9HHR: Glycoprotein

Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its post-fusion conformation in complex with 8G5F11 Fab. Determined by electron microscopy at 2.81 Å resolution. Released 29 Oct 2025.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Vesicular stomatitis virus, Mus sp.
Chains: 9
Atoms: 15,492
Mol. weight: 313.16 kDa
Released: 29 Oct 2025

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

Secondary structure: helices and β-sheets

9HHR contains 55 α-helices and 177 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: 16 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	1
β-strand	15-16	2	1
α-helix	17-18	2
α-helix	25-28	4
β-strand	39-46	8	2
α-helix	50-52	3
β-strand	53-67	15	3
β-strand	80-85	6	3
α-helix	86-88	3
α-helix	89-100	12
α-helix	110-112	3
β-strand	121-137	17	3
β-strand	142-144	3	3
β-strand	148	1	4
α-helix	149-151	3
β-strand	152-153	2	3
β-strand	157-159	3	3
β-strand	160	1	4
β-strand	165-169	5	3
α-helix	173-177	5
α-helix	178-180	3
β-strand	181-188	8	2
β-strand	205-206	2	2
β-strand	219-222	4	5
β-strand	227-230	4	5
β-strand	236-237	2	5
β-strand	238-239	2	2
α-helix	243-248	6
α-helix	250-252	3
β-strand	260-261	2	6
α-helix	262-263	2
α-helix	267-293	27
α-helix	299-302	4
β-strand	311-318	8	1
β-strand	323-335	13	1
β-strand	339-340	2	7
β-strand	344-347	4	1
β-strand	353-355	3	1
β-strand	361-363	3	7
β-strand	366-368	3	7
β-strand	374-376	3	7
β-strand	379-381	3	7
α-helix	382-383	2
α-helix	384-399	16
β-strand	403-404	2	6
β-strand	422-425	4	3

Chain B: 18 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	8
β-strand	15-16	2	8
α-helix	17-18	2
α-helix	25-28	4
β-strand	37-46	10	9
α-helix	47-48	2
α-helix	50-52	3
β-strand	53-70	18	10
β-strand	77-85	9	10
α-helix	86-88	3
α-helix	89-99	11
α-helix	110-111	2
β-strand	118-137	20	10
β-strand	142-144	3	10
β-strand	148	1	11
α-helix	149-151	3
β-strand	152-153	2	10
β-strand	157-159	3	10
β-strand	160	1	11
β-strand	165-169	5	10
α-helix	173-178	6
β-strand	181-190	10	9
α-helix	195-197	3
β-strand	204-206	3	9
β-strand	213-214	2	9
β-strand	219-222	4	12
β-strand	227-230	4	12
β-strand	236-237	2	12
β-strand	238-239	2	9
α-helix	242-248	7
α-helix	253-254	2
β-strand	260-261	2	13
α-helix	262-263	2
α-helix	266-293	28
α-helix	299-305	7
β-strand	311-318	8	8
β-strand	323-335	13	8
β-strand	339-340	2	14
β-strand	344-347	4	8
β-strand	353-355	3	8
β-strand	361-363	3	14
β-strand	366-368	3	14
α-helix	370-372	3
β-strand	374-376	3	14
β-strand	379-381	3	14
α-helix	382-383	2
α-helix	384-399	16
β-strand	403-404	2	13
β-strand	423-425	3	10

Chain C: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	15
β-strand	15-16	2	15
α-helix	17-18	2
β-strand	37-40	4	16
β-strand	43-46	4	17
α-helix	50-52	3
β-strand	53-67	15	18
β-strand	68	1	19
β-strand	79-85	7	18
α-helix	86-88	3
α-helix	89-100	12
α-helix	110-111	2
β-strand	120	1	19
β-strand	126-137	12	18
β-strand	142-144	3	18
β-strand	148	1	20
α-helix	149-151	3
β-strand	152-153	2	18
β-strand	157-159	3	18
β-strand	160	1	20
β-strand	165-169	5	18
α-helix	173-178	6
β-strand	181-184	4	17
β-strand	187-190	4	16
β-strand	204-206	3	16
β-strand	213-214	2	16
β-strand	219-223	5	21
β-strand	226-230	5	21
β-strand	236-237	2	21
β-strand	238-239	2	17
α-helix	242-248	7
α-helix	253-254	2
β-strand	260-261	2	22
α-helix	262-263	2
α-helix	265-293	29
α-helix	299-305	7
β-strand	311-319	9	15
β-strand	322-335	14	15
β-strand	339-340	2	23
β-strand	344-347	4	15
β-strand	350-355	6	15
β-strand	361-363	3	23
β-strand	366-368	3	23
α-helix	370-372	3
β-strand	374-376	3	23
β-strand	379-381	3	23
α-helix	382-383	2
α-helix	384-399	16
β-strand	403-404	2	22
β-strand	422-425	4	18

