8K0D: The heavy chain of 1E5

Cryo-EM structure of conformation 2 of complex of Nipah virus attachment G with 1E5 neutralizing antibody. Determined by electron microscopy at 2.94 Å resolution. Released 1 May 2024.

Method: Electron microscopy
Resolution: 2.94 Å
Organisms: Macaca mulatta, Nipah virus
Chains: 6
Atoms: 13,282
Mol. weight: 188.85 kDa
Released: 1 May 2024

Explore 8K0D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K0D contains 39 α-helices and 170 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: 9 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	13
α-helix	204-206	3
β-strand	217-218	2	14
β-strand	225	1	15
β-strand	228	1	15
β-strand	230-237	8	14
β-strand	244-257	14	14
β-strand	263-271	9	14
α-helix	276-278	3
β-strand	279-287	9	16
β-strand	290-297	8	16
β-strand	313-320	8	16
α-helix	328-331	4
β-strand	333-336	4	16
β-strand	340-341	2	17
β-strand	347-350	4	17
β-strand	354	1	16
β-strand	356-358	3	17
β-strand	361-371	11	17
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	17
α-helix	418-420	3
β-strand	426-430	5	17
β-strand	431	1	18
α-helix	432	1
β-strand	442-447	6	19
β-strand	450-455	6	19
β-strand	463	1	20
β-strand	466-471	6	19
β-strand	475	1	18
β-strand	476-479	4	19
β-strand	486	1	20
β-strand	509	1	13
β-strand	511-515	5	21
β-strand	520-526	7	21
β-strand	533	1	22
β-strand	535-540	6	21
β-strand	545-550	6	21
β-strand	557	1	22
β-strand	558-567	10	13
β-strand	572-582	11	13
β-strand	587-591	5	13
β-strand	593-596	4	13
α-helix	597-598	2

Chain B: 10 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	36
α-helix	204-206	3
β-strand	217-218	2	37
β-strand	225	1	38
β-strand	228	1	38
β-strand	230-237	8	37
α-helix	243	1
β-strand	244-257	14	37
β-strand	263-271	9	37
α-helix	276-278	3
β-strand	279-287	9	39
β-strand	290-297	8	39
β-strand	313-320	8	39
α-helix	328-331	4
β-strand	333-335	3	39
α-helix	336	1
β-strand	340-341	2	40
β-strand	347-350	4	40
β-strand	354	1	39
β-strand	356-358	3	40
β-strand	361-371	11	40
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	40
α-helix	418-420	3
β-strand	426-430	5	40
β-strand	431	1	41
α-helix	432	1
β-strand	442-447	6	42
β-strand	450-455	6	42
β-strand	463	1	43
β-strand	466-471	6	42
β-strand	475	1	41
β-strand	476-479	4	42
β-strand	486	1	43
β-strand	509	1	36
β-strand	511-515	5	44
β-strand	520-526	7	44
β-strand	533	1	45
β-strand	535-540	6	44
β-strand	545-550	6	44
β-strand	557	1	45
β-strand	558-567	10	36
β-strand	572-582	11	36
β-strand	587-591	5	36
β-strand	593-596	4	36
α-helix	597-598	2

Chain C: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	11-12	2	24
β-strand	20-25	6	23
β-strand	34-40	7	25
β-strand	47-52	6	25
β-strand	59-61	3	25
β-strand	69-70	2	26
β-strand	79-82	4	23
β-strand	83-84	2	26
α-helix	89-91	3
β-strand	93-103	11	25
α-helix	112	1
β-strand	113-119	7	25
β-strand	123-125	3	25
β-strand	126-127	2	24
α-helix	130-132	3
β-strand	133	1	27
β-strand	136-140	5	28
β-strand	147-148	2	28
β-strand	151-159	9	28
β-strand	161	1	29
β-strand	162	1	27
β-strand	167-170	4	30
β-strand	179-181	3	28
α-helix	182-184	3
β-strand	185-186	2	29
β-strand	192-193	2	29
β-strand	195-201	7	28
α-helix	202-204	3
β-strand	211-216	6	30
β-strand	221-226	6	30
α-helix	229-231	3

