6VY4: Hendra receptor binding protein head domain

Crystal structure of Hendra receptor binding protein head domain in complex with human neutralizing antibody HENV-32. Determined by X-ray diffraction at 2.0 Å resolution. Released 30 Dec 2020.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Hendra henipavirus, Homo sapiens
Chains: 6
Atoms: 13,613
Mol. weight: 193.52 kDa
Ligands: NAG, IPA
Released: 30 Dec 2020

Explore 6VY4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6VY4 contains 49 α-helices and 152 β-strands across 6 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: 12 helices, 32 β-strands

Element	Residues	Length	Sheet
α-helix	195-197	3
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
α-helix	276-278	3
β-strand	279-287	9	3
β-strand	290-297	8	3
α-helix	303-305	3
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
α-helix	418-420	3
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	465-471	7	6
β-strand	475	1	5
β-strand	476-479	4	6
β-strand	509	1	1
β-strand	511-515	5	7
β-strand	520-526	7	7
β-strand	533	1	8
β-strand	535-541	7	7
β-strand	544-550	7	7
β-strand	557	1	8
β-strand	558-568	11	1
β-strand	571-580	10	1
β-strand	589-596	8	1
α-helix	597-598	2
α-helix	603-610	8

Chain B: 9 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	201-202	2	9
α-helix	204-206	3
β-strand	215-225	11	10
β-strand	228-237	10	10
β-strand	244-257	14	10
β-strand	263-271	9	10
α-helix	276-278	3
β-strand	279-287	9	11
β-strand	290-297	8	11
α-helix	310-312	3
β-strand	314-320	7	11
β-strand	332-336	5	11
β-strand	339-341	3	12
β-strand	347-350	4	12
β-strand	354	1	11
β-strand	356-358	3	12
β-strand	361-371	11	12
α-helix	372-374	3
α-helix	379-381	3
α-helix	394-397	4
β-strand	407-417	11	12
β-strand	425-430	6	12
β-strand	431	1	13
α-helix	432	1
β-strand	442-447	6	14
β-strand	450-455	6	14
β-strand	465-471	7	14
β-strand	475	1	13
β-strand	476-479	4	14
β-strand	509	1	9
β-strand	511-515	5	15
β-strand	520-526	7	15
β-strand	533	1	16
β-strand	535-540	6	15
β-strand	545-550	6	15
β-strand	557	1	16
β-strand	558-568	11	9
β-strand	571-582	12	9
β-strand	587-596	10	9
α-helix	597-598	2
α-helix	607-610	4

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	10-12	3	18
β-strand	18-25	8	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	59	1	18
β-strand	68-73	6	17
β-strand	78-83	6	17
α-helix	88-90	3
β-strand	92-100	9	18
β-strand	104-108	5	18
β-strand	112-116	5	18
α-helix	119-121	3
β-strand	122	1	19
α-helix	123-124	2
β-strand	125-129	5	20
β-strand	143-150	8	20
β-strand	151	1	19
β-strand	156-159	4	21
β-strand	164	1	21
β-strand	168-170	3	20
α-helix	171-173	3
β-strand	174-175	2	20
β-strand	181-187	7	20
β-strand	200-205	6	21
α-helix	206-208	3
β-strand	210-215	6	21

Chain D: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	22
β-strand	10-13	4	23
β-strand	19-24	6	22
α-helix	28-30	3
β-strand	34-38	5	23
β-strand	45-48	4	23
β-strand	49	1	24
β-strand	53	1	24
β-strand	62-67	6	22
β-strand	70-75	6	22
α-helix	80-82	3
β-strand	84-92	9	23
β-strand	97-100	4	23
β-strand	104-108	5	23
β-strand	117-121	5	25
α-helix	122-124	3
α-helix	125-128	4
β-strand	133-140	8	25
β-strand	148-150	3	26
β-strand	162-164	3	25
α-helix	165-167	3
β-strand	168-169	2	27
β-strand	175-176	2	27
β-strand	177-183	7	25
α-helix	185-190	6
β-strand	194-199	6	26
β-strand	205-209	5	26

