7TY0: Glycoprotein G

Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (local refinement of the stalk region). Determined by electron microscopy at 3.5 Å resolution. Released 9 Mar 2022.

Method: Electron microscopy
Resolution: 3.5 Å
Organisms: Nipah henipavirus, Mus sp.
Chains: 8
Atoms: 10,640
Mol. weight: 395.65 kDa
Ligands: NAG
Released: 9 Mar 2022

Explore 7TY0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7TY0 contains 48 α-helices and 121 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.

Chain A: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	97-99	3
α-helix	100-105	6
α-helix	106-114	9
α-helix	115-119	5
α-helix	120-145	26
α-helix	151-153	3
β-strand	154	1	1
α-helix	155-157	3
β-strand	159-161	3	2
α-helix	165-167	3

Chain B: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
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
β-strand	153	1	2
β-strand	159-161	3	1

Chain C: 13 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	98-100	3
α-helix	101-105	5
α-helix	106-114	9
α-helix	115-119	5
α-helix	120-145	26
α-helix	150-152	3
β-strand	154-155	2	1
β-strand	158-161	4	1
β-strand	178-179	2	21
β-strand	201-202	2	21
α-helix	204-206	3
β-strand	215-225	11	22
β-strand	228-237	10	22
α-helix	243	1
β-strand	244-257	14	22
β-strand	263-271	9	22
α-helix	276-278	3
β-strand	279-287	9	23
β-strand	290-297	8	23
β-strand	314-320	7	23
β-strand	332-337	6	23
β-strand	340-341	2	24
β-strand	347-350	4	24
β-strand	356-358	3	24
β-strand	361-371	11	24
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	24
β-strand	426-430	5	24
β-strand	431	1	25
α-helix	432	1
β-strand	442-447	6	26
β-strand	450-455	6	26
β-strand	463	1	27
β-strand	465-471	7	26
β-strand	475	1	25
β-strand	476-479	4	26
β-strand	486	1	27
β-strand	509	1	21
β-strand	512-515	4	28
β-strand	520-526	7	28
β-strand	533	1	29
β-strand	535-541	7	28
β-strand	544-550	7	28
β-strand	557	1	29
β-strand	558-568	11	21
β-strand	571-581	11	21
β-strand	588-596	9	21

Chain D: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
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
α-helix	150-152	3
β-strand	153-155	3	2
β-strand	158-161	4	2
β-strand	178-180	3	12
β-strand	200-202	3	12
α-helix	204-206	3
β-strand	216-225	10	13
β-strand	228-236	9	13
β-strand	245-257	13	13
β-strand	263-271	9	13
α-helix	276-278	3
β-strand	279-287	9	14
β-strand	290-297	8	14
α-helix	307-309	3
β-strand	314-320	7	14
α-helix	328-330	3
β-strand	332-336	5	14
β-strand	340-341	2	15
β-strand	347-350	4	15
β-strand	354	1	14
β-strand	356-358	3	15
β-strand	361-371	11	15
α-helix	394-397	4
β-strand	407-417	11	15
β-strand	426-430	5	15
β-strand	431	1	16
β-strand	442-447	6	17
β-strand	450-455	6	17
β-strand	463	1	18
β-strand	465-471	7	17
β-strand	475	1	16
β-strand	476-479	4	17
β-strand	486	1	18
β-strand	509	1	12
β-strand	512-515	4	19
β-strand	520-526	7	19
β-strand	533	1	20
β-strand	535-541	7	19
β-strand	544-550	7	19
β-strand	557	1	20
β-strand	558-568	11	12
β-strand	571-581	11	12
β-strand	588-596	9	12
α-helix	597-598	2

Chain J: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	3
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	33-38	6	4
β-strand	46-51	6	4
α-helix	54-56	3
β-strand	60-61	2	4
β-strand	70-74	5	3
β-strand	80-85	6	3
α-helix	90-92	3
β-strand	94-102	9	4
β-strand	105-109	5	4
β-strand	113-115	3	4

Chain K: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	5
β-strand	10	1	6
β-strand	19-25	7	5
α-helix	29-31	3
β-strand	33-38	6	6
β-strand	46-51	6	6
α-helix	54-56	3
β-strand	60-62	3	6
β-strand	70-75	6	5
α-helix	76-78	3
β-strand	80-85	6	5
β-strand	94-102	9	6
β-strand	105-109	5	6
β-strand	113-115	3	6

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	11-12	2	8
β-strand	19-25	7	7
α-helix	31-33	3
β-strand	37-42	6	8
β-strand	49-53	5	8
β-strand	57-58	2	8
β-strand	66-71	6	7
β-strand	74-79	6	7
α-helix	84-86	3
β-strand	88-94	7	8
α-helix	100	1
β-strand	101	1	8
β-strand	106-109	4	8

Chain O: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	19-25	7	9
β-strand	30-31	2	10
β-strand	34-35	2	10
β-strand	37-42	6	11
β-strand	49-52	4	11
β-strand	58	1	11
β-strand	66-71	6	9
β-strand	74-79	6	9
α-helix	84-86	3
β-strand	88-94	7	11
β-strand	101-102	2	11
β-strand	106-108	3	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	A, B, C, D	protein	539	Nipah henipavirus	Q9IH62 (AlphaFold model)
Igh protein	J, K	protein	458	Mus sp.	I6L985 (AlphaFold model)
nAH Fab light chain	N, O	protein	218	Mus sp.

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

>7TY0_1 Glycoprotein G (chains A, B, C, D)
HHHHHHIQNYTRSTDNQAVIKDALQGIQQQIKGLADKIGTEIGPKVSLIDTSSTITIPAN
IGLLGSKISQSTASINENVNEKCKFTLPPLKIHECNISCPNPLPFREYRPQTEGVSNLVG
LPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRG
VSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDP
ILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLY
FPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGEN
PKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNT
VISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDN
EILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCY

Sequence of entity 2 (J, K), FASTA

>7TY0_2 Igh protein (chains J, K)
EVKLEESGGGLVQPGGSMKLSCVASGFSFSYYWMNWVRQSPEKGLEWVAEIRLKSNNYGT
HYAESVKGRFTISRDDSKSSVYLQMNNLRPEDTGIYYCTRVITTVFAYWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSSVFIFP
PKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTAQTQPREEQFNSTFRSVS
ELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTISKTKGRPKAPQVYTIPPPKEQMAKDKVS
LTCMITDFFPEDITVEWQWNGQPAENYKNTQPIMDTDGSYFVYSKLNVQKSNWEAGNTFT
CSVLHEGLHNHHTEKSLSHSPGKGGSGGGSWSHPQFEK

Sequence of entity 3 (N, O), FASTA

>7TY0_3 nAH Fab light chain (chains N, O)
DIVLTQSPASLAVSLGQRATISCRASESVHDYGISFMNWFQQKPGQPPKLLIYSASNQGS
GVPARFSGSGSGTDFSLNIHPMEEDDIAMYFCQQSKEVPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Primary citation

Architecture and antigenicity of the Nipah virus attachment glycoprotein. Wang, Z., Amaya, M., Addetia, A. et al. Science (2022) 375:1373-1378. DOI 10.1126/science.abm5561 · 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
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…

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