Chain D: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	31
β-strand	10-13	4	32
β-strand	19-29	11	31
β-strand	33-38	6	32
β-strand	45-49	5	32
β-strand	53-54	2	32
β-strand	62-65	4	31
β-strand	68-75	8	31
α-helix	80-82	3
β-strand	85-90	6	32
β-strand	97	1	25
β-strand	98	1	32
β-strand	102-106	5	32
β-strand	110	1	33
β-strand	113-117	5	34
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	34
β-strand	139	1	33
β-strand	144-149	6	35
β-strand	153-154	2	35
β-strand	158-162	5	34
α-helix	163-166	4
β-strand	172-181	10	34
α-helix	182-186	5
β-strand	190-196	7	35
β-strand	205-209	5	35

Chain E: 5 helices, 26 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	34-40	7	3
β-strand	47-52	6	3
β-strand	59-61	3	3
β-strand	69-71	3	1
β-strand	74	1	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-103	11	3
β-strand	113-119	7	3
β-strand	123-125	3	3
β-strand	126-127	2	2
α-helix	130-132	3
β-strand	133	1	4
β-strand	136-140	5	5
β-strand	147	1	5
β-strand	151-159	9	5
β-strand	161	1	6
β-strand	162	1	4
β-strand	167-170	4	7
β-strand	179-181	3	5
α-helix	182-184	3
β-strand	185-186	2	6
β-strand	192-193	2	6
β-strand	195-201	7	5
α-helix	202-204	3
β-strand	212-216	5	7
β-strand	221-224	4	7
α-helix	229-231	3

Chain F: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-29	11	8
β-strand	33-38	6	9
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-65	4	8
β-strand	68-75	8	8
β-strand	85-90	6	9
β-strand	97	1	3
β-strand	98	1	9
β-strand	102-106	5	9
β-strand	110	1	10
β-strand	113-117	5	11
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	11
β-strand	139	1	10
β-strand	144-149	6	12
β-strand	152-153	2	12
β-strand	158-162	5	11
β-strand	172-181	10	11
α-helix	182-186	5
β-strand	190-196	7	12
β-strand	204-209	6	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
The heavy chain of 1E5	C, E	protein	242	Macaca mulatta
The light chain of 1E5	D, F	protein	213	Macaca mulatta
Glycoprotein G	A, B	protein	402	Nipah virus	Q9IH62 (AlphaFold model)

Sequence of entity 1 (C, E), FASTA

>8K0D_1 The heavy chain of 1E5 (chains C, E)
QVQLQESGPGVVKPSETLSLTCAVSGGSISDTYRWSWIRQPPGKGLEWIGYIYGSATSTY
YNPSLSSRVTISKDMSKNQFSLNLNSVTAADTAVYYCARDYQYYYSGSYPTPHNWFDVWG
PGVLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVH
TFPAVLQSSGLYSLSSVVTVPSSGLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHHHHH
HH

Sequence of entity 2 (D, F), FASTA

>8K0D_2 The light chain of 1E5 (chains D, F)
DIQMTQSPSSLSASVGDRVTITCRASQGIIDYLSWYQQKPGKAPKLLISTASNLESGVPS
RFSGSGSGTEFTLTISSLQPEDFATYSCLQGYTTPYTFGQGTKVEIKTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>8K0D_3 Glycoprotein G (chains A, B)
PKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRGVSKQRIIGVGEVLDRG
DEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDPILNSTYWSGSLMMTRL
AVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLYFPAVGFLVRTEFKYND
SNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGENPKVVFIEISDQRLSIG
SPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNTVISRPGQSQCPRFNTC
PEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDNEILYRAQLASEDTNAQ
KTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQC

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
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
8K0C 3.18 Å, Cryo-EM structure of conformation 1 of complex of Nipah virus attachment glycoprotein G…
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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