5U68: PDB entry 5U68

Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus. Determined by X-ray diffraction at 3.08 Å resolution. Released 15 Feb 2017.

Method: X-ray diffraction
Resolution: 3.08 Å
Organisms: Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 15,642
Mol. weight: 279.41 kDa
Released: 15 Feb 2017

Explore 5U68 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U68 contains 65 α-helices and 161 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: 16 helices, 27 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	76-96	21
α-helix	149-158	10
α-helix	163-170	8
β-strand	176-180	5	2
β-strand	186-194	9	2
α-helix	195-200	6
α-helix	218-239	22
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	333-336	4	3
β-strand	340-344	5	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	373-376	4	1
α-helix	377-380	4
α-helix	381-384	4
β-strand	394	1	4
β-strand	395-398	4	3
β-strand	404-407	4	5
β-strand	411-416	6	5
β-strand	422-426	5	6
β-strand	430-434	5	6
α-helix	435-436	2
β-strand	438-443	6	5
β-strand	449-452	4	6
β-strand	455-458	4	6
α-helix	459-460	2
β-strand	465-469	5	1
α-helix	474-477	4
α-helix	480-482	3
β-strand	487	1	3
β-strand	491	1	4
α-helix	492-505	14

Chain B: 17 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	7
β-strand	38-60	23	7
α-helix	76-96	21
α-helix	139-141	3
α-helix	149-157	9
α-helix	163-170	8
β-strand	176-180	5	7
β-strand	186-194	9	7
α-helix	196-202	7
α-helix	218-239	22
β-strand	243-244	2	7
α-helix	254-262	9
α-helix	268-276	9
α-helix	278-281	4
α-helix	282-284	3
β-strand	286-291	6	7
β-strand	296-318	23	7
β-strand	320-322	3	8
β-strand	333-336	4	8
β-strand	340-344	5	7
β-strand	349-352	4	7
β-strand	358-361	4	7
β-strand	364-368	5	7
α-helix	369-371	3
β-strand	373-375	3	7
α-helix	377-380	4
α-helix	381-384	4
β-strand	394	1	9
β-strand	395-398	4	8
β-strand	404-407	4	10
β-strand	411-416	6	10
β-strand	422-426	5	11
β-strand	430-434	5	11
α-helix	435-436	2
β-strand	438-443	6	10
β-strand	449-452	4	11
β-strand	455-458	4	11
α-helix	459-460	2
β-strand	465-469	5	7
α-helix	474-477	4
β-strand	487	1	8
β-strand	491	1	9
α-helix	492-504	13

Chain C: 17 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	29-33	5	12
β-strand	38-49	12	12
β-strand	51-60	10	13
α-helix	76-96	21
α-helix	139-141	3
β-strand	144	1	5
β-strand	146	1	6
α-helix	149-157	9
α-helix	163-170	8
β-strand	176-180	5	13
β-strand	186-194	9	13
α-helix	195-200	6
α-helix	218-240	23
β-strand	243-244	2	13
α-helix	254-262	9
α-helix	268-276	9
α-helix	278-281	4
β-strand	286-293	8	13
β-strand	296-305	10	13
β-strand	308-318	11	12
β-strand	320-322	3	14
β-strand	333-336	4	14
β-strand	340-344	5	12
β-strand	348-352	5	12
β-strand	359-361	3	12
β-strand	364-368	5	12
α-helix	369-371	3
β-strand	373-376	4	12
α-helix	377-380	4
α-helix	381-384	4
β-strand	394	1	15
β-strand	395-398	4	14
β-strand	404-407	4	16
β-strand	411-416	6	16
β-strand	422-426	5	17
β-strand	430-434	5	17
α-helix	435-436	2
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	466-469	4	12
α-helix	474-477	4
α-helix	480-482	3
β-strand	487	1	14
β-strand	491	1	15
α-helix	492-504	13