Chain D: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	24
β-strand	11-12	2	25
β-strand	18-25	8	24
β-strand	34-40	7	26
β-strand	46-53	8	26
β-strand	58-60	3	26
α-helix	62-64	3
β-strand	71-73	3	24
β-strand	78-83	6	24
β-strand	92-98	7	26
β-strand	112	1	26
β-strand	116-118	3	26
β-strand	119-120	2	25

Chain E: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	27
β-strand	12	1	28
β-strand	19-23	5	29
β-strand	24	1	27
β-strand	33-38	6	30
β-strand	40	1	31
β-strand	42	1	31
β-strand	46-49	4	30
β-strand	54	1	30
α-helix	55	1
β-strand	62-67	6	29
β-strand	69-75	7	29
α-helix	80-82	3
β-strand	85-90	6	30
β-strand	98	1	30
β-strand	103	1	30
β-strand	105	1	28

Chain F: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	32
β-strand	11-12	2	33
β-strand	16-18	3	34
β-strand	21-25	5	32
β-strand	35-40	6	35
β-strand	46-52	7	35
β-strand	58-60	3	35
α-helix	62-64	3
β-strand	68	1	34
β-strand	71-73	3	32
β-strand	78-80	3	32
β-strand	83-86	4	34
β-strand	92-98	7	35
β-strand	112	1	35
β-strand	116-118	3	35
β-strand	119-120	2	33

Chain G: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	36
β-strand	12	1	37
β-strand	19-24	6	36
β-strand	33-38	6	38
β-strand	46-49	4	38
β-strand	53-54	2	38
β-strand	62-67	6	36
β-strand	70-75	6	36
α-helix	80-82	3
β-strand	85-90	6	38
β-strand	98	1	38
β-strand	103	1	38
β-strand	105	1	37

Chain H: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	39
β-strand	19-23	5	40
β-strand	33-38	6	39
β-strand	45-49	5	39
β-strand	53-54	2	39
β-strand	62-65	4	40
β-strand	71-75	5	40
β-strand	85-90	6	39
β-strand	97	1	41
β-strand	98	1	39
β-strand	103	1	39

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 vh	D, F, L	protein	229	Mus sp.
8G5F11 vl	E, G, H	protein	214	Mus sp.

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

>9HHR_1 Glycoprotein (chains A, B, C)
KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCH
ASKWVTTCDFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVT
DAEAVIVQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSN
LISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCKHWGVRLPSGVWFEMA
DKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV
DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDW
APYEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDD
ESLFFGDTGLSKNPIELVEGWFSSWKSSIASFFFIIGLIIGLFLVLRVGIHLCIKLKHTK
KRQIYTDIEMNRLGK

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

>9HHR_2 8G5F11 VH (chains D, F, L)
DVQLQESGPDLVKPSQSLSLTCTVTGYSITSGYSWHWNRQFPGNKLEWMGYIHYSGLTNY
NPSLKSRISITRHTSKNQFFLQLNSVTTEDTATYYCVRGGYDGRDYYAMDFWGQGTSVTV
SSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTIN

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

>9HHR_3 8G5F11 VL (chains E, G, H)
DIVMTQSHKFMSTSVGDRVSITCKASQDVDNDVAWYQQKPGQSPKLLIYWASTRHTGVPD
RFTGSGSGTDFTLTISDVQSEDLSDYFCQQYSSYPFTFGGGTRLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Cryo-EM structure of VSV-Indiana (MUDD-SUMMERS strain) glycoprotein under its acidic conformation. 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
9HH9 2.93 Å, Cryo-EM structure of VSV-Indiana glycoprotein (MUDD-SUMMERS strain) in its pre-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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