6APD: Fusion glycoprotein F0,Envelope glycoprotein

Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425. Determined by X-ray diffraction at 4.1 Å resolution. Released 21 Mar 2018.

Method: X-ray diffraction
Resolution: 4.1 Å
Organisms: Respiratory syncytial virus, Human immunodeficiency virus 1, Homo sapiens
Chains: 15
Atoms: 30,005
Mol. weight: 474.12 kDa
Released: 21 Mar 2018

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

Secondary structure: helices and β-sheets

6APD contains 137 α-helices and 359 β-strands across 15 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: 17 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
α-helix	139-141	3
β-strand	144	1	3
α-helix	149-158	10
α-helix	163-170	8
β-strand	177-180	4	2
β-strand	186-194	9	2
α-helix	195-202	8
α-helix	204-207	4
β-strand	211-213	3	4
α-helix	218-238	21
β-strand	243-244	2	2
α-helix	254-263	10
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	320-322	3	5
β-strand	333-336	4	5
β-strand	340-345	6	1
β-strand	348-352	5	1
α-helix	355-357	3
β-strand	359-361	3	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	5
β-strand	404-407	4	6
β-strand	411-416	6	6
β-strand	422-426	5	7
β-strand	430-434	5	7
α-helix	435-436	2
β-strand	438-443	6	6
β-strand	449-452	4	7
β-strand	455-458	4	7
β-strand	465-469	5	1
α-helix	474-477	4
β-strand	490-491	2	5
α-helix	492-514	23

Chain B: 18 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	8
β-strand	38-44	7	8
β-strand	45-49	5	9
β-strand	51-60	10	10
α-helix	74-96	23
α-helix	139-141	3
β-strand	144	1	11
α-helix	149-158	10
α-helix	161-170	10
β-strand	176-180	5	10
β-strand	186-194	9	10
α-helix	195-202	8
α-helix	204-207	4
β-strand	211-213	3	12
α-helix	218-238	21
β-strand	243-244	2	10
α-helix	254-263	10
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-293	8	10
β-strand	296-305	10	10
β-strand	308-309	2	9
β-strand	313-318	6	8
β-strand	320-322	3	13
α-helix	328-330	3
β-strand	333-336	4	13
β-strand	340-345	6	8
β-strand	348-352	5	8
α-helix	355-357	3
β-strand	359-361	3	9
β-strand	364-368	5	9
α-helix	369-371	3
β-strand	373-376	4	8
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	13
β-strand	404-407	4	3
β-strand	411-416	6	3
β-strand	422-426	5	14
β-strand	430-434	5	14
α-helix	435-436	2
β-strand	438-443	6	3
β-strand	449-452	4	14
β-strand	455-458	4	14
β-strand	465-469	5	8
α-helix	474-477	4
β-strand	490-491	2	13
α-helix	492-514	23

Chain C: 17 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	15
β-strand	38-49	12	15
β-strand	51-60	10	16
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	16
β-strand	186-194	9	16
α-helix	196-202	7
α-helix	204-207	4
β-strand	211-213	3	17
α-helix	218-238	21
β-strand	243-244	2	16
α-helix	254-263	10
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-293	8	16
β-strand	296-305	10	16
β-strand	308-318	11	15
β-strand	321-322	2	18
β-strand	333-336	4	18
β-strand	340-345	6	15
β-strand	348-352	5	15
α-helix	355-357	3
β-strand	359-361	3	15
β-strand	364-368	5	15
α-helix	369-371	3
β-strand	373-375	3	15
α-helix	377-380	4
α-helix	381-384	4
β-strand	394-398	5	18
β-strand	404-407	4	11
β-strand	411-416	6	11
β-strand	422-426	5	19
β-strand	430-434	5	19
α-helix	435-436	2
β-strand	438-443	6	11
β-strand	449-452	4	19
β-strand	455-458	4	19
β-strand	465-469	5	15
α-helix	474-477	4
β-strand	490-491	2	18
α-helix	492-516	25

Chain D: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	20
α-helix	7-9	3
β-strand	10-12	3	21
β-strand	17-25	9	20
β-strand	33-39	7	21
β-strand	45-52	8	21
β-strand	56-59	4	21
β-strand	67-72	6	20
β-strand	77-82A	7	20
α-helix	84-86	3
β-strand	88-93	6	21
β-strand	98-99	2	4
β-strand	100D-100F	3	4
β-strand	103	1	21
β-strand	107-111	5	21
α-helix	114-116	3
β-strand	117	1	22
β-strand	120-124	5	23
β-strand	135-145	11	23
β-strand	146	1	22
β-strand	150-154	5	24
β-strand	163-165	3	23
α-helix	166-168	3
β-strand	169-170	2	23
β-strand	176-185	10	23
α-helix	186-188	3
β-strand	194-200	7	24
β-strand	205-211	7	24

Chains E and I: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	10-13	4	26
α-helix	18	1
β-strand	19-25	7	25
α-helix	30-32	3
β-strand	34-38	5	26
β-strand	45-49	5	26
β-strand	53-54	2	26
α-helix	55	1
β-strand	62-67	6	25
β-strand	70-75	6	25
α-helix	80-82	3
β-strand	85-92	8	26
β-strand	95-98	4	26
β-strand	102-106	5	26
β-strand	111	1	27
α-helix	112-113	2
β-strand	114-118	5	28
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	28
β-strand	140	1	27
β-strand	144-150	7	29
β-strand	153-155	3	29
β-strand	159-163	5	28
α-helix	164-167	4
β-strand	173-182	10	28
α-helix	183-186	4
β-strand	192-198	7	29
β-strand	205-209	5	29