Chain E: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	18
β-strand	30-31	2	19
β-strand	36-44	9	18
α-helix	48-50	3
β-strand	52-58	7	20
β-strand	64-70	7	20
β-strand	77-79	3	20
α-helix	81-83	3
β-strand	87-92	6	18
α-helix	93-95	3
β-strand	97-103	7	18
β-strand	111-119	9	20
β-strand	129-133	5	20
β-strand	137-139	3	20
β-strand	140-141	2	19
β-strand	167	1	21
β-strand	168-169	2	22
β-strand	172-175	4	23
β-strand	180-186	7	22
β-strand	192	1	24
β-strand	196	1	24
β-strand	199-203	5	23
β-strand	210-213	4	23
β-strand	214	1	25
β-strand	218	1	25
β-strand	228-232	5	22
β-strand	235-241	7	22
α-helix	245-247	3
β-strand	249-255	7	23
β-strand	263-264	2	23
β-strand	265	1	21
β-strand	269-272	4	23

Chain F: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	22-24	3	26
β-strand	30-31	2	27
β-strand	36-44	9	26
α-helix	48-50	3
β-strand	52-58	7	28
β-strand	64-70	7	28
β-strand	77-79	3	28
α-helix	81-83	3
β-strand	87-92	6	26
α-helix	93-95	3
β-strand	97-103	7	26
α-helix	107-109	3
β-strand	111-119	9	28
β-strand	129-133	5	28
β-strand	137-139	3	28
β-strand	140-141	2	27
β-strand	168-169	2	29
β-strand	172-175	4	30
β-strand	180-186	7	29
α-helix	191-194	4
β-strand	199-203	5	30
β-strand	210-213	4	30
β-strand	214	1	31
β-strand	218	1	31
β-strand	227-232	6	29
β-strand	235-241	7	29
α-helix	245-247	3
β-strand	249-255	7	30
β-strand	263-264	2	30
β-strand	268-272	5	30

Chain G: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	22-26	5	32
β-strand	30-31	2	33
β-strand	36-44	9	32
α-helix	48-50	3
β-strand	53-58	6	34
β-strand	64-70	7	34
β-strand	77-79	3	34
α-helix	81-83	3
β-strand	87-92	6	32
α-helix	93-95	3
β-strand	97-103	7	32
β-strand	111-119	9	34
β-strand	129-133	5	34
β-strand	137-139	3	34
β-strand	140-141	2	33
β-strand	167	1	35
β-strand	168-169	2	36
β-strand	172-175	4	37
β-strand	180-186	7	36
α-helix	191-194	4
β-strand	198-203	6	37
β-strand	210-213	4	37
β-strand	214	1	38
β-strand	218	1	38
β-strand	227-232	6	36
β-strand	235-241	7	36
α-helix	245-247	3
β-strand	249-255	7	37
β-strand	263-264	2	37
β-strand	265	1	35
β-strand	268-272	5	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein	A, B, C	protein	562	Human respiratory syncytial virus A (strain A2), Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), P03420
MPE8	E, F, G	protein	294	Homo sapiens

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

>5U68_1 Chimera protein of Fusion glycoprotein F0 and Envelope glycoprotein (chains A, B, C)
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPATNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVCKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTFKVLDLKNYIDKQLLPILNKQSCSISNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLTNSELLSLINDMPITNDQKKLMSNNVQIVRQQSYSIMCIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEVNLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGVDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLSAIGGYIPEAPRDGQAYVRKDGEWVLL
STFLGGLVPRGSSAHHHHHHHH

Sequence of entity 2 (E, F, G), FASTA

>5U68_2 MPE8 (chains E, F, G)
MELGLRWVFLVAILEGVQCEVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAP
GKGLEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARARA
TGYNSITPYFDIWGQGTLVTVSSGTGGSGGGGSGGGGSGGGASQSVVTQTPSVSGAPGQR
VTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYDNNNRPSGVPDRFSASKSGTSASLAI
TGLQAEDEADYYCQSYDRSLSGVFGTGTKVTVLGSGENLYFQSGGSGGHHHHHH

Primary citation

Structural basis for antibody cross-neutralization of respiratory syncytial virus and human metapneumovirus. Wen, X., Mousa, J.J., Bates, J.T. et al. Nat Microbiol (2017) 2:16272-16272. DOI 10.1038/nmicrobiol.2016.272 · 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)
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…
6OUS 3.4 Å, Structure of fusion glycoprotein from human respiratory syncytial virus

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