6VY6: Hendra receptor binding protein head domain

Crystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-26. Determined by X-ray diffraction at 2.6 Å resolution. Released 6 Jan 2021.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Hendra henipavirus, Homo sapiens
Chains: 3
Atoms: 6,803
Mol. weight: 97.67 kDa
Ligands: NAG, ZN
Released: 6 Jan 2021

Explore 6VY6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VY6 contains 22 α-helices and 79 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: 9 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	1
α-helix	204-206	3
β-strand	215-225	11	2
β-strand	228-237	10	2
α-helix	243	1
β-strand	244-257	14	2
β-strand	263-271	9	2
β-strand	279-287	9	3
β-strand	290-297	8	3
α-helix	303-306	4
α-helix	310-312	3
β-strand	314-320	7	3
β-strand	332-337	6	3
β-strand	339-341	3	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
β-strand	425-430	6	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	9
β-strand	535-540	6	8
β-strand	545-550	6	8
β-strand	557	1	9
β-strand	558-568	11	1
β-strand	571-580	10	1
β-strand	589-596	8	1
α-helix	597-598	2

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	11
β-strand	46-51	6	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	114-117	4	11
β-strand	121-125	5	11
α-helix	128-130	3
β-strand	131	1	12
α-helix	132-133	2
β-strand	134-138	5	13
β-strand	149-159	11	13
β-strand	160	1	12
β-strand	165-168	4	14
β-strand	173	1	14
β-strand	177-179	3	13
α-helix	180-182	3
β-strand	183-184	2	13
β-strand	190-199	10	13
α-helix	200-204	5
β-strand	209-214	6	14
α-helix	215-217	3
β-strand	219-224	6	14

Chain L: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	15
β-strand	10-13	4	16
β-strand	19-24	6	15
α-helix	28-30	3
β-strand	34-38	5	16
β-strand	45-48	4	16
β-strand	49	1	17
β-strand	53	1	17
β-strand	62-67	6	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	85-92	8	16
β-strand	97-100	4	16
β-strand	104-108	5	16
β-strand	114	1	18
α-helix	115-116	2
β-strand	117-121	5	19
α-helix	125-129	5
β-strand	133-142	10	19
β-strand	143	1	18
β-strand	148-153	6	20
β-strand	156-158	3	20
β-strand	162-164	3	19
α-helix	165-167	3
β-strand	168-169	2	19
β-strand	175-183	9	19
α-helix	185-189	5
β-strand	194-200	7	20
β-strand	203-209	7	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
receptor binding protein	A	protein	433	Hendra henipavirus	O89343 (AlphaFold model)
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

Sequence of entity 1 (A), FASTA

>6VY6_1 receptor binding protein (chains A)
PNQICLQKTTSTILKPRLISYTLPINTREGVCITDPLLAVDNGFFAYSHLEKIGSCTRGI
AKQRIIGVGEVLDRGDKVPSMFMTNVWTPPNPSTIHHCSSTYHEDFYYTLCAVSHVGDPI
LNSTSWTESLSLIRLAVRPKSDSGDYNQKYIAITKVERGKYDKVMPYGPSGIKQGDTLYF
PAVGFLPRTEFQYNDSNCPIIHCKYSKAENCRLSMGVNSKSHYILRSGLLKYNLSLGGDI
ILQFIEIADNRLTIGSPSKIYNSLGQPVFYQASYSWDTMIKLGDVDTVDPLRVQWRNNSV
ISRPGQSQCPRFNVCPEVCWEGTYNDAFLIDRLNWVSAGVYLNSNQTAENPVFAVFKDNE
ILYQVPLAEDDTNAQKTITDCFLLENVIWCISLVEIYDTGDSVIRPKLFAVKIPAQCSES
ENLYFQGHHHHHH

Sequence of entity 2 (H), FASTA

>6VY6_2 Anti-Hendra receptor binding protein antibody HENV-26 Fab heavy chain (chains H)
EVQLLESGGGLIQPGGSLRLSCAASGFTFSRFTMSWVRQPPGKGPEWVSGISGSGGHTYY
ADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAKDGFVGQQLMRRGPWWFDPWGQG
TLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>6VY6_3 Anti-Hendra receptor binding protein antibody HENV-26 Fab light chain (chains L)
SYVLTQPPSVSVAPGQTARISCGGNNIGNKGVHWYQQKPGQAPVVVVYDDSDRPSGIPER
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSSSDHVVFGGGTKLTVLGQPKANPTVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
ZN	Zinc ion	Zn	1

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

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 O89343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6VY4 2.0 Å, Crystal structure of Hendra receptor binding protein head domain in complex with human…
6PD4 2.2 Å, Crystal Structure of Hendra Virus Attachment G Glycoprotein
6CMG 2.7 Å, Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent…
6PDL 2.7 Å, Crystal Structure of Hendra Virus Attachment G Glycoprotein in Complex with Receptor…
6CMI 2.72 Å, Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent…
7SYY 2.74 Å, Hendra virus G protein head domain in complex with cross-neutralizing murine antibody…
7SYZ 2.86 Å, Hendra virus G protein head domain in complex with cross-neutralizing murine antibody…
2X9M 2.9 Å, Hendra virus attachment glycoprotein
8VF1 3.0 Å, Crystal Structure of the Hendra Virus Attachment G glycoprotein (HeV-G)
8JR3 3.22 Å, Crystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N in complex…
2VSK 3.3 Å, Hendra virus attachment glycoprotein in complex with human cell surface receptor ephrinB2
8JR5 3.3 Å, Crystal structure of Hendra Virus attachment(G) glycoprotein mutant S586N

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