9MY8: D7 Herpes Virus Simplex Neutralizing Nanobody

D7 Herpes Virus Simplex Neutralizing Nanobody Bound to HSV Glycoprotein gD. Determined by electron microscopy at 2.3 Å resolution. Released 13 Aug 2025.

Method: Electron microscopy
Resolution: 2.3 Å
Organisms: Lama glama, Homo sapiens, Human herpesvirus 2
Chains: 4
Atoms: 7,403
Mol. weight: 99.67 kDa
Released: 13 Aug 2025

Explore 9MY8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MY8 contains 24 α-helices and 63 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: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	11-12	2	14
β-strand	18-23	6	13
β-strand	33-39	7	15
β-strand	46-52	7	15
β-strand	57-59	3	15
β-strand	67-70	4	13
β-strand	79-82	4	13
α-helix	87-89	3
β-strand	91-98	8	15
β-strand	109	1	15
β-strand	113-115	3	15
β-strand	116-117	2	14

Chain B: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	30-31	2
β-strand	35-37	3	16
α-helix	44-46	3
α-helix	50-51	2
β-strand	56-60	5	16
β-strand	69-71	3	17
α-helix	77-82	6
α-helix	86-89	4
β-strand	92-103	12	16
β-strand	106-119	14	16
α-helix	123	1
β-strand	129-131	3	16
α-helix	132-133	2
β-strand	134-135	2	16
β-strand	142-144	3	17
β-strand	151-153	3	17
α-helix	158-160	3
β-strand	162-170	9	16
β-strand	173-181	9	16
α-helix	193-194	2
α-helix	199-201	3
β-strand	203	1	16
α-helix	205-210	6
α-helix	219	1
β-strand	220-221	2	16
α-helix	225-239	15

Chain H: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	19-25	7	1
α-helix	29-31	3
β-strand	32-39	8	3
β-strand	45-52	8	3
β-strand	57-60	4	3
β-strand	69-73	5	1
β-strand	78-82	5	1
α-helix	88-90	3
β-strand	92-100	9	3
β-strand	117-118	2	3
β-strand	122-124	3	3
β-strand	125-126	2	2
β-strand	135-137	3	4
β-strand	152-160	9	4
β-strand	166	1	5
α-helix	181-183	3
β-strand	184	1	4
α-helix	185	1
β-strand	191-198	8	4
α-helix	202-206	5
β-strand	214	1	5

Chain L: 4 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	6
β-strand	12	1	7
β-strand	19-24	6	6
β-strand	34	1	8
β-strand	48-49	2	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
β-strand	84	1	10
β-strand	89-91	3	8
β-strand	96-98	3	8
β-strand	104	1	10
β-strand	105	1	7
α-helix	111-113	3
β-strand	115-118	4	11
α-helix	123-126	4
β-strand	133-139	7	11
β-strand	147-150	4	12
β-strand	154-155	2	12
β-strand	173-178	6	11
α-helix	183-188	6
β-strand	192-195	4	12
β-strand	207-209	3	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Anti-Nb Fab Heavy chain	H	protein	244	Lama glama
Ig-like domain-containing protein	L	protein	214	Lama glama	Q7Z3Y4 (AlphaFold model)
D7 Neutralizing Nanobody against HSV Glycoprotein D	A	protein	125	Homo sapiens
Glycoprotein D	B	protein	327	Human herpesvirus 2	Q69467

Sequence of entity 1 (H), FASTA

>9MY8_1 Anti-Nb Fab Heavy chain (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFNFSYYSIHWVRQAPGKGLEWVAYISSSSSYTSY
ADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCARGYQYWQYHASWYWNGGLDYWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGSHH
HHHH

Sequence of entity 2 (L), FASTA

>9MY8_2 Ig-like domain-containing protein (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQSVSSAVAWYQQKPGKAPKLLIYSASSLYSGVPS
RFSGSRSGTDFTLTISSLQPEDFATYYCQQSSSSLITFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>9MY8_3 D7 Neutralizing Nanobody against HSV Glycoprotein D (chains A)
EVQLVESGGGLVQPGGSLRLSCSASGSIPSIWIMYWYRQAPGKGRELVAQITNFGTTVYA
DSVKGRFTISSDASKNTVYLQMNSLRAEDTAVYYCNLDVTLGPSRGAYWGKGTPVTVSSH
HHHHH

Sequence of entity 4 (B), FASTA

>9MY8_4 Glycoprotein D (chains B)
KYALADPSLKMADPNRFRGKNLPVLDQLTDPPGVKRVYHIQPSLEDPFQPPSIPITVYYA
VLERACRSVLLHAPSEAPQIVRGASDEARKHTYNLTIAWYRMGDNCAIPITVMEYTECPY
NKSLGVCPIRTQPRWSYYDSFSAVSEDNLGFLMHAPAFETAGTYLRLVKINDWTEITQFI
LEHRARASCKYALPLRIPPAACLTSKAYQQGVTVDSIGMLPRFIPENQRTVALYSLKIAG
WHGPKPPYTSTLLPPELSDTTNATQPELVPEDPEDSALLEDPAGTVSSQIPPNWHIPSIQ
DVAPHGGGSHHHHHHHHGSDYKDDDDK

Primary citation

Identification and engineering of potent bispecific antibodies that protect against herpes simplex virus recurrent disease. Lee, C.V., Viadiu, H., Kalamkar, A. et al. Cell Rep (2025) 44:116063-116063. DOI 10.1016/j.celrep.2025.116063 · PubMed

Other PDB entries of the same protein (UniProt Q7Z3Y4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5VSI 1.51 Å, CH1/Ckappa Fab mutant 15.1
6MY4 1.69 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M,LC-S30bR]
6MY5 1.73 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M,LC-S30bR]
4PUB 1.75 Å, Crystal structure of Fab DX-2930
1L7I 1.8 Å, Crystal Structure of the anti-ErbB2 Fab2C4
6MXS 1.95 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98F,HC-G99M]
6MXR 2.04 Å, Crystal structure of the dimeric bH1-Fab variant [HC-Y33W,HC-D98M,HC-G99M]
4OGY 2.1 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom…
5VR9 2.15 Å, CH1/Ckappa Fab based on Matuzumab
4OGX 2.4 Å, Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom…
8CWJ 2.45 Å, Fab arms of antibodies 4C12-B12 and CR3022 bound to pangolin receptor binding domain…
1PG7 2.5 Å, Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab

Browse structure collections

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