8DPL: 2.1.1D5 heavy chain variable domain

Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv and 6D6 scFv bound. Determined by electron microscopy at 2.53 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 2.53 Å
Organisms: Homo sapiens, Mus musculus, Ebola virus - Mayinga, Zaire, 1976
Chains: 15
Atoms: 16,872
Mol. weight: 295.73 kDa
Ligands: NAG
Released: 19 Jul 2023

Explore 8DPL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DPL contains 36 α-helices and 204 β-strands across 15 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.

Chains A, F and K: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	18-25	8	11
β-strand	34-39	6	13
β-strand	45-51	7	13
β-strand	60-62	3	13
β-strand	70-75	6	11
β-strand	80-85	6	11
α-helix	90-92	3
β-strand	94-103	10	13
β-strand	107-110	4	13
β-strand	114-116	3	13
β-strand	117-118	2	12

Chains B, G and L: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	14
β-strand	9-12	4	15
β-strand	18-23	6	14
α-helix	26-30	5
β-strand	36-40	5	15
β-strand	47-50	4	15
β-strand	51	1	16
β-strand	55	1	16
β-strand	64-69	6	14
β-strand	72-77	6	14
β-strand	87-93	7	15
β-strand	101-103	3	15
β-strand	107-111	5	15

Chains C, H and O: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	17
β-strand	17-25	9	17
α-helix	29-31	3
β-strand	34-39	6	18
β-strand	45-51	7	18
β-strand	58-60	3	18
β-strand	68-73	6	17
β-strand	78-84	7	17
α-helix	88-90	3
β-strand	93-99	7	18
β-strand	105-108	4	18
α-helix	109-111	3
β-strand	112-113	2	18
β-strand	142-144	3	19
β-strand	148	1	20
β-strand	157-167	11	19
β-strand	171-176	6	20
β-strand	183-187	5	20
β-strand	191-192	2	20
β-strand	200-213	14	19
β-strand	223-228	6	20
β-strand	237	1	20
β-strand	241-242	2	20

Chains D, I and M: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	36-39	4	37
β-strand	42-45	4	37
β-strand	63-69	7	37
α-helix	70-73	4
α-helix	79-83	5
β-strand	86-89	4	38
β-strand	96-98	3	37
β-strand	101	1	37
β-strand	102-103	2	39
β-strand	105	1	40
β-strand	108-114	7	41
β-strand	120	1	41
α-helix	123	1
β-strand	124	1	42
α-helix	125-126	2
β-strand	135	1	40
β-strand	137-144	8	41
β-strand	151-154	4	38
β-strand	159-161	3	37
β-strand	165-167	3	37
β-strand	172	1	42
β-strand	176	1	41
β-strand	177-185	9	37
β-strand	216-223	8	41
β-strand	231-232	2	41

Chains E, J and N: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	515-520	6	39
α-helix	539-541	3
β-strand	543-548	6	39
α-helix	552-575	24
β-strand	580-581	2	37
α-helix	584-596	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
2.1.1D5 heavy chain variable domain	A, F, K	protein	120	Homo sapiens
2.1.1D5 light chain variable domain	B, G, L	protein	112	Homo sapiens
6D6 single-chain variable fragment	C, H, O	protein	243	Mus musculus
Glycoprotein GP1	D, I, M	protein	280	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)
Glycoprotein GP2	E, J, N	protein	136	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)

Sequence of entity 1 (A, F, K), FASTA

>8DPL_1 2.1.1D5 heavy chain variable domain (chains A, F, K)
EVQLVESGGGLVKPGGSLRLSCAASGFTFSNAWMNWVRQAPGKGLEWVGRIKSKTDGGAA
DYAAPVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYFCTTVYRYNYDSVWGQGTLVTVSS

Sequence of entity 2 (B, G, L), FASTA

>8DPL_2 2.1.1D5 light chain variable domain (chains B, G, L)
QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVYWYQQLPGTAPKLLIYGNSNRPSGV
PDRFSGSKSGTSASLAITGLQAEDEADYYCQSFDSSLRDSWVFGGGTKLTVL

Sequence of entity 3 (C, H, O), FASTA

>8DPL_3 6D6 single-chain variable fragment (chains C, H, O)
QVQLQQSGTELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPRNGRTDF
SEKFKSKATLTVDTSSSTAFIQLSSLTSEDSAVYYCARWGYYGSSDYWGQGTALTVSSGT
GGSGGGGSGGGGSGGGASDIVVTQSHKFMSTSVGDRVSITCKASQDVSVAVAWYQQKTGQ
SPKLLIYSASYRITGVPDRFTGSGSGTDFTFTISSVQAEDMAVYYCQQHYSTPPWTFGGG
TKL

Sequence of entity 4 (D, I, M), FASTA

>8DPL_4 Glycoprotein GP1 (chains D, I, M)
IPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGV
PPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFA
FHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSG
YYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGK
LIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVS

Sequence of entity 5 (E, J, N), FASTA

>8DPL_5 Glycoprotein GP2 (chains E, J, N)
EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQL
ANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITD
KIDQIIHDFVDKTLPD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3

Primary citation

The evolution and determinants of neutralization of potent head-binding antibodies against Ebola virus. Yu, X., Hastie, K.M., Davis, C.W. et al. Cell Rep (2023) 42:113366-113366. DOI 10.1016/j.celrep.2023.113366 · 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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