9HH9: Glycoprotein

Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its pre-fusion conformation in complex with 8G5F11 Fab. Determined by electron microscopy at 2.93 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 2.93 Å
Organisms: Vesicular stomatitis virus, Mus sp.
Chains: 9
Atoms: 15,613
Mol. weight: 313.16 kDa
Released: 22 Oct 2025

Explore 9HH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9HH9 contains 56 α-helices and 191 β-strands across 9 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: 17 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	15-16	2	1
α-helix	17-18	2
β-strand	23-24	2	2
α-helix	25-28	4
β-strand	37-45	9	3
α-helix	49-51	3
β-strand	54	1	4
β-strand	56-65	10	5
β-strand	82-84	3	5
α-helix	86-88	3
α-helix	89-101	13
β-strand	123-131	9	5
β-strand	134	1	4
β-strand	135-136	2	6
β-strand	143-144	2	6
β-strand	148	1	7
α-helix	149-151	3
β-strand	152-153	2	6
β-strand	157-159	3	5
β-strand	160	1	7
β-strand	166-169	4	5
β-strand	182-190	9	3
α-helix	195-197	3
β-strand	204-207	4	3
β-strand	210-214	5	3
β-strand	219-222	4	8
β-strand	227-230	4	8
β-strand	236-237	2	8
β-strand	238-239	2	3
α-helix	242-247	6
β-strand	252	1	8
α-helix	257-259	3
β-strand	263	1	1
α-helix	269-271	3
α-helix	274-293	20
β-strand	296-297	2	9
α-helix	299-303	5
β-strand	311-319	9	1
β-strand	322-335	14	1
β-strand	339-340	2	10
β-strand	344-345	2	11
β-strand	346-347	2	1
β-strand	354-355	2	11
β-strand	361-363	3	10
β-strand	366-368	3	10
α-helix	370-372	3
β-strand	374-376	3	10
β-strand	379-381	3	10
α-helix	383-386	4
β-strand	390-391	2	12
α-helix	392-393	2
α-helix	394-396	3
β-strand	400-401	2	9
β-strand	403	1	1
α-helix	408-413	6

Chain B: 18 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	13
β-strand	15-16	2	13
β-strand	23-24	2	14
α-helix	25-28	4
β-strand	37-45	9	15
α-helix	49-51	3
β-strand	53-54	2	16
β-strand	56-69	14	17
β-strand	77-84	8	17
α-helix	86-88	3
α-helix	89-101	13
β-strand	119-122	4	17
β-strand	125-131	7	17
β-strand	134-136	3	16
β-strand	143-144	2	16
β-strand	148	1	18
α-helix	149-151	3
β-strand	152-153	2	16
β-strand	157-159	3	17
β-strand	160	1	18
β-strand	166-169	4	17
α-helix	180-181	2
β-strand	182-190	9	15
α-helix	195-197	3
β-strand	204-206	3	15
β-strand	213-214	2	15
β-strand	219-222	4	19
β-strand	227-230	4	19
β-strand	236-237	2	19
β-strand	238-239	2	15
α-helix	242-248	7
α-helix	250-251	2
β-strand	252	1	19
α-helix	253-254	2
β-strand	263	1	13
α-helix	269-271	3
α-helix	274-293	20
β-strand	297	1	20
α-helix	299-302	4
β-strand	311-319	9	13
β-strand	322-335	14	13
β-strand	339-340	2	21
β-strand	346-347	2	13
β-strand	361-363	3	21
β-strand	366-368	3	21
α-helix	370-372	3
β-strand	374-375	2	21
β-strand	380-381	2	21
α-helix	383-386	4
β-strand	390-391	2	2
α-helix	392-393	2
β-strand	400	1	20
β-strand	403	1	13
α-helix	410-416	7
α-helix	418	1
β-strand	424-425	2	17

Chain C: 20 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	22
α-helix	14	1
β-strand	15-16	2	22
α-helix	17	1
β-strand	23-24	2	12
α-helix	25-28	4
β-strand	37-45	9	23
α-helix	48-50	3
β-strand	56-64	9	24
β-strand	66-67	2	25
β-strand	70	1	26
β-strand	76	1	26
β-strand	80-84	5	24
α-helix	86-88	3
α-helix	89-97	9
α-helix	110	1
β-strand	121-122	2	25
β-strand	125-130	6	24
β-strand	135-136	2	27
β-strand	143-144	2	27
β-strand	148	1	28
α-helix	149-151	3
β-strand	152	1	27
β-strand	157-159	3	24
β-strand	160	1	28
β-strand	166-169	4	24
α-helix	181	1
β-strand	182-190	9	23
β-strand	205	1	29
β-strand	206	1	23
β-strand	213	1	29
α-helix	215-217	3
β-strand	221-222	2	30
β-strand	227-228	2	30
β-strand	229-230	2	31
β-strand	236-237	2	31
β-strand	238	1	23
α-helix	242-245	4
β-strand	263	1	22
α-helix	269-271	3
α-helix	274-292	19
β-strand	297	1	32
α-helix	299-302	4
α-helix	303-305	3
β-strand	311-319	9	22
β-strand	322-335	14	22
β-strand	339-340	2	33
β-strand	346-347	2	22
β-strand	353	1	22
β-strand	361-363	3	33
β-strand	366-368	3	33
α-helix	370-372	3
β-strand	374-376	3	33
β-strand	379-381	3	33
α-helix	383-385	3
β-strand	390-391	2	14
α-helix	392-393	2
β-strand	400	1	32
β-strand	403	1	22
α-helix	410-413	4
α-helix	414-416	3
β-strand	423-425	3	24

