5JQB: Ebola glycoprotein

Crystal structure of Ebola glycoprotein in complex with ibuprofen. Determined by X-ray diffraction at 2.68 Å resolution. Released 29 Jun 2016.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Ebola virus - Mayinga, Zaire, 1976
Chains: 2
Atoms: 3,238
Mol. weight: 57.43 kDa
Ligands: NAG, IBP
Released: 29 Jun 2016

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

Secondary structure: helices and β-sheets

5JQB contains 14 α-helices and 26 β-strands across 2 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: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	35-38	4	1
β-strand	43-46	4	1
α-helix	60-62	3
β-strand	63-69	7	1
α-helix	70-73	4
α-helix	79-83	5
β-strand	86-89	4	2
β-strand	96-98	3	1
β-strand	101-103	3	1
β-strand	105-114	10	3
β-strand	120	1	3
α-helix	123	1
β-strand	124	1	4
α-helix	125-126	2
α-helix	130-132	3
β-strand	135-144	10	3
β-strand	151-154	4	2
β-strand	159-161	3	1
β-strand	165-167	3	1
β-strand	169	1	2
α-helix	170-171	2
β-strand	172	1	4
β-strand	176	1	3
β-strand	177-185	9	1
β-strand	216-223	8	3
β-strand	231-235	5	3
β-strand	240-243	4	3
α-helix	250-263	14
β-strand	273-277	5	3
β-strand	307-309	3	3
β-strand	473-476	4	3

Chain B: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	515-520	6	1
α-helix	539-541	3
β-strand	543-548	6	1
α-helix	551-553	3
α-helix	554-575	22
β-strand	580-581	2	1
α-helix	584-597	14
α-helix	613-622	10
α-helix	623-625	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1	A	protein	330	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)
Envelope glycoprotein 2	B	protein	168	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5JQB_1 Envelope glycoprotein 1,Envelope glycoprotein 1,Envelope glycoprotein 1 (chains A)
ETGRSIPLGVIHNSALQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWG
FRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPC
AGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATE
DPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRS
NTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVSTHHQDTGEESASSGK
LGLITNTIAGVAGLITGGRRTRRXXXXXXX

Sequence of entity 2 (B), FASTA

>5JQB_2 Envelope glycoprotein 2 (chains B)
EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYIEGLMHNQDGLICGLRQL
ANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITD
KIDQIIHDFVDGSGYIPEAPRDGQAYVRKDGEWVLLSTFLGTHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
IBP	Ibuprofen	C13 H18 O2	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Toremifene interacts with and destabilizes the Ebola virus glycoprotein. Zhao, Y., Ren, J., Harlos, K. et al. Nature (2016) 535:168-172. DOI 10.1038/nature18615 · PubMed

Other PDB entries of the same protein (UniProt Q05320 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2EBO 1.9 Å, Core structure of GP2 from ebola virus
6HS4 2.05 Å, Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118
6F5U 2.07 Å, Crystal structure of ebolavirus glycoprotein in complex with bepridil
6F6N 2.15 Å, Crystal structure of ebolavirus glycoprotein in complex with sertraline
6G9I 2.19 Å, Crystal structure of Ebolavirus glycoprotein in complex with clomipramine
5JQ3 2.23 Å, Crystal structure of Ebola glycoprotein
7SSQ 2.25 Å, Crystal Structure of Ebola zaire Envelope glycoprotein GP in complex with compound…
6G9B 2.26 Å, Crystal structure of Ebolavirus glycoprotein in complex with imipramine
7JPI 2.28 Å, Crystal structure of EBOV glycoprotein with modified HR2 stalk at 2.3A resolution
6F6S 2.29 Å, CRYSTAL STRUCTURE OF EBOLAVIRUS GLYCOPROTEIN IN COMPLEX WITH benztropine
6HRO 2.3 Å, Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a
6G95 2.31 Å, Crystal structure of Ebolavirus glycoprotein in complex with thioridazine

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