6CXC: R4.C6 Fab Heavy Chain

3.9A Cryo-EM structure of murine antibody bound at a novel epitope of respiratory syncytial virus fusion protein. Determined by electron microscopy at 3.9 Å resolution. Released 31 Jul 2019.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Mus musculus, Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1
Chains: 12
Atoms: 15,196
Mol. weight: 444.56 kDa
Ligands: NAG
Released: 31 Jul 2019

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

Secondary structure: helices and β-sheets

6CXC contains 55 α-helices and 142 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	16
β-strand	38-40	3	16
β-strand	41-42	2	17
β-strand	47-59	13	18
α-helix	83-93	11
α-helix	94-96	3

Chain B: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	154-156	3
α-helix	157-201	45
α-helix	204-213	10
α-helix	214-216	3
α-helix	217-223	7
α-helix	228-239	12
β-strand	243-244	2	18
α-helix	255-263	9
α-helix	268-276	9
α-helix	278-282	5
β-strand	286-292	7	18
β-strand	297-309	13	18
β-strand	314-315	2	17
β-strand	321	1	19
β-strand	334	1	19
β-strand	335-336	2	20
β-strand	341-345	5	21
β-strand	348-352	5	21
β-strand	366-368	3	18
β-strand	373-375	3	21
α-helix	377-382	6
β-strand	395-396	2	20
β-strand	404-407	4	22
β-strand	411-416	6	22
β-strand	422-426	5	23
β-strand	430-434	5	23
β-strand	438-443	6	22
β-strand	449-452	4	23
β-strand	455-458	4	23
α-helix	461	1
β-strand	462	1	24
α-helix	463	1
β-strand	466-467	2	24
α-helix	486-500	15
α-helix	502-509	8
α-helix	510-513	4

Chain C: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	25
β-strand	38-40	3	25
β-strand	41-42	2	26
β-strand	46-59	14	27
α-helix	83-93	11

Chain D: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	162-175	14
α-helix	177-201	25
α-helix	204-213	10
α-helix	214-216	3
α-helix	217-226	10
α-helix	228-239	12
β-strand	243-244	2	27
α-helix	254-263	10
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-292	7	27
β-strand	297-311	15	27
β-strand	314-315	2	26
β-strand	321	1	28
β-strand	334	1	28
β-strand	335	1	29
β-strand	341-345	5	30
β-strand	348-352	5	30
β-strand	366-367	2	27
β-strand	373-375	3	30
α-helix	377-383	7
β-strand	396	1	29
β-strand	404-407	4	31
β-strand	411-416	6	31
β-strand	422-426	5	32
β-strand	430-434	5	32
β-strand	438-443	6	31
β-strand	449-452	4	32
β-strand	455-458	4	32
α-helix	461	1
β-strand	462	1	18
α-helix	463	1
β-strand	466-469	4	18
α-helix	486-509	24
α-helix	510-513	4

Chain E: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	33
β-strand	38-40	3	33
β-strand	41-42	2	34
β-strand	46-59	14	24
α-helix	83-93	11
α-helix	94-96	3

Chain F: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	159-201	43
α-helix	204-213	10
α-helix	214-216	3
α-helix	217-226	10
α-helix	228-239	12
β-strand	243-244	2	24
α-helix	255-263	9
α-helix	268-276	9
α-helix	278-283	6
β-strand	286-292	7	24
β-strand	297-311	15	24
β-strand	314-315	2	34
β-strand	335	1	35
β-strand	341-345	5	36
β-strand	348-352	5	36
β-strand	366-367	2	24
β-strand	373-375	3	36
α-helix	377-383	7
β-strand	396	1	35
β-strand	404-407	4	37
β-strand	412-416	5	37
β-strand	422-426	5	38
β-strand	430-434	5	38
β-strand	438-442	5	37
β-strand	449-452	4	38
β-strand	455-458	4	38
α-helix	461	1
β-strand	462	1	27
α-helix	463	1
β-strand	466-467	2	27
α-helix	486-509	24

Chains G, I and X: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	6
β-strand	8-10	3	7
β-strand	16	1	6
β-strand	20-22	3	6
β-strand	32-38	7	8
β-strand	42-50	9	8
β-strand	55-56	2	8
β-strand	66-71	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	91-95	5	8
β-strand	104	1	8
β-strand	109	1	8
β-strand	110-112	3	7

Chains J, K and Y: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	119-120	2	9
β-strand	133-138	6	9
β-strand	147-152	6	10
β-strand	159-163	5	10
β-strand	167-168	2	10
α-helix	169	1
β-strand	176-180	5	9
β-strand	184-189	6	9
α-helix	194-196	3
β-strand	199-204	6	10
β-strand	212	1	10
β-strand	216-217	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
R4.C6 Fab Heavy Chain	G, I, X	protein	118	Mus musculus
R4.C6 Fab Light Chain	J, K, Y	protein	122	Mus musculus
Fusion glycoprotein F0, Envelope glycoprotein chimera	A, B, C, D, E, F	protein	548	Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), P03420

Sequence of entity 1 (G, I, X), FASTA

>6CXC_1 R4.C6 Fab Heavy Chain (chains G, I, X)
MAEVQLQQSGPELVKPGASVKISCKASGYAFSNSWMSWVKQRPGKGLEWIGRLFPADGDI
TYNGHFKDKAALTADKSSNTAYIQLSSLTSEDSAVYFCARMDNSEVFWGQGTLVTVSA

Sequence of entity 2 (J, K, Y), FASTA

>6CXC_2 R4.C6 Fab Light Chain (chains J, K, Y)
MADILLTQSQKFMSTSVGDRVSITCKASQNVRTGVSWYQRKPGQSPKALIYLASNRHTGV
PDRFTGRGSGTDFTLTISEVQSEDLADYFCLQHWTVPYTFGGGTKLEIKRTAAAPSRANS
FK

Sequence of entity 3 (A, B, C, D, E, F), FASTA

>6CXC_3 Fusion glycoprotein F0, Envelope glycoprotein chimera (chains A, B, C, D, E, F)
QNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIELSNIKENKCNGTDAKVKLIKQELDK
YKNAVTELQLLMQSTPATNNRARRELPRFMNYTLNNAKKTNVTLSKKQKQQFLGFLLGVG
SAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVSLSNGVSVLTSKVLDLKNYIDKQLLP
IVNKQSCSISNIETVIEFQQKNNRLLEITREFSVNAGVTTPVSTYMLTNSELLSLINDMP
ITNDQKKLMSNNVQIVRQQSYSIMSIIKEEVLAYVVQLPLYGVIDTPCWKLHTSPLCTTN
TKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKVQSNRVFCDTMNSLTLPSEVNLCNVD
IFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKTKCTASNKNRGIIKTFSNGCDYVSNK
GVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDPLVFPSDEFDASISQVNEKINQSLAF
IRKSDELLHNVNAGKSTTNIMGALVPRGSPGSGYIPEAPRDGQAYVRKDGEWVLLSTFLG
SSHHHHHH

Ligands and cofactors

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

Primary citation

Structure basis of neutralization by a novel site II/IV antibody against respiratory syncytial virus fusion protein. Xie, Q., Wang, Z., Ni, F. et al. PLoS One (2019) 14:e0210749-e0210749. DOI 10.1371/journal.pone.0210749 · 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…

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