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	18-25	8	28
β-strand	34-39	6	29
β-strand	45-51	7	29
β-strand	59	1	29
β-strand	68-73	6	28
β-strand	78-83	6	28
α-helix	88-90	3
β-strand	92-100	9	29
β-strand	104-108	5	29
β-strand	112-116	5	29
α-helix	120-121	2
β-strand	122	1	30
α-helix	123-124	2
β-strand	125-129	5	31
β-strand	140-150	11	31
β-strand	151	1	30
β-strand	156-159	4	32
α-helix	160-162	3
β-strand	164	1	32
β-strand	168-170	3	31
α-helix	171-173	3
β-strand	174-175	2	31
β-strand	181-190	10	31
α-helix	191-195	5
β-strand	200-205	6	32
α-helix	206-208	3
β-strand	210-215	6	32

Chain L: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	33
β-strand	10-13	4	34
β-strand	19-24	6	33
α-helix	28-30	3
β-strand	34-38	5	34
β-strand	45-48	4	34
β-strand	49	1	35
β-strand	53	1	35
β-strand	62-67	6	33
β-strand	70-75	6	33
α-helix	80-82	3
β-strand	85-92	8	34
β-strand	97-100	4	34
β-strand	104-108	5	34
α-helix	111-113	3
β-strand	114	1	36
α-helix	115-116	2
β-strand	117-121	5	37
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	37
β-strand	143	1	36
β-strand	148-153	6	38
β-strand	156-158	3	38
β-strand	162-164	3	37
α-helix	165-167	3
β-strand	168-169	2	37
β-strand	175-183	9	37
α-helix	185-190	6
β-strand	194-200	7	38
β-strand	203-209	7	38

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
receptor binding protein	A, B	protein	433	Hendra henipavirus	O89343 (AlphaFold model)
Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain	C, H	protein	221	Homo sapiens
Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain	D, L	protein	214	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>6VY4_1 receptor binding protein (chains A, B)
PNQICLQKTTSTILKPRLISYTLPINTREGVCITDPLLAVDNGFFAYSHLEKIGSCTRGI
AKQRIIGVGEVLDRGDKVPSMFMTNVWTPPNPSTIHHCSSTYHEDFYYTLCAVSHVGDPI
LNSTSWTESLSLIRLAVRPKSDSGDYNQKYIAITKVERGKYDKVMPYGPSGIKQGDTLYF
PAVGFLPRTEFQYNDSNCPIIHCKYSKAENCRLSMGVNSKSHYILRSGLLKYNLSLGGDI
ILQFIEIADNRLTIGSPSKIYNSLGQPVFYQASYSWDTMIKLGDVDTVDPLRVQWRNNSV
ISRPGQSQCPRFNVCPEVCWEGTYNDAFLIDRLNWVSAGVYLNSNQTAENPVFAVFKDNE
ILYQVPLAEDDTNAQKTITDCFLLENVIWCISLVEIYDTGDSVIRPKLFAVKIPAQCSES
ENLYFQGHHHHHH

Sequence of entity 2 (C, H), FASTA

>6VY4_2 Anti-Hendra receptor binding protein antibody HENV-32 Fab heavy chain (chains C, H)
QVQLVQSGAEVKKPGSSVKVSCKVSGGIFNRETINWVRQAPGQGLEWMGRITPIVDVPNY
PRKFRGRVTITADKSTSTVYMELSGLRFEDTAIYFCARFRGHNYFDPWGQGTLVTVSSAS
FKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (D, L), FASTA

>6VY4_3 Anti-Hendra receptor binding protein antibody HENV-32 Fab light chain (chains D, L)
SYVLTQPPSVSVAPGQTARITCGGNNIGGKSVHWYQQKPGQAPVLVVYDDRDRPSGIPER
FSGSNSGDTASLTISRVDAGDEADYFCQVWDNASDEAVFGGGTKLTVLGQPKANPTVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9
IPA	Isopropyl alcohol	C3 H8 O	3

Water and common crystallization additives (SO4) 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:

6PD4 2.2 Å, Crystal Structure of Hendra Virus Attachment G Glycoprotein
6VY6 2.6 Å, Crystal structure of Hendra receptor binding protein head domain in complex with human…
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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