Chain F: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	30
α-helix	7-9	3
β-strand	10-12	3	31
β-strand	17-25	9	30
β-strand	33-39	7	31
β-strand	45-52	8	31
β-strand	56-59	4	31
α-helix	61-63	3
β-strand	67-72	6	30
β-strand	77-82A	7	30
α-helix	84-86	3
β-strand	88-93	6	31
β-strand	97-99	3	17
β-strand	100D-100F	3	17
β-strand	103	1	31
β-strand	107-111	5	31
α-helix	114-116	3
β-strand	117	1	32
β-strand	120-124	5	33
β-strand	135-145	11	33
β-strand	146	1	32
β-strand	151-154	4	34
β-strand	163-165	3	33
α-helix	166-168	3
β-strand	169-170	2	33
β-strand	176-185	10	33
α-helix	186-188	3
β-strand	194-200	7	34
β-strand	205-211	7	34

Chain G: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	35
β-strand	10-13	4	36
α-helix	18	1
β-strand	19-25	7	35
α-helix	30-32	3
β-strand	34-38	5	36
β-strand	45-49	5	36
β-strand	53-54	2	36
α-helix	55	1
β-strand	62-67	6	35
β-strand	70-75	6	35
α-helix	80-82	3
β-strand	85-92	8	36
β-strand	95-98	4	36
β-strand	102-106	5	36
β-strand	111	1	37
α-helix	112-113	2
β-strand	114-118	5	38
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	38
β-strand	140	1	37
β-strand	144-150	7	39
β-strand	153-155	3	39
β-strand	159-163	5	38
β-strand	173-182	10	38
α-helix	183-186	4
β-strand	192-198	7	39
β-strand	205-209	5	39

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	40
α-helix	7-9	3
β-strand	10-11	2	41
β-strand	17-25	9	40
α-helix	29-31	3
β-strand	33-39	7	41
β-strand	45-52	8	41
β-strand	56-59	4	41
α-helix	61-63	3
β-strand	67-72	6	40
β-strand	77-82A	7	40
α-helix	84-86	3
β-strand	88-93	6	41
β-strand	97-99	3	12
β-strand	100D-100F	3	12
β-strand	103	1	41
β-strand	107-110	4	41
α-helix	114-116	3
β-strand	117	1	42
α-helix	118-119	2
β-strand	120-124	5	43
β-strand	135-145	11	43
β-strand	146	1	42
β-strand	150-154	5	44
β-strand	163-165	3	43
α-helix	166-168	3
β-strand	169-170	2	43
β-strand	176-185	10	43
α-helix	186-188	3
β-strand	194-200	7	44
β-strand	205-211	7	44

5 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
Fusion glycoprotein F0,Envelope glycoprotein	A, B, C	protein	573	Respiratory syncytial virus, Human immunodeficiency virus 1	P03420, P10104
AM22 Fab Heavy Chain,IGH@ protein	D, F, H	protein	228	Homo sapiens	Q6GMX6 (AlphaFold model)
AM22 Fab Light Chain,Uncharacterized protein	E, G, I	protein	215	Homo sapiens	Q8TCD0 (AlphaFold model)
Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain	J, K, N	protein	226	Homo sapiens	A0A0B4J1V1, P0DOX5
IGL@ protein	L, M, O	protein	218	Homo sapiens	Q6GMX4

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

>6APD_1 Fusion glycoprotein F0,Envelope glycoprotein (chains A, B, C)
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKEIKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSIPNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL
STFLGSMEVLFQGPGHHHHHHHHSAWSHPQFEK

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

>6APD_2 AM22 Fab Heavy Chain,IGH@ protein (chains D, F, H)
QVQLVQSGAEVKKPGATVKVSCKISGHTLIKLSIHWVRQAPGKGLEWMGGYEGEVDEIFY
AQKFQHRLTVIADTATDTVYMELGRLTSDDTAVYFCGTLGVTVTEAGLGIDDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

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

>6APD_3 AM22 Fab Light Chain,Uncharacterized protein (chains E, G, I)
EIVLTQSPGTLSLSPGERATLSCRASQIVSRNHLAWYQQKPGQAPRLLIFGASSRATGIP
VRFSGSGSGTDFTLTINGLAPEDFAVYYCLSSDSSIFTFGQGTKVDFKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (J, K, N), FASTA

>6APD_4 Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain (chains J, K, N)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYIYY
ADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARLGYCSGGSCHFDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 5 (L, M, O), FASTA

>6APD_5 IGL@ protein (chains L, M, O)
QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYGNSNRPSGV
PDRFSGSKSGTSASLAITGLQAEDEADYYCQSYDSSLSGFYVFGTGTKVTVLGQPKAAPS
VTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAA
SSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation. Goodwin, E., Gilman, M.S.A., Wrapp, D. et al. Immunity (2018) 48:339-349.e5. DOI 10.1016/j.immuni.2018.01.005 · 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
8DG9 2.24 Å, Cryo-EM Structure of RSV prefusion F trimer in complex with three MxR Fabs
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

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