3D12: Nipah Virus G Attachment Glycoprotein

Crystal Structures of Nipah Virus G Attachment Glycoprotein in Complex with its Receptor Ephrin-B3. Determined by X-ray diffraction at 3.0 Å resolution. Released 19 Aug 2008.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Nipah virus, Mus musculus
Chains: 4
Atoms: 9,598
Mol. weight: 135.76 kDa
Ligands: NAG
Released: 19 Aug 2008

Explore 3D12 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D12 contains 27 α-helices and 92 β-strands across 4 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, 35 β-strands

Element	Residues	Length	Sheet
β-strand	178-180	3	1
β-strand	201-202	2	1
α-helix	204-206	3
β-strand	215-225	11	2
β-strand	228-237	10	2
β-strand	244-257	14	2
β-strand	263-271	9	2
β-strand	279-286	8	3
β-strand	290-297	8	3
α-helix	307-309	3
β-strand	314-320	7	3
α-helix	328-331	4
β-strand	332-333	2	3
β-strand	340-341	2	4
β-strand	347-350	4	4
β-strand	354	1	3
β-strand	356-358	3	4
β-strand	361-371	11	4
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	4
α-helix	424-425	2
β-strand	426-430	5	4
β-strand	431	1	5
α-helix	432	1
β-strand	442-447	6	6
β-strand	450-455	6	6
β-strand	463	1	7
β-strand	465-471	7	6
β-strand	475	1	5
β-strand	476-479	4	6
β-strand	486	1	7
β-strand	509	1	1
β-strand	511-515	5	8
β-strand	520-526	7	8
β-strand	533	1	1
β-strand	535-541	7	8
β-strand	544-550	7	8
β-strand	557-568	12	1
β-strand	572-581	10	1
β-strand	588	1	2
β-strand	591-596	6	1
α-helix	597-598	2

Chain B: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
β-strand	33-34	2	9
β-strand	49-50	2	10
α-helix	52-53	2
β-strand	57-62	6	9
β-strand	80-84	5	10
α-helix	87-90	4
β-strand	93	1	11
α-helix	94-95	2
β-strand	99-103	5	10
β-strand	111-116	6	9
β-strand	134-139	6	10
β-strand	152	1	11
α-helix	155-158	4
β-strand	162-166	5	10

Chain D: 8 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	177	1	12
β-strand	179-180	2	13
β-strand	201-202	2	13
α-helix	204-206	3
β-strand	215-225	11	12
β-strand	228-237	10	12
β-strand	244-257	14	12
β-strand	263-271	9	12
β-strand	279-286	8	14
β-strand	290-297	8	14
α-helix	307-309	3
β-strand	314-320	7	14
β-strand	334-335	2	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	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	15
α-helix	424-425	2
β-strand	426-430	5	15
β-strand	431	1	16
α-helix	432	1
β-strand	442-447	6	17
β-strand	450-455	6	17
β-strand	465-468	4	17
β-strand	469-471	3	18
β-strand	475	1	16
β-strand	476-477	2	18
β-strand	509	1	13
β-strand	511-515	5	19
β-strand	520-526	7	19
β-strand	533	1	13
β-strand	535-541	7	19
β-strand	544-550	7	19
β-strand	557-568	12	13
β-strand	571-581	11	13
β-strand	588	1	12
β-strand	589-596	8	13
α-helix	597-598	2

Chain E: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	30-32	3
β-strand	33-34	2	20
β-strand	49-50	2	21
α-helix	52-53	2
β-strand	57-62	6	20
β-strand	78	1	22
β-strand	80-84	5	21
α-helix	87-90	4
β-strand	93	1	23
β-strand	99-103	5	21
β-strand	111-116	6	20
α-helix	129-130	2
β-strand	134-139	6	21
β-strand	143	1	22
β-strand	152	1	23
α-helix	155-158	4
β-strand	162-166	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hemagglutinin-neuraminidase	A, D	protein	428	Nipah virus	Q9IH62 (AlphaFold model)
Ephrin-B3	B, E	protein	141	Mus musculus	O35393 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>3D12_1 Hemagglutinin-neuraminidase (chains A, D)
EGVSNLVGLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLE
RIGSCSRGVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLC
AVSTVGDPILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSG
IKQGDTLYFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLK
YNLSDGENPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPL
VVNWRNNTVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENP
VFTVFKDNEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAV
KIPEQCTA

Sequence of entity 2 (B, E), FASTA

>3D12_2 Ephrin-B3 (chains B, E)
SLEPVYWNSANKRFQAEGGYVLYPQIGDRLDLLCPRARPPGPHSSPSYEFYKLYLVEGAQ
GRRCEAPPAPNLLLTCDRPDLDLRFTIKFQEYSPNLWGHEFRSHHDYYIIATSDGTREGL
ESLQGGVCLTRGMKVLLRVGQ

Ligands and cofactors

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

Water and common crystallization additives (SO4) are not listed.

Primary citation

Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3. Xu, K., Rajashankar, K.R., Chan, Y.P. et al. Proc Natl Acad Sci U S A (2008) 105:9953-9958. DOI 10.1073/pnas.0804797105 · 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
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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