5I2M: Glycoprotein G

Crystal structure of vsv-indiana (mudd-summers strain) glycoprotein under its acidic conformation. Determined by X-ray diffraction at 2.4 Å resolution. Released 24 Feb 2016.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Vesicular stomatitis Indiana virus (strain Mudd-Summers)
Chains: 3
Atoms: 10,314
Mol. weight: 143.84 kDa
Ligands: PE4, CA
Released: 24 Feb 2016

Explore 5I2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5I2M contains 55 α-helices and 101 β-strands across 3 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: 19 helices, 33 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	37-46	10	2
α-helix	47-48	2
α-helix	50-52	3
β-strand	53-54	2	3
β-strand	56-70	15	4
β-strand	76-85	10	4
α-helix	86-88	3
α-helix	89-100	12
α-helix	110-112	3
β-strand	119-131	13	4
β-strand	134-136	3	3
β-strand	143-144	2	3
β-strand	148	1	5
α-helix	149-151	3
β-strand	152-153	2	3
β-strand	157-159	3	4
β-strand	160	1	5
β-strand	165-169	5	4
α-helix	173-178	6
β-strand	181-190	10	2
α-helix	195-197	3
β-strand	204-207	4	2
β-strand	210-214	5	2
β-strand	219-223	5	6
β-strand	226-230	5	6
β-strand	236-237	2	6
β-strand	238-239	2	2
α-helix	242-248	7
α-helix	250-251	2
β-strand	252	1	6
α-helix	253-254	2
β-strand	260-261	2	7
α-helix	264-293	30
α-helix	299-305	7
β-strand	311-319	9	1
β-strand	322-335	14	1
β-strand	339-340	2	8
β-strand	344-347	4	1
β-strand	353-355	3	1
β-strand	361-363	3	8
β-strand	366-368	3	8
α-helix	370-372	3
β-strand	374-376	3	8
β-strand	379-381	3	8
α-helix	384-399	16
α-helix	401-402	2
β-strand	403-404	2	7
α-helix	405	1

Chain B: 19 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	9
β-strand	15-16	2	9
α-helix	17-18	2
α-helix	25-28	4
β-strand	37-46	10	10
α-helix	47-48	2
α-helix	50-52	3
β-strand	53-54	2	11
β-strand	56-70	15	12
β-strand	76-85	10	12
α-helix	86-88	3
α-helix	89-100	12
α-helix	110-112	3
β-strand	119-131	13	12
β-strand	134-137	4	11
β-strand	142-144	3	11
β-strand	148	1	13
α-helix	149-151	3
β-strand	152-153	2	11
β-strand	157-159	3	12
β-strand	160	1	13
β-strand	166-169	4	12
α-helix	173-178	6
β-strand	181-190	10	10
α-helix	195-197	3
β-strand	204-207	4	10
β-strand	210-214	5	10
β-strand	219-223	5	14
β-strand	226-230	5	14
β-strand	235	1	15
β-strand	236-237	2	14
β-strand	238-239	2	10
α-helix	242-248	7
α-helix	250-251	2
β-strand	252	1	14
α-helix	253-254	2
β-strand	260-261	2	15
α-helix	264-293	30
α-helix	299-305	7
β-strand	311-319	9	9
β-strand	322-335	14	9
β-strand	339-340	2	16
β-strand	344-347	4	9
β-strand	353-355	3	9
β-strand	361-363	3	16
β-strand	366-368	3	16
α-helix	370-372	3
β-strand	374-376	3	16
β-strand	379-381	3	16
α-helix	384-399	16
α-helix	401-402	2
β-strand	403-404	2	15
α-helix	405	1

Chain C: 17 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	17
β-strand	15-16	2	17
α-helix	17-18	2
α-helix	25-28	4
β-strand	37-46	10	18
α-helix	47-48	2
β-strand	53-54	2	19
β-strand	56-70	15	20
β-strand	76-85	10	20
α-helix	86-88	3
α-helix	89-100	12
α-helix	110-112	3
β-strand	119-131	13	20
β-strand	134-137	4	19
β-strand	142-144	3	19
β-strand	148	1	21
α-helix	149-151	3
β-strand	152-153	2	19
β-strand	157-159	3	20
β-strand	160	1	21
β-strand	166-169	4	20
α-helix	173-178	6
β-strand	181-190	10	18
α-helix	195-197	3
β-strand	204-207	4	18
β-strand	210-214	5	18
β-strand	219-223	5	22
β-strand	226-230	5	22
β-strand	235	1	23
β-strand	236-237	2	22
β-strand	238-239	2	18
α-helix	242-248	7
α-helix	250-251	2
β-strand	252	1	22
α-helix	253-254	2
β-strand	260-261	2	23
α-helix	264-293	30
α-helix	299-305	7
β-strand	311-319	9	17
β-strand	322-335	14	17
β-strand	339-340	2	24
β-strand	344-347	4	17
β-strand	353-355	3	17
β-strand	361-363	3	24
β-strand	366-368	3	24
α-helix	370-372	3
β-strand	374-376	3	24
β-strand	379-381	3	24
α-helix	382-383	2
α-helix	384-399	16
β-strand	403-404	2	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glycoprotein G	A, B, C	protein	422	Vesicular stomatitis Indiana virus (strain Mudd-Summers)	P0C2X0

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

>5I2M_1 Glycoprotein G (chains A, B, C)
KFTIVFPHNQKGNWKNVPSNYHYCPSSSDLNWHNDLIGTALQVKMPKSHKAIQADGWMCH
ASKWVTTCDFRWYGPKYITHSIRSFTPSVEQCKESIEQTKQGTWLNPGFPPQSCGYATVT
DAEAVIVQVTPHHVLVDEYTGEWVDSQFINGKCSNYICPTVHNSTTWHSDYKVKGLCDSN
LISMDITFFSEDGELSSLGKEGTGFRSNYFAYETGGKACKMQYCKHWGVRLPSGVWFEMA
DKDLFAAARFPECPEGSSISAPSQTSVDVSLIQDVERILDYSLCQETWSKIRAGLPISPV
DLSYLAPKNPGTGPAFTIINGTLKYFETRYIRVDIAAPILSRMVGMISGTTTERELWDDW
APYEDVEIGPNGVLRTSSGYKFPLYMIGHGMLDSDLHLSSKAQVFEHPHIQDAASQLPDD
ES

Ligands and cofactors

ID	Name	Formula	Copies
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	5
CA	Calcium ion	Ca	1

Primary citation

Crystal structure of the low-pH form of the vesicular stomatitis virus glycoprotein G. Roche, S., Bressanelli, S., Rey, F.A. et al. Science (2006) 313:187-191. DOI 10.1126/SCIENCE.1127683 · PubMed

Other PDB entries of the same protein (UniProt P0C2X0), best resolution first:

5I2S 3.0 Å, Prefusion form of the vesicular stomatitis virus glycoprotein G ectodomain
5OY9 3.6 Å, Vsv G CR3

Browse structure collections

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