7TXZ: Glycoprotein G

Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing antibody Fab fragment (local refinement of the distal region). Determined by electron microscopy at 3.2 Å resolution. Released 9 Mar 2022.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Nipah henipavirus, Mus sp.
Chains: 8
Atoms: 11,303
Mol. weight: 396.65 kDa
Ligands: NAG
Released: 9 Mar 2022

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

Secondary structure: helices and β-sheets

7TXZ contains 38 α-helices and 130 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: 13 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	132-145	14
α-helix	151-152	2
β-strand	153-154	2	1
α-helix	155-157	3
β-strand	159-161	3	2
α-helix	165-167	3
β-strand	178-179	2	3
β-strand	201-202	2	3
α-helix	204-206	3
β-strand	215-225	11	4
β-strand	228-237	10	4
α-helix	240-242	3
β-strand	244-257	14	4
β-strand	263-271	9	4
β-strand	279-287	9	5
β-strand	290-297	8	5
β-strand	314-320	7	5
α-helix	328-330	3
β-strand	332-336	5	5
β-strand	340-341	2	6
β-strand	347-350	4	6
β-strand	354	1	5
β-strand	356-358	3	6
β-strand	361-371	11	6
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	6
α-helix	424-425	2
β-strand	426-430	5	6
β-strand	431	1	7
α-helix	432	1
β-strand	442-447	6	8
β-strand	450-455	6	8
β-strand	465-471	7	8
β-strand	475	1	7
β-strand	476-479	4	8
β-strand	509	1	3
β-strand	512-515	4	9
β-strand	520-526	7	9
β-strand	533	1	10
β-strand	535-541	7	9
β-strand	544-550	7	9
β-strand	557	1	10
β-strand	558-568	11	3
β-strand	571-581	11	3
β-strand	588-596	9	3
α-helix	597-598	2

Chain B: 11 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	133-145	13
α-helix	151-152	2
β-strand	153	1	2
β-strand	159-161	3	1
α-helix	162-164	3
α-helix	169-171	3
β-strand	177	1	11
β-strand	179-180	2	12
β-strand	201-203	3	12
α-helix	210-212	3
β-strand	215-225	11	11
β-strand	228-237	10	11
β-strand	244-257	14	11
β-strand	263-271	9	11
β-strand	279-287	9	13
β-strand	290-297	8	13
β-strand	314-320	7	13
α-helix	328-331	4
β-strand	332-336	5	13
β-strand	340-341	2	14
β-strand	347-350	4	14
β-strand	354	1	13
β-strand	356-358	3	14
β-strand	361-371	11	14
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	14
β-strand	426-430	5	14
β-strand	431	1	15
α-helix	432	1
β-strand	442-447	6	16
β-strand	450-455	6	16
β-strand	463	1	17
β-strand	465-471	7	16
β-strand	475	1	15
β-strand	476-479	4	16
β-strand	486	1	17
β-strand	509	1	12
β-strand	512-515	4	18
β-strand	520-526	7	18
β-strand	533	1	19
β-strand	535-541	7	18
β-strand	544-550	7	18
β-strand	557	1	19
β-strand	558-568	11	12
β-strand	571-580	10	12
β-strand	588	1	11
β-strand	591-596	6	12
α-helix	597-598	2

Chain C: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	133-145	13
α-helix	150-152	3
β-strand	153-154	2	1
β-strand	159-161	3	1

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	133-145	13
α-helix	151-152	2
β-strand	153-155	3	2
β-strand	158-161	4	2

Chain E: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	10-11	2	21
β-strand	18-25	8	20
α-helix	29-31	3
β-strand	33-40	8	21
β-strand	44-51	8	21
α-helix	54-56	3
β-strand	60-62	3	21
β-strand	67	1	20
β-strand	70-75	6	20
β-strand	80-85	6	20
α-helix	90-92	3
β-strand	94-102	9	21
β-strand	105-109	5	21
β-strand	113-116	4	21

Chain F: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	22
β-strand	10-13	4	23
β-strand	19-25	7	22
β-strand	30-31	2	24
β-strand	34-35	2	24
β-strand	37-42	6	23
β-strand	49-52	4	23
β-strand	53	1	25
β-strand	57	1	25
β-strand	66-71	6	22
β-strand	74-79	6	22
α-helix	84-86	3
β-strand	88-94	7	23
α-helix	100	1
β-strand	101-102	2	23
β-strand	106-110	5	23

Chain H: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	10-11	2	27
β-strand	18-25	8	26
α-helix	29-31	3
β-strand	33-40	8	27
β-strand	44-51	8	27
α-helix	54-56	3
β-strand	60-62	3	27
β-strand	67	1	26
β-strand	70-75	6	26
α-helix	76-78	3
β-strand	80-85	6	26
α-helix	90-92	3
β-strand	94-102	9	27
β-strand	105-109	5	27
β-strand	113-116	4	27

Chain L: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	28
β-strand	10-13	4	29
β-strand	19-25	7	28
β-strand	30-31	2	30
β-strand	34-35	2	30
β-strand	37-42	6	29
β-strand	49-52	4	29
β-strand	53	1	31
β-strand	57	1	31
β-strand	66-71	6	28
β-strand	74-79	6	28
β-strand	88-94	7	29
α-helix	100	1
β-strand	101-102	2	29
β-strand	106-110	5	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	A, B, C, D	protein	539	Nipah henipavirus	Q9IH62 (AlphaFold model)
nAH1.3 Fab heavy chain	E, H	protein	458	Mus sp.
nAH1.3 Fab light chain	F, L	protein	218	Mus sp.

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

>7TXZ_1 Glycoprotein G (chains A, B, C, D)
HHHHHHIQNYTRSTDNQAVIKDALQGIQQQIKGLADKIGTEIGPKVSLIDTSSTITIPAN
IGLLGSKISQSTASINENVNEKCKFTLPPLKIHECNISCPNPLPFREYRPQTEGVSNLVG
LPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSRG
VSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGDP
ILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTLY
FPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGEN
PKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNNT
VISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKDN
EILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCY

Sequence of entity 2 (E, H), FASTA

>7TXZ_2 nAH1.3 Fab heavy chain (chains E, H)
EVKLEESGGGLVQPGGSMKLSCVASGFSFSYYWMNWVRQSPEKGLEWVAEIRLKSNNYGT
HYAESVKGRFTISRDDSKSSVYLQMNNLRPEDTGIYYCTRVITTVFAYWGQGTLVTVSAA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDCGCKPCICTVPEVSSVFIFP
PKPKDVLTITLTPKVTCVVVDISKDDPEVQFSWFVDDVEVHTAQTQPREEQFNSTFRSVS
ELPIMHQDWLNGKEFKCRVNSAAFPAPIEKTISKTKGRPKAPQVYTIPPPKEQMAKDKVS
LTCMITDFFPEDITVEWQWNGQPAENYKNTQPIMDTDGSYFVYSKLNVQKSNWEAGNTFT
CSVLHEGLHNHHTEKSLSHSPGKGGSGGGSWSHPQFEK

Sequence of entity 3 (F, L), FASTA

>7TXZ_3 nAH1.3 Fab light chain (chains F, L)
DIVLTQSPASLAVSLGQRATISCRASESVHDYGISFMNWFQQKPGQPPKLLIYSASNQGS
GVPARFSGSGSGTDFSLNIHPMEEDDIAMYFCQQSKEVPYTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

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

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…
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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