4	28
β-strand	455-458	4	28
α-helix	459-460	2
β-strand	465-469	5	26
α-helix	474-477	4
β-strand	490-491	2	27
α-helix	492-512	21

Chains D, F and H: 3 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	29
β-strand	11-12	2	30
β-strand	18	1	31
β-strand	21-23	3	29
α-helix	29-31	3
β-strand	34-39	6	32
β-strand	45-51	7	32
β-strand	57-59	3	32
β-strand	67	1	31
β-strand	70-72	3	29
β-strand	77-79	3	29
β-strand	82	1	31
α-helix	84-86	3
β-strand	88-94	7	32
α-helix	100A-100C	3
β-strand	102-103	2	32
β-strand	107-109	3	32
β-strand	110-111	2	30

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	33
β-strand	5	1	34
β-strand	9-13	4	35
β-strand	19-24	6	34
β-strand	33-38	6	35
β-strand	45-48	4	35
β-strand	49	1	36
β-strand	53	1	36
α-helix	54-55	2
β-strand	62	1	34
β-strand	65-67	3	34
β-strand	70-75	6	34
α-helix	80-82	3
β-strand	84-92	9	35
β-strand	95B-98	4	35
β-strand	99	1	33
β-strand	102-106	5	35

Chain G: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	22
β-strand	5	1	23
β-strand	9-13	4	24
β-strand	19-24	6	23
β-strand	33-38	6	24
β-strand	45-48	4	24
β-strand	49	1	25
β-strand	53	1	25
α-helix	54-55	2
β-strand	62	1	23
β-strand	65-67	3	23
β-strand	70-75	6	23
α-helix	80-82	3
β-strand	85-92	8	24
β-strand	95B-98	4	24
β-strand	99	1	22
β-strand	102-106	5	24

Chain L: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	10
β-strand	5	1	11
β-strand	9-13	4	12
β-strand	19-24	6	11
β-strand	34-38	5	12
β-strand	45-48	4	12
β-strand	49	1	13
β-strand	53	1	13
α-helix	54-55	2
β-strand	62	1	11
β-strand	65-67	3	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	85-92	8	12
β-strand	95B-98	4	12
β-strand	99	1	10
β-strand	102-106	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusion glycoprotein F0	A, B, C	protein	569	Respiratory syncytial virus A2	P03420
mAb MxR Heavy Chain, VH region	D, F, H	protein	120	Homo sapiens
mAb MxR Light Chain, VL region	E, G, L	protein	111	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>8DG9_1 Fusion glycoprotein F0 (chains A, B, C)
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL
STFLGLNDIFEAQKIEWHEGSHHHHHHHH

Sequence of entity 2 (D, F, H), FASTA

>8DG9_2 mAb MxR Heavy Chain, VH region (chains D, F, H)
EVQVVESGGGLVKPGGSLRLSCAASGFPFSSYKMDWVRQAPGKGLEWVSSISASGSYINY
ADSVKGRFTISRDNAKNSLYLQMKSLRADDTAVYFCARDGGRELSPFEKWGQGILVTVSS

Sequence of entity 3 (E, G, L), FASTA

>8DG9_3 mAb MxR Light Chain, VL region (chains E, G, L)
QSVLTQPPSVSGAPGQRVTISCTGTNSNIGTGYDVHWYQQLPGTAPKVVLFDNNNRPSGV
PDRFSGSKSGTSAALAITGLQAEDEAVYYCQSYDKSLGGWVFGGGTKLTVL

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Cross-protective antibodies against common endemic respiratory viruses. Caban, M., Rodarte, J.V., Bibby, M. et al. Nat Commun (2023) 14:798-798. DOI 10.1038/s41467-023-36459-3 · PubMed

Other PDB entries of the same protein (UniProt P03420), best resolution first:

29QJ 1.32 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex…
6OJ7 1.45 Å, Respiratory syncytial virus fusion glycoprotein N-terminal heptad repeat domain+VIQKI…
3KPE 1.47 Å, Solution structure of the respiratory syncytial virus (RSV)six-helix bundle complexed…
9RA5 1.63 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain in complex…
3O41 1.95 Å, Crystal Structure of 101F Fab Bound to 15-mer Peptide Epitope
9VWE 2.06 Å, Cryo-EM structure of RSV pre-F (strain A2) in complex with Fabs 1A2 and 2D10
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
7LVW 2.1 Å, Structure of RSV F in Complex with VHH Cl184
6NTX 2.2 Å, Respiratory syncytial virus fusion protein N-terminal heptad repeat domain+VIQKI
8PHI 2.29 Å, Crystal structure of prefusion-stabilized RSV F Variant DS-Cav1 in complex with Lonafarnib
5C69 2.3 Å, Crystal Structure of Prefusion-stabilized RSV F variant PR-DM
5EA4 2.3 Å, Crystal Structure of Inhibitor JNJ-49153390 in Complex with Prefusion RSV F Glycoprotein

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