6VY5: Nipah receptor binding protein head domain

Crystal structure of Nipah receptor binding protein head domain in complex with human neutralizing antibody HENV-26. Determined by X-ray diffraction at 3.4 Å resolution. Released 6 Jan 2021.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Homo sapiens, Nipah henipavirus
Chains: 3
Atoms: 6,252
Mol. weight: 97.19 kDa
Ligands: NAG
Released: 6 Jan 2021

Explore 6VY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VY5 contains 21 α-helices and 76 β-strands across 3 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: 7 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	12
α-helix	204-206	3
β-strand	217-225	9	13
β-strand	228-235	8	13
β-strand	248-257	10	13
β-strand	263-271	9	13
α-helix	276-278	3
β-strand	279-286	8	14
β-strand	290-297	8	14
β-strand	314-320	7	14
α-helix	323-324	2
β-strand	332-335	4	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
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	465-471	7	17
β-strand	475	1	16
β-strand	476-479	4	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	535-540	6	18
β-strand	545-550	6	18
β-strand	557	1	19
β-strand	558-567	10	12
β-strand	572-581	10	12
β-strand	588-589	2	12
β-strand	592-596	5	12

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	3
β-strand	114-117	4	3
β-strand	121-123	3	3
β-strand	124-125	2	2
α-helix	129-130	2
β-strand	131	1	4
β-strand	134-138	5	5
β-strand	152-159	8	5
β-strand	160	1	4
β-strand	165-168	4	6
α-helix	169-171	3
β-strand	177-179	3	5
α-helix	180-182	3
β-strand	183-184	2	5
β-strand	190-196	7	5
β-strand	208-214	7	6
α-helix	215-217	3
β-strand	219-225	7	6

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	7
β-strand	10-13	4	8
β-strand	18-25	8	7
α-helix	28-30	3
β-strand	34-38	5	8
β-strand	45-48	4	8
β-strand	49	1	9
β-strand	53	1	9
α-helix	54-55	2
β-strand	62-67	6	7
β-strand	70-76	7	7
α-helix	80-82	3
β-strand	85-92	8	8
β-strand	97-100	4	8
β-strand	104-108	5	8
α-helix	111-113	3
β-strand	117-121	5	10
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	10
β-strand	148-153	6	11
β-strand	156-157	2	11
β-strand	163-164	2	10
α-helix	165-167	3
β-strand	168-169	2	10
β-strand	175-183	9	10
α-helix	185-190	6
β-strand	194-199	6	11
β-strand	204-209	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain	H	protein	230	Homo sapiens
Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain	L	protein	214	Homo sapiens
receptor binding protein	A	protein	433	Nipah henipavirus	Q9IH62 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>6VY5_1 Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain (chains H)
EVQLLESGGGLIQPGGSLRLSCAASGFTFSRFTMSWVRQPPGKGPEWVSGISGSGGHTYY
ADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAKDGFVGQQLMRRGPWWFDPWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 2 (L), FASTA

>6VY5_2 Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain (chains L)
SYVLTQPPSVSVAPGQTARISCGGNNIGNKGVHWYQQKPGQAPVVVVYDDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHVVFGGGTKLTVLGQPKANPTVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 3 (A), FASTA

>6VY5_3 receptor binding protein (chains A)
GLPNNICLQKTSNQILKPKLISYTLPVVGQSGTCITDPLLAMDEGYFAYSHLERIGSCSR
GVSKQRIIGVGEVLDRGDEVPSLFMTNVWTPPNPNTVYHCSAVYNNEFYYVLCAVSTVGD
PILNSTYWSGSLMMTRLAVKPKSNGGGYNQHQLALRSIEKGRYDKVMPYGPSGIKQGDTL
YFPAVGFLVRTEFKYNDSNCPITKCQYSKPENCRLSMGIRPNSHYILRSGLLKYNLSDGE
NPKVVFIEISDQRLSIGSPSKIYDSLGQPVFYQASFSWDTMIKFGDVLTVNPLVVNWRNN
TVISRPGQSQCPRFNTCPEICWEGVYNDAFLIDRINWISAGVFLDSNQTAENPVFTVFKD
NEILYRAQLASEDTNAQKTITNCFLLKNKIWCISLVEIYDTGDNVIRPKLFAVKIPEQCT
ENLYFQGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Primary citation

Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein. Dong, J., Cross, R.W., Doyle, M.P. et al. Cell (2020) 183:1536-1550.e17. DOI 10.1016/j.cell.2020.11.023 · 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…
7TY0 3.5 Å, Nipah Virus attachment (G) glycoprotein ectodomain in complex with nAH1.3 neutralizing…

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