Chain D: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	34
β-strand	21	1	35
β-strand	24	1	36
β-strand	36-38	3	37
β-strand	45-46	2	37
β-strand	48	1	38
β-strand	54	1	38
α-helix	55	1
β-strand	70	1	36
β-strand	73	1	35
β-strand	85-87	3	37
β-strand	88	1	39
β-strand	97	1	40
β-strand	99	1	39
β-strand	103	1	37
β-strand	104	1	34

Chain E: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	41
β-strand	12	1	42
β-strand	16-19	4	43
β-strand	24-25	2	41
β-strand	35-40	6	40
β-strand	46-52	7	40
β-strand	58-60	3	40
β-strand	68-72	5	43
β-strand	79-86	8	43
β-strand	93	1	44
β-strand	94-98	5	40
β-strand	112	1	40
β-strand	117	1	44
β-strand	120	1	42

Chain F: 0 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	45
β-strand	10-11	2	46
β-strand	21-22	2	47
β-strand	25	1	45
β-strand	33-37	5	48
β-strand	45-48	4	48
β-strand	54	1	48
β-strand	72-73	2	47
β-strand	86-90	5	48
β-strand	103-104	2	46

Chain G: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	49
β-strand	16-20	5	50
β-strand	23-25	3	49
β-strand	35-40	6	51
β-strand	46-52	7	51
β-strand	58-60	3	51
β-strand	68-72	5	50
β-strand	79-86	8	50
β-strand	92-98	7	51
β-strand	112	1	51
β-strand	117-118	2	51

Chain H: 0 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	52
β-strand	19-21	3	53
β-strand	33-36	4	54
β-strand	38	1	55
β-strand	46-48	3	54
β-strand	73-75	3	53
β-strand	85	1	55
β-strand	88-90	3	54
β-strand	97	1	52

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein	A, B, C	protein	495	Vesicular stomatitis virus	B7UCZ5 (AlphaFold model)
8G5F11 vl	D, F, H	protein	214	Mus sp.
8G5F11 vh	E, G, I	protein	229	Mus sp.

Sequence of entity 1 (A, B, C), FASTA

>9HH9_1 Glycoprotein (chains A, B, C)
KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCH
ASKWVTTCDFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVT
DAEAVIVQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSN
LISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCKHWGVRLPSGVWFEMA
DKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV
DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDW
APYEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDD
ESLFFGDTGLSKNPIELVEGWFSSWKSSIASFFFIIGLIIGLFLVLRVGIHLCIKLKHTK
KRQIYTDIEMNRLGK

Sequence of entity 2 (D, F, H), FASTA

>9HH9_2 8G5F11 VL (chains D, F, H)
DIVMTQSHKFMSTSVGDRVSITCKASQDVDNDVAWYQQKPGQSPKLLIYWASTRHTGVPD
RFTGSGSGTDFTLTISDVQSEDLSDYFCQQYSSYPFTFGGGTRLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (E, G, I), FASTA

>9HH9_3 8G5F11 VH (chains E, G, I)
DVQLQESGPDLVKPSQSLSLTCTVTGYSITSGYSWHWNRQFPGNKLEWMGYIHYSGLTNY
NPSLKSRISITRHTSKNQFFLQLNSVTTEDTATYYCVRGGYDGRDYYAMDFWGQGTSVTV
SSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTIN

Primary citation

Cryo-EM structures of VSV G alone and in complex with a neutralizing antibody. Albertini, A., Minoves, M.J., OuldAli, M. et al. To be published.

Other PDB entries of the same protein (UniProt B7UCZ5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TIT 2.07 Å, Vsv G_440
5OYL 2.25 Å, Vsv G CR2
9HHR 2.81 Å, Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its post-fusion…
9I8Q 2.93 Å, Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its pre-fusion…
9HGN 2.94 Å, Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its acidic…

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