8F6X: PDB entry 8F6X

cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8. Determined by electron microscopy at 3.25 Å resolution. Released 2 Aug 2023.

Method: Electron microscopy
Resolution: 3.25 Å
Organisms: Human metapneumovirus, Escherichia phage T2, Homo sapiens
Chains: 6
Atoms: 14,952
Mol. weight: 267.37 kDa
Ligands: NAG
Released: 2 Aug 2023

Explore 8F6X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F6X contains 49 α-helices and 158 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: 14 helices, 29 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	68-83	16
β-strand	92	1	3
α-helix	113-129	17
α-helix	131-143	13
β-strand	146-150	5	2
β-strand	156-161	6	2
α-helix	165-168	4
α-helix	169-173	5
α-helix	174-176	3
α-helix	188-196	9
α-helix	198-209	12
β-strand	213-214	2	2
α-helix	224-233	10
α-helix	238-246	9
α-helix	248-254	7
β-strand	256-263	8	2
β-strand	266-275	10	2
β-strand	278-288	11	1
β-strand	291-295	5	4
β-strand	298-304	7	4
β-strand	308-312	5	1
β-strand	317-320	4	1
β-strand	327-329	3	1
β-strand	332-336	5	1
β-strand	341-342	2	1
α-helix	345-351	7
β-strand	362	1	5
β-strand	363-366	4	4
β-strand	372-374	3	6
β-strand	375	1	7
β-strand	380-383	4	6
β-strand	390-393	4	8
β-strand	399-402	4	8
β-strand	408-410	3	6
β-strand	417-420	4	8
β-strand	423-426	4	8
α-helix	427-428	2
β-strand	433-437	5	1
α-helix	443-445	3
β-strand	459	1	5

Chain B: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	9
β-strand	29-40	12	9
β-strand	42-51	10	10
α-helix	68-80	13
β-strand	92	1	11
α-helix	113-129	17
α-helix	131-143	13
β-strand	146-150	5	10
β-strand	156-161	6	10
α-helix	165-168	4
α-helix	169-173	5
α-helix	174-176	3
α-helix	188-196	9
α-helix	198-209	12
β-strand	213-214	2	10
α-helix	224-233	10
α-helix	238-246	9
α-helix	248-254	7
β-strand	256-263	8	10
β-strand	266-275	10	10
β-strand	278-288	11	9
β-strand	291-295	5	12
β-strand	298-304	7	12
β-strand	308-312	5	9
β-strand	317-320	4	9
β-strand	327-329	3	9
β-strand	332-336	5	9
β-strand	341-342	2	9
α-helix	345-351	7
β-strand	362	1	13
β-strand	363-366	4	12
β-strand	372-374	3	14
β-strand	375	1	3
β-strand	380-383	4	14
β-strand	390-394	5	15
β-strand	398-402	5	15
α-helix	403-404	2
β-strand	408-410	3	14
β-strand	417-420	4	15
β-strand	423-426	4	15
α-helix	427-428	2
β-strand	433-437	5	9
α-helix	443-445	3
β-strand	459	1	13

Chain C: 15 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	20-24	5	16
β-strand	29-40	12	16
β-strand	42-51	10	17
α-helix	68-83	16
β-strand	92	1	7
α-helix	113-129	17
α-helix	131-143	13
β-strand	146-150	5	17
β-strand	156-161	6	17
α-helix	165-167	3
α-helix	168-173	6
α-helix	174-176	3
α-helix	188-196	9
α-helix	198-209	12
β-strand	213-214	2	17
α-helix	224-233	10
α-helix	238-245	8
α-helix	248-254	7
β-strand	256-263	8	17
β-strand	266-275	10	17
β-strand	278-288	11	16
β-strand	291-295	5	18
β-strand	298-303	6	18
β-strand	308-312	5	16
β-strand	317-320	4	16
β-strand	327-329	3	16
β-strand	332-336	5	16
β-strand	341-342	2	16
α-helix	345-351	7
β-strand	362-363	2	19
β-strand	364-366	3	18
β-strand	372-374	3	20
β-strand	375	1	11
β-strand	380-383	4	20
β-strand	390-393	4	21
β-strand	401-402	2	21
α-helix	403-404	2
β-strand	408-410	3	20
β-strand	417-420	4	21
β-strand	423-426	4	21
α-helix	427-428	2
β-strand	433-437	5	16
α-helix	443-445	3
β-strand	458-459	2	19

Chain D: 1 helix, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	22
β-strand	17-25	9	22
β-strand	33-39	7	23
β-strand	41	1	24
β-strand	43	1	24
β-strand	45-51	7	23
β-strand	60	1	23
β-strand	68-73	6	22
β-strand	78-84	7	22
β-strand	92-99	8	23
β-strand	100	1	25
β-strand	110	1	25
β-strand	114	1	23
β-strand	118-120	3	23
β-strand	149-150	2	26
β-strand	153-154	2	27
β-strand	162-167	6	26
β-strand	180-184	5	27
β-strand	191-194	4	27
β-strand	208-213	6	26
β-strand	216-221	6	26
α-helix	226-228	3
β-strand	231-236	6	27
β-strand	244-245	2	27
β-strand	249-251	3	27

