6DC5: RSV prefusion F

RSV prefusion F in complex with AM22 Fab. Determined by X-ray diffraction at 3.5 Å resolution. Released 10 Jul 2019.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1, Homo sapiens
Chains: 9
Atoms: 20,286
Mol. weight: 333.48 kDa
Ligands: NAG, CD
Released: 10 Jul 2019

Explore 6DC5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DC5 contains 93 α-helices and 219 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: 14 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	1
β-strand	38-49	12	1
β-strand	51-60	10	2
α-helix	74-96	23
β-strand	144	1	3
α-helix	149-159	11
α-helix	163-170	8
β-strand	176-180	5	2
β-strand	186-194	9	2
α-helix	196-202	7
α-helix	204-207	4
β-strand	211-214	4	4
α-helix	217-240	24
β-strand	243-244	2	2
α-helix	254-262	9
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-293	8	2
β-strand	296-305	10	2
β-strand	308-318	11	1
β-strand	321-322	2	5
β-strand	333-336	4	5
β-strand	340-345	6	1
β-strand	348-352	5	1
β-strand	359-361	3	1
β-strand	364-368	5	1
α-helix	369-371	3
β-strand	373-375	3	1
α-helix	377-383	7
β-strand	394-398	5	5
β-strand	404-407	4	6
β-strand	411-415	5	6
β-strand	422-425	4	7
β-strand	433-434	2	7
β-strand	439-443	5	6
β-strand	449-452	4	7
β-strand	455-458	4	7
α-helix	459-460	2
β-strand	465-469	5	1
α-helix	474-477	4
β-strand	490-491	2	5
α-helix	492-508	17

Chain B: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	17-25	9	19
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	46-52	7	20
β-strand	56-59	4	20
β-strand	67-72	6	19
β-strand	77-82A	7	19
α-helix	84-86	3
β-strand	88-93	6	20
β-strand	97-99	3	4
β-strand	100C-100F	4	4
β-strand	103	1	20
β-strand	107-111	5	20
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	151-154	4	23
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	176-185	10	22
α-helix	186-190	5
β-strand	194-200	7	23
α-helix	201-203	3
β-strand	205-211	7	23

Chain C: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-13	4	25
β-strand	18-25	8	24
α-helix	30-32	3
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	70-76	7	24
α-helix	80-82	3
β-strand	85-91	7	25
β-strand	96-98	3	25
β-strand	102-106	5	25
β-strand	111	1	26
α-helix	112-113	2
β-strand	114-118	5	27
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	27
β-strand	140	1	26
β-strand	144-150	7	28
β-strand	153-154	2	28
α-helix	155	1
β-strand	159-163	5	27
α-helix	164-167	4
β-strand	173-182	10	27
α-helix	183-187	5
β-strand	191-198	8	28
β-strand	205-210	6	28

Chain D: 16 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	8
β-strand	38-49	12	8
β-strand	51-60	10	9
α-helix	74-97	24
α-helix	139-141	3
β-strand	144	1	10
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	9
β-strand	186-194	9	9
α-helix	196-202	7
α-helix	204-207	4
β-strand	211-214	4	11
α-helix	217-240	24
β-strand	243-244	2	9
α-helix	247-248	2
α-helix	254-262	9
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-293	8	9
β-strand	296-305	10	9
β-strand	308-318	11	8
β-strand	321-322	2	12
α-helix	328-330	3
β-strand	333-336	4	12
β-strand	340-345	6	8
β-strand	348-352	5	8
β-strand	359-361	3	8
β-strand	364-368	5	8
α-helix	369-371	3
β-strand	373-375	3	8
α-helix	377-382	6
β-strand	394-398	5	12
β-strand	404-407	4	3
β-strand	411-415	5	3
β-strand	422-426	5	13
β-strand	430-434	5	13
α-helix	435-436	2
β-strand	439-443	5	3
β-strand	449-452	4	13
β-strand	455-458	4	13
β-strand	465-469	5	8
β-strand	490-491	2	12
α-helix	492-511	20

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	29
α-helix	7-9	3
β-strand	10-12	3	30
β-strand	17-25	9	29
α-helix	29-31	3
β-strand	33-39	7	30
β-strand	45-52	8	30
β-strand	56-59	4	30
β-strand	67-72	6	29
β-strand	77-82A	7	29
α-helix	84-86	3
β-strand	88-93	6	30
β-strand	97-99	3	11
β-strand	100C-100F	4	11
β-strand	103	1	30
β-strand	107-111	5	30
β-strand	117	1	31
α-helix	118-119	2
β-strand	120-124	5	32
β-strand	135-145	11	32
β-strand	146	1	31
β-strand	151-154	4	33
α-helix	155-157	3
β-strand	159	1	33
β-strand	163-165	3	32
α-helix	166-168	3
β-strand	169-170	2	32
β-strand	176-185	10	32
α-helix	186-188	3
β-strand	195-200	6	33
α-helix	201-203	3
β-strand	205-210	6	33

Chain F: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	34
β-strand	10-13	4	35
α-helix	18	1
β-strand	19-25	7	34
α-helix	30-32	3
β-strand	33-38	6	35
β-strand	45-49	5	35
β-strand	53-54	2	35
α-helix	55	1
β-strand	62-67	6	34
β-strand	70-75	6	34
α-helix	80-82	3
β-strand	85-91	7	35
β-strand	96-98	3	35
β-strand	102-106	5	35
β-strand	111	1	36
α-helix	112-113	2
β-strand	114-118	5	37
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	37
β-strand	140	1	36
β-strand	145-150	6	38
β-strand	153-154	2	38
α-helix	155	1
β-strand	159-163	5	37
α-helix	164-167	4
β-strand	173-182	10	37
α-helix	183-186	4
β-strand	191-197	7	38
β-strand	205-210	6	38

