6W16: Human metapneumovirus monomeric fusion protein

Crystal structure of a human metapneumovirus monomeric fusion protein complexed with 458 Fab. Determined by X-ray diffraction at 3.1 Å resolution. Released 3 Jun 2020.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Human metapneumovirus, Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,265
Mol. weight: 107.13 kDa
Ligands: NAG
Released: 3 Jun 2020

Explore 6W16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W16 contains 27 α-helices and 72 β-strands across 3 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 F: 14 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	1
β-strand	29-40	12	1
β-strand	42-51	10	2
α-helix	66-87	22
α-helix	115-129	15
α-helix	131-140	10
β-strand	146-150	5	2
α-helix	151	1
β-strand	156-162	7	2
α-helix	164-167	4
α-helix	168-173	6
α-helix	174-176	3
α-helix	187-196	10
α-helix	198-208	11
β-strand	213-214	2	2
α-helix	224-232	9
α-helix	238-246	9
α-helix	248-253	6
β-strand	256-262	7	2
β-strand	266-275	10	2
β-strand	278-288	11	1
β-strand	293-295	3	3
β-strand	298-300	3	3
β-strand	303-304	2	4
β-strand	308-312	5	1
β-strand	317-320	4	1
β-strand	326-329	4	1
β-strand	332-336	5	1
α-helix	337-339	3
β-strand	341-343	3	1
β-strand	363-364	2	4
β-strand	372-376	5	5
β-strand	379-383	5	5
β-strand	390-393	4	6
β-strand	402-403	2	6
β-strand	408-411	4	5
β-strand	417-420	4	6
β-strand	424-426	3	6
α-helix	427-428	2

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	7
β-strand	12-13	2	8
β-strand	19-26	8	7
α-helix	30-36	3
β-strand	39-44	6	9
β-strand	51-56	6	9
β-strand	65-67	3	9
α-helix	69-71	3
β-strand	76-81	6	7
β-strand	86-91	6	7
α-helix	96-98	3
β-strand	100-106	7	9
β-strand	118	1	9
β-strand	122-124	3	9
β-strand	125-126	2	8
β-strand	132	1	10
α-helix	133-134	2
β-strand	135-139	5	11
β-strand	150-160	11	11
β-strand	161	1	10
β-strand	166-169	4	12
β-strand	178-180	3	11
α-helix	181-183	3
β-strand	184-185	2	11
β-strand	191-200	10	11
β-strand	210-215	6	12
α-helix	216-218	3
β-strand	220-225	6	12

Chain L: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-13	4	14
β-strand	19-25	7	13
β-strand	36	1	15
β-strand	39-44	6	14
β-strand	51-55	5	14
β-strand	66-67	2	14
α-helix	68	1
β-strand	76-83	6	13
β-strand	84	1	15
β-strand	86-91	6	13
α-helix	96-98	3
β-strand	101-106	6	14
β-strand	117-118	2	14
β-strand	122-126	5	14
β-strand	131	1	16
α-helix	132-133	2
β-strand	134-138	5	17
α-helix	139-141	3
α-helix	142-145	4
β-strand	149-159	11	17
β-strand	160	1	16
β-strand	165-170	6	18
β-strand	174	1	18
β-strand	179-183	5	17
α-helix	184-187	4
β-strand	193-202	10	17
α-helix	203-207	5
β-strand	211	1	19
β-strand	212-217	6	18
β-strand	225-227	3	18
β-strand	230	1	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fusion glycoprotein F0,Envelope glycoprotein fusion	F	protein	539	Human metapneumovirus, Human immunodeficiency virus 1	M1E1E4 (AlphaFold model), Q6W8S4
458 Fab heavy chain	H	protein	219	Homo sapiens
458 Fab light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (F), FASTA

>6W16_1 Fusion glycoprotein F0,Envelope glycoprotein fusion (chains F)
MSWKVMIIISLLITPQHGLKESYLEESCSTITEGYLSVLRTGWYTNVFTLEVGDVENLTC
TDGPSLIKTELDLTKSALRELKTVSADQLAREEQIENPRQSKKRKRRVATAAAVTAGIAI
AKTIRLESEVNAIKGALKTTNEAVSTLGNGVRVLATAVRELKEFVSKNLTSAINKNKCDI
ADLKMAVSFSQFNRRFLNVVRQFSDNAGITPAISLDLMTDAELARAVSYMPTSAGQIKLM
LENRAMVRRKGFGILIGVYGSSVIYMVQLPIFGVIDTPCWIIKAAPSCSEKDGNYACLLR
EDQGWYCKNAGSTVYYPNEKDCETRGDHVFCDTAAGINVAEQSRECNINISTTNYPCKVS
TGRHPISMVALSPLGALVACYKGVSCSIGSNRVGIIKQLPKGCSYITNQDADTVTIDNTV
YQLSKVEGEQHVIKGRPVSSSFDPIRFPEDQFNVALDQVFESIENSQALVDQSNKILNSA
EKGNTSGRENLYFQGGGGGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGGTEGRHHHHHH

Sequence of entity 2 (H), FASTA

>6W16_2 458 Fab heavy chain (chains H)
QGKLVESGGGVIQPGRSLRLSCAASGFDFSRYGLHWVRQAPGKGLEWVAVIVYAGSNKYY
ADSVKGRFTISKDNSKNTMHLQMSDLRTEDTAVYYCARDQAFDLWGQGTMVTVSSASTKG
PSVFPLAPSSKSTGGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSL
SSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 3 (L), FASTA

>6W16_3 458 Fab light chain (chains L)
DIQMTQSPASLSASVGDRVTITCQASQGISRSVNWYQQKPGKAPKLLIFDASHLERGVPS
RFSGSGYGTDFTFTISSLQPEDIATYYCQQYDNLRISFGQGTRLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Antibody recognition of the Pneumovirus fusion protein trimer interface. Huang, J., Diaz, D., Mousa, J.J. PLoS Pathog (2020) 16:e1008942-e1008942. DOI 10.1371/journal.ppat.1008942 · 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…
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

Browse structure collections

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