Chain E: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	28
β-strand	7	1	29
β-strand	17-23	7	29
β-strand	24-25	2	28
β-strand	33-39	7	30
β-strand	45-51	7	30
β-strand	60	1	30
β-strand	68-73	6	29
β-strand	78-84	7	29
α-helix	88-90	3
β-strand	92-100	9	30
β-strand	110-114	5	30
β-strand	118-120	3	30
β-strand	149-150	2	31
β-strand	153-156	4	32
β-strand	162-167	6	31
β-strand	180-184	5	32
β-strand	191-194	4	32
β-strand	208-213	6	31
β-strand	216-221	6	31
α-helix	226-228	3
β-strand	231-235	5	32
α-helix	244	1
β-strand	245	1	32
α-helix	246	1
β-strand	249-253	5	32

Chain F: 0 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	33
β-strand	11-12	2	34
β-strand	17-25	9	33
β-strand	35-39	5	35
β-strand	45-50	6	35
β-strand	60	1	35
β-strand	68-73	6	33
β-strand	78-84	7	33
β-strand	92-97	6	35
β-strand	100	1	36
β-strand	110	1	36
β-strand	114	1	35
β-strand	118-120	3	35
β-strand	121-122	2	34
β-strand	150	1	37
β-strand	153-154	2	38
β-strand	162-165	4	39
β-strand	166	1	37
β-strand	180-184	5	38
β-strand	191-194	4	38
β-strand	208-211	4	39
β-strand	218-221	4	39
β-strand	231-236	6	38
β-strand	244-245	2	38
β-strand	249-251	3	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin	A, B, C	protein	522	Human metapneumovirus, Escherichia phage T2	G3KCK8, P10104
MPE8 Single chain variable fragment	D, E, F	protein	306	Homo sapiens

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

>8F6X_1 Structurally designed HMPV F protein HMPV_v3B_D12_DS454,Fibritin (chains A, B, C)
MSWKVMIIISLLITPQHGLKESYLEESCSTITEGYLSVLRTGWYTNVFTLEVGDVENLTC
TDGPSLIKTELDLTKSALRELKTCSADQGSGGSGATAAAVTAGIAIAKTIRLESEVNAIK
GCLKTTNECVSTLGNGVRVLATAVRELKEFVSKNLTSAINKNKCDIPDLKMAVSFSQFNR
RFLNVVRQFSDNAGITPAISLDLMTDAELARAVSYMPTSAGQIKLMLENRCMVRRKGFGI
LIGVYGSSVIYMVQLPIFGVIDTPCWIIKAAPSCSEKDGNYACLLREDQGWYCKNAGSTV
YYPNDKDCETRGDHVFCDTAAGINVAEQSRECNINISTTNYPCKVSTGRHPISMVALSPL
GALVACYKGVSCSIGSNRVGIIKQLPKGCSYITNQDADTVTIDNTVYQLSKVEGEQHVIK
GRPVSSSFDPIKFPECQFNCALDQVFESIENSQALVDQSNKILNSAESAIGGYIPEAPRD
GQAYVRKDGEWVLLSTFLGGLVPRGSHHHHHHSAWSHPQFEK

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

>8F6X_2 MPE8 Single chain variable fragment (chains D, E, F)
MELGLRWVFLVAILEGVQCEVQLVESGGGLVKPGGSLRLSCAASGFTFSSYSMNWVRQAP
GKGLEWVSSISASSSYSDYADSAKGRFTISRDNAKTSLFLQMNSLRAEDTAIYFCARARA
TGYSSITPYFDIWGQGTLVTVSSGTGGSGGGGSGGGGSGGGASQSVVTQTPSVSGAPGQR
VTISCTGSSSNIGAGYDVHWYQQLPGTAPKLLIYDNNNRPSGVPDRFSASKSGTSASLAI
TGLQAEDEADYYCQSYDRNLSGVFGTGTKVTVLGSGENLYFQSGGSGGHHHHHHHHSAWS
HPQFEK

Ligands and cofactors

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

Primary citation

cryo-EM structure of a structurally designed Human metapneumovirus F protein in complex with antibody MPE8. Ou, L., Kwong, P.D. To be published.

Other PDB entries of the same protein (UniProt G3KCK8), best resolution first:

8T9Z 3.0 Å, Structural of M8C10 Fab in complex human metapneumovirus fusion protein
4DAG 3.39 Å, Structure of the Human Metapneumovirus Fusion Protein with Neutralizing Antibody…

Browse structure collections

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