8K0C: Heavy chain of 1E5 Fab fragments

Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G with 1E5 neutralizing antibody. Determined by electron microscopy at 3.18 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 3.18 Å
Organisms: Macaca mulatta, Nipah virus
Chains: 8
Atoms: 15,262
Mol. weight: 223.1 kDa
Released: 1 May 2024

Explore 8K0C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K0C contains 54 α-helices and 180 β-strands across 8 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.

Chains A and B: 12 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	98-99	2
α-helix	100-105	6
α-helix	106-114	9
α-helix	115-119	5
α-helix	120-145	26
β-strand	178-179	2	16
β-strand	200-202	3	16
α-helix	204-206	3
β-strand	217-222	6	17
β-strand	225	1	18
β-strand	228	1	18
β-strand	230-237	8	17
β-strand	244-255	12	17
β-strand	265-271	7	17
α-helix	276-278	3
β-strand	279-286	8	19
β-strand	291-297	7	19
β-strand	313-319	7	19
α-helix	328-331	4
β-strand	334-335	2	19
β-strand	340-341	2	20
β-strand	347-350	4	20
β-strand	354	1	19
β-strand	356-358	3	20
β-strand	361-371	11	20
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	20
α-helix	418-420	3
β-strand	426-430	5	20
β-strand	431	1	21
α-helix	432	1
β-strand	442-447	6	22
β-strand	450-455	6	22
β-strand	463	1	23
β-strand	466-471	6	22
β-strand	475	1	21
β-strand	476-479	4	22
β-strand	486	1	23
β-strand	509	1	16
β-strand	512-515	4	24
β-strand	520-526	7	24
β-strand	533	1	25
β-strand	535-540	6	24
β-strand	545-550	6	24
β-strand	557	1	25
β-strand	558-568	11	16
β-strand	572-581	10	16
β-strand	588-591	4	16
β-strand	593-596	4	16

Chains C and D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	97-100	4
α-helix	101-105	5
α-helix	106-114	9
α-helix	115-119	5
α-helix	120-145	26

Chains E and G: 5 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	20-25	6	1
β-strand	35-39	5	3
β-strand	47-48	2	3
β-strand	52	1	3
β-strand	59	1	3
β-strand	69-70	2	4
β-strand	73-74	2	1
β-strand	79-82	4	1
β-strand	83-84	2	4
α-helix	89-91	3
β-strand	93-94	2	5
β-strand	96-103	8	3
β-strand	113-119	7	3
β-strand	124-125	2	5
β-strand	126-127	2	2
α-helix	130-132	3
β-strand	133	1	6
β-strand	136-140	5	7
β-strand	147-148	2	7
β-strand	151-159	9	7
β-strand	161	1	8
β-strand	162	1	6
β-strand	167-170	4	9
β-strand	179-181	3	7
α-helix	182-184	3
β-strand	185-186	2	8
β-strand	192-193	2	8
β-strand	195-201	7	7
α-helix	202-204	3
β-strand	211-216	6	9
β-strand	221-226	6	9
α-helix	229-231	3

Chains F and H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	10
β-strand	10-12	3	11
β-strand	19-25	7	10
β-strand	29	1	12
β-strand	33-38	6	11
β-strand	44-49	6	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-65	4	10
β-strand	68	1	12
β-strand	72-75	4	10
β-strand	85-90	6	11
β-strand	98	1	11
β-strand	102-105	4	11
β-strand	110	1	13
β-strand	113-117	5	14
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	14
β-strand	139	1	13
β-strand	144-149	6	15
β-strand	153-154	2	15
β-strand	158-162	5	14
α-helix	163-166	4
β-strand	172-181	10	14
α-helix	182-186	5
β-strand	190-196	7	15
β-strand	204-209	6	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of 1E5 Fab fragments	E, G	protein	242	Macaca mulatta
Light chain of 1E5 Fab fragments	F, H	protein	213	Macaca mulatta
Glycoprotein G	A, B	protein	505	Nipah virus	Q9IH62 (AlphaFold model)
Glycoprotein G	C, D	protein	58	Nipah virus	Q9IH62 (AlphaFold model)

Sequence of entity 1 (E, G), FASTA

>8K0C_1 Heavy chain of 1E5 Fab fragments (chains E, G)
QVQLQESGPGVVKPSETLSLTCAVSGGSISDTYRWSWIRQPPGKGLEWIGYIYGSATSTY
YNPSLSSRVTISKDMSKNQFSLNLNSVTAADTAVYYCARDYQYYYSGSYPTPHNWFDVWG
PGVLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSGLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHH
HH

Sequence of entity 2 (F, H), FASTA

>8K0C_2 Light chain of 1E5 Fab fragments (chains F, H)
DIQMTQSPSSLSASVGDRVTITCRASQGIIDYLSWYQQKPGKAPKLLISTASNLESGVPS
RFSGSGSGTEFTLTISSLQPEDFATYSCLQGYTTPYTFGQGTKVEIKTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>8K0C_3 Glycoprotein G (chains A, B)
LADKIGTEIGPKVSLIDTSSTITIPANIGLLGSKISQSTASINENVNEKCKFTLPPLKIH
ECNISCPNPLPFREYRPQTEGVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTC
ITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNP
NTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLA
LRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCR
LSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQA
SFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDR
INWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCIS
LVEIYDTGDNVIRPKLFAVKIPEQC

Sequence of entity 4 (C, D), FASTA

>8K0C_4 Glycoprotein G (chains C, D)
GLADKIGTEIGPKVSLIDTSSTITIPANIGLLGSKISQSTASINENVNEKCKFTLPPL

Primary citation

A potent Henipavirus cross-neutralizing antibody reveals a dynamic fusion-triggering pattern of the G-tetramer. Fan, P., Sun, M., Zhang, X. et al. Nat Commun (2024) 15:4330-4330. DOI 10.1038/s41467-024-48601-w · PubMed

Other PDB entries of the same protein (UniProt Q9IH62 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VSM 1.8 Å, Nipah virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
2VWD 2.25 Å, Nipah Virus Attachment Glycoprotein
3D11 2.31 Å, Crystal Structures of the Nipah G Attachment Glycoprotein
8JA5 2.79 Å, Crystal structure of Nipah Virus attachment (G) glycoprotein in complex with…
8K3C 2.88 Å, Nipah virus Attachment glycoprotein with 41-6 antibody fragment
8K0D 2.94 Å, Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5…
9LU3 3.0 Å, LN1F9 Fab bound to Nipah Virus attachment (G) glycoprotein head domain
3D12 3.0 Å, Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor…
9LUE 3.03 Å, Cryo-EM structure of the Nipah G head domain in complex with three Fabs
7TXZ 3.2 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…
6VY5 3.4 Å, Crystal structure of Nipah receptor binding protein head domain in complex with human…
7TY0 3.5 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…

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