9DVD: Cryo EM structure of Hendra G ectodomain

Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270. Determined by electron microscopy at 2.9 Å resolution. Released 15 Oct 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Henipavirus hendraense, Homo sapiens
Chains: 4
Atoms: 5,965
Mol. weight: 90.27 kDa
Ligands: NAG, BMA
Released: 15 Oct 2025

Explore 9DVD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DVD contains 6 α-helices and 79 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: 4 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	176-177	2
β-strand	178-179	2	1
β-strand	200-201	2	2
β-strand	215-222	8	3
β-strand	225	1	3
β-strand	228-237	10	3
β-strand	244-254	11	3
β-strand	257	1	4
β-strand	263	1	4
β-strand	266-271	6	3
β-strand	279-280	2	5
β-strand	285-287	3	5
β-strand	290-297	8	5
β-strand	314-319	6	5
β-strand	332-336	5	5
β-strand	341	1	6
β-strand	348-350	3	7
β-strand	361-371	11	7
α-helix	379-381	3
α-helix	394-399	6
β-strand	400	1	7
β-strand	407-417	11	7
β-strand	427	1	6
β-strand	428-430	3	7
β-strand	442-447	6	8
β-strand	450-455	6	8
β-strand	463	1	9
β-strand	465-468	4	8
β-strand	469-471	3	10
β-strand	476-477	2	10
β-strand	486	1	9
β-strand	505	1	11
β-strand	509	1	2
β-strand	511	1	12
β-strand	521-526	6	12
β-strand	533	1	13
β-strand	535-540	6	12
β-strand	545-550	6	12
β-strand	557	1	13
β-strand	561-564	4	2
β-strand	567-568	2	1
β-strand	571-572	2	1
β-strand	573-578	6	2
β-strand	581	1	13
β-strand	591-596	6	2
α-helix	597-598	2

Chain B: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	29	1	14
α-helix	30-32	3
β-strand	33-34	2	14
β-strand	43	1	15
β-strand	47	1	15
β-strand	48-49	2	16
β-strand	57-62	6	14
β-strand	77-81	5	16
α-helix	83-88	6
β-strand	99-100	2	16
β-strand	108-113	6	14
β-strand	120	1	11
β-strand	133-136	4	16
β-strand	159-161	3	16

Chain H: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	17
β-strand	10-12	3	18
β-strand	17-20	4	17
β-strand	23-25	3	17
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	60-61	2	18
β-strand	68-73	6	17
β-strand	78-84	7	17
β-strand	92-98	7	18
β-strand	110	1	17
β-strand	113-117	5	18

Chain L: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	19
β-strand	5	1	20
β-strand	9-12	4	21
β-strand	18-23	6	20
β-strand	32-37	6	21
β-strand	44-48	5	21
β-strand	52	1	21
β-strand	61-66	6	20
β-strand	69-74	6	20
β-strand	84-90	7	21
β-strand	96-98	3	21
β-strand	99	1	19
β-strand	102-106	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	A	protein	429	Henipavirus hendraense	F4YH71
Ephrin-B2	B	protein	138	Homo sapiens	P52799 (AlphaFold model)
Fan HENV-270 heavy chain	H	protein	120	Homo sapiens
Fan HENV-270 light chain	L	protein	108	Homo sapiens

Sequence of entity 1 (A), FASTA

>9DVD_1 Glycoprotein (chains A)
ISQGVSDLVGLPNQICLQKTTSTILKPRLISYTLPINTREGVCITDPLLAVDNGFFAYSH
LEKIGSCTRGIAKQRIIGVGEVLDRGDKVPSMFMTNVWTPPNPSTIHHCSSTYHEDFYYT
LCAVSHVGDPILNSTSWTESLSLIRLAVRPKSDSGDYNQKYIAITKVERGKYDKVMPYGP
SGIKQGDTLYFPAVGFLPRTEFQYNDSNCPIIHCKYSKAENCRLSMGVNSKSHYILRSGL
LKYNLSLGGDIILQFIEIADNRLTIGSPSKIYNSLGQPVFYQASYSWDTMIKLGDVDTVD
PLRVQWRNNSVISRPGQSQCPRFNVCPEVCWEGTYNDAFLIDRLNWVSAGVYLNSNQTAE
NPVFAVFKDNEILYQVPLAEDDTNAQKTITDCFLLENVIWCISLVEIYDTGDSVIRPKLF
AVKIPAQCS

Sequence of entity 2 (B), FASTA

>9DVD_2 Ephrin-B2 (chains B)
SIVLEPIYWNSSNSKFLPGQGLVLYPQIGDKLDIICPKVDSKTVGQYEYYKVYMVDKDQA
DRCTIKKENTPLLNCAKPDQDIKFTIKFQEFSPNLWGLEFQKNKDYYIISTSNGSLEGLD
NQEGGVCQTRAMKILMKV

Sequence of entity 3 (H), FASTA

>9DVD_3 Fan HENV-270 heavy chain (chains H)
QVQLVQSGSELKKPGASVKVSCKASGYTFTSYAVNWVRQAPGQGLEWVGWMSTNTGDPIY
AQGFTGRFVFSLDTSVSTAYLQISSLKAEDSGVYYCAREGLRGRAFDIWGQGTMVTVSSA

Sequence of entity 4 (L), FASTA

>9DVD_4 Fan HENV-270 light chain (chains L)
SYELTQPPSVSVSPGQTARITCSGDKLGDKYAAWYQQKPGQSPVLVIYQNTKRPSGIPER
FSGSSSGNTATLTISGTQAMDEADYFCQAWDSRTNWVFGGGTKLTVLG

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
BMA	beta-D-mannopyranose	C6 H12 O6	1

Primary citation

Cryo EM structure of Hendra G ectodomain in complex with Ephrin-B2 and Fab HENV-270. Binshtein, E., Crowe, J.E. To be published.

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