Chain G: 15 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	14
β-strand	38-49	12	14
β-strand	51-60	10	15
α-helix	74-96	23
α-helix	139-141	3
β-strand	144	1	6
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	15
β-strand	186-194	9	15
α-helix	196-202	7
α-helix	204-207	4
β-strand	211-214	4	16
α-helix	217-239	23
β-strand	243-244	2	15
α-helix	254-262	9
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-293	8	15
β-strand	296-305	10	15
β-strand	308-318	11	14
β-strand	321-322	2	17
β-strand	333-336	4	17
β-strand	341-345	5	14
β-strand	348-352	5	14
β-strand	359-361	3	14
β-strand	364-368	5	14
α-helix	369-371	3
β-strand	373-375	3	14
α-helix	377-382	6
β-strand	394-398	5	17
β-strand	406-407	2	10
β-strand	411-415	5	10
β-strand	422-426	5	18
β-strand	430-434	5	18
β-strand	439-443	5	10
β-strand	449-452	4	18
β-strand	455-458	4	18
α-helix	459-460	2
β-strand	465-469	5	14
α-helix	474-477	4
β-strand	490-491	2	17
α-helix	492-508	17

Chain H: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	39
β-strand	10-12	3	40
β-strand	17-20	4	39
β-strand	22-25	4	39
α-helix	29-31	3
β-strand	33-39	7	40
β-strand	45-52	8	40
β-strand	56-59	4	40
β-strand	67-72	6	39
β-strand	77-82A	7	39
α-helix	84-86	3
β-strand	88-93	6	40
β-strand	97-99	3	16
β-strand	100C-100F	4	16
β-strand	103	1	40
β-strand	107-111	5	40
β-strand	117	1	41
α-helix	118-119	2
β-strand	120-124	5	42
α-helix	125-127	3
β-strand	135-145	11	42
β-strand	146	1	41
β-strand	151-154	4	43
α-helix	155-157	3
β-strand	159	1	43
β-strand	163-165	3	42
α-helix	166-168	3
β-strand	169-170	2	42
β-strand	176-185	10	42
α-helix	186-188	3
β-strand	195-200	6	43
α-helix	201-203	3
β-strand	205-210	6	43

1 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
RSV fusion glycoprotein	A, D, G	protein	568	Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), P03420
Fab AM22 heavy chain	B, E, H	protein	228	Homo sapiens	Q6GMX6 (AlphaFold model)
Fab AM22 light chain	C, F, I	protein	215	Homo sapiens	Q8TCD0 (AlphaFold model)

Sequence of entity 1 (A, D, G), FASTA

>6DC5_1 RSV fusion glycoprotein (chains A, D, G)
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL
STFLGGLVPRGSHHHHHHSAWSHPQFEK

Sequence of entity 2 (B, E, H), FASTA

>6DC5_2 Fab AM22 heavy chain (chains B, E, H)
QVQLVQSGAEVKKPGATVKVSCKISGHTLIKLSIHWVRQAPGKGLEWMGGYEGEVDEIFY
AQKFQHRLTVIADTATDTVYMELGRLTSDDTAVYFCGTLGVTVTEAGLGIDDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (C, F, I), FASTA

>6DC5_3 Fab AM22 light chain (chains C, F, I)
EIVLTQSPGTLSLSPGERATLSCRASQIVSRNHLAWYQQKPGQAPRLLIFGASSRATGIP
VRFSGSGSGTDFTLTINGLAPEDFAVYYCLSSDSSIFTFGPGTKVDFKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

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

Water and common crystallization additives (PEG) are not listed.

Primary citation

Alternative conformations of a major antigenic site on RSV F. Jones, H.G., Battles, M.B., Lin, C.C. et al. PLoS Pathog (2019) 15:e1007944-e1007944. DOI 10.1371/journal.ppat.1007944 · PubMed

Other PDB entries of the same protein (UniProt M1E1E4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BJM 2.07 Å, Crystal Structure of Inhibitor 5c in Complex with Prefusion RSV F Glycoprotein
6VKE 2.1 Å, Crystal Structure of Inhibitor JNJ-40012665 in Complex with Prefusion RSV F Glycoprotein
6A0Z 2.33 Å, Crystal structure of broadly neutralizing antibody 13D4 bound to H5N1 influenza…
5KWW 2.5 Å, Crystal Structure of Inhibitor JNJ-53718678 In Complex with Prefusion RSV F Glycoprotein
6VKD 2.5 Å, Crystal Structure of Inhibitor JNJ-36689282 in Complex with Prefusion RSV F Glycoprotein
6VKC 2.6 Å, Crystal Structure of Inhibitor JNJ-36811054 in Complex with Prefusion RSV F Glycoprotein
7ZRV 2.8 Å, cryo-EM structure of omicron spike in complex with de novo designed binder, full map
7AD1 2.92 Å, Cryo-EM structure of a prefusion stabilized SARS-CoV-2 Spike (D614N, R682S, R685G,…
7QTI 3.04 Å, SARS-CoV-2 S Omicron Spike B.1.1.529 - 3-P2G3 and 1-P5C3 Fabs (Global)
5U68 3.08 Å, Structural basis for antibody cross-neutralization of respiratory syncytial virus and…
6W16 3.1 Å, Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458…
7FJN 3.25 Å, Cryo-EM structure of South African (B.1.351) SARS-CoV-2 spike glycoprotein in complex…

Browse structure collections

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