3CSY: Trimeric prefusion Ebola virus glycoprotein

Crystal structure of the trimeric prefusion Ebola virus glycoprotein in complex with a neutralizing antibody from a human survivor. Determined by X-ray diffraction at 3.4 Å resolution. Released 8 Jul 2008.

Method: X-ray diffraction
Resolution: 3.4 Å
Organisms: Homo sapiens, Ebola virus - Mayinga, Zaire, 1976
Chains: 16
Atoms: 23,539
Mol. weight: 406.07 kDa
Released: 8 Jul 2008

Explore 3CSY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3CSY contains 81 α-helices and 291 β-strands across 16 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: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
α-helix	44	1
β-strand	45-51	7	2
β-strand	57-59	3	2
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-95	8	2
α-helix	96	1
β-strand	100H-103	4	2
β-strand	107-111	5	2
β-strand	117	1	3
β-strand	120-124	5	4
β-strand	133	1	4
β-strand	138-147	10	4
β-strand	148	1	3
β-strand	153-157	4	5
β-strand	171-173	3	4
α-helix	174-176	3
β-strand	185-193	9	4
β-strand	207	1	6
β-strand	208-212	5	5
α-helix	213-215	3
β-strand	217-219	3	5
β-strand	222	1	6

Chain B: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-14	5	8
β-strand	19-25	7	7
β-strand	27C	1	9
β-strand	31	1	9
β-strand	33-38	6	8
β-strand	44-49	6	8
β-strand	53-54	2	8
β-strand	62-67	6	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-107	6	8
β-strand	111	1	10
β-strand	118	1	11
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	145-150	6	12
β-strand	153-154	2	12
α-helix	155	1
β-strand	159-163	5	11
β-strand	173-182	10	11
α-helix	183-186	4
β-strand	192-197	6	12
β-strand	205-209	5	12

Chain C: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	13
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	15
α-helix	44	1
β-strand	45-51	7	15
β-strand	57-59	3	15
α-helix	61-63	3
β-strand	67-72	6	13
β-strand	77-82	6	13
α-helix	84-86	3
β-strand	88-90	3	14
β-strand	91-95	5	15
α-helix	96	1
β-strand	100H-103	4	15
β-strand	107-111	5	14
β-strand	117	1	16
β-strand	120-124	5	17
β-strand	133	1	17
β-strand	137-147	11	17
β-strand	148	1	16
β-strand	153-157	4	18
β-strand	171-174	4	17
β-strand	185-194	10	17
β-strand	207-212	6	18
α-helix	213-215	3
β-strand	217-222	6	18

Chain D: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	19
β-strand	10-14	5	20
β-strand	19-25	7	19
β-strand	27C-27D	2	21
β-strand	30-31	2	21
β-strand	33-38	6	20
β-strand	45-49	5	20
β-strand	53-54	2	20
α-helix	55	1
β-strand	62-67	6	19
β-strand	70-75	6	19
α-helix	80-82	3
β-strand	84-90	7	20
α-helix	96	1
β-strand	97-98	2	20
β-strand	102-107	6	20
β-strand	111	1	22
β-strand	118	1	23
α-helix	122-125	4
β-strand	129-139	11	23
β-strand	140	1	22
β-strand	145-150	6	24
β-strand	153-154	2	24
β-strand	159-163	5	23
α-helix	164-165	2
β-strand	173-182	10	23
α-helix	183-187	5
β-strand	192-197	6	24
β-strand	205-209	5	24

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	25
β-strand	10-12	3	26
β-strand	18-25	8	25
α-helix	29-31	3
β-strand	34-39	6	26
β-strand	45-51	7	26
β-strand	57-59	3	26
α-helix	61-63	3
β-strand	68-72	5	25
β-strand	77-82	6	25
α-helix	84-86	3
β-strand	88-95	8	26
α-helix	96	1
β-strand	100H-103	4	26
β-strand	107-111	5	26
β-strand	117	1	27
α-helix	118-119	2
β-strand	120-124	5	28
β-strand	133	1	28
β-strand	137-147	11	28
β-strand	148	1	27
β-strand	153-157	4	29
β-strand	171-173	3	28
α-helix	174-176	3
β-strand	177-178	2	28
β-strand	185-194	10	28
α-helix	195-198	4
β-strand	207	1	30
β-strand	208-212	5	29
α-helix	213-215	3
β-strand	217-219	3	29
β-strand	222	1	30

Chain F: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	31
β-strand	10-14	5	32
β-strand	19-24	6	31
β-strand	27C	1	33
β-strand	31	1	33
β-strand	33-38	6	32
β-strand	45-49	5	32
β-strand	53-54	2	32
β-strand	62-67	6	31
β-strand	70-75	6	31
β-strand	84-90	7	32
α-helix	96	1
β-strand	97-98	2	32
β-strand	102-107	6	32
β-strand	111	1	34
β-strand	116-118	3	35
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	35
β-strand	140	1	34
β-strand	145-150	6	36
β-strand	153-154	2	36
β-strand	159-163	5	35
β-strand	173-182	10	35
α-helix	183-187	5
β-strand	192-197	6	36
β-strand	205-209	5	36

Chain G: 9 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	37
β-strand	10-12	3	38
β-strand	18-25	8	37
α-helix	29-31	3
β-strand	34-39	6	38
β-strand	45-51	7	38
β-strand	57-59	3	38
α-helix	61-63	3
β-strand	67-72	6	37
α-helix	73-75	3
β-strand	77-82	6	37
α-helix	84-86	3
β-strand	88-95	8	38
α-helix	96	1
β-strand	100H-103	4	38
β-strand	107-111	5	38
β-strand	117	1	39
α-helix	118-119	2
β-strand	120-124	5	40
β-strand	133	1	40
β-strand	137-147	11	40
β-strand	148	1	39
β-strand	153	1	41
β-strand	157	1	42
β-strand	171-173	3	40
α-helix	174-176	3
β-strand	177-178	2	40
β-strand	185-194	10	40
α-helix	196-198	3
β-strand	207	1	43
β-strand	208	1	42
β-strand	210-212	3	41
α-helix	213-215	3
β-strand	217-219	3	41
β-strand	222	1	43

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	44
β-strand	10-14	5	45
β-strand	19-25	7	44
β-strand	27C	1	46
β-strand	31	1	46
β-strand	33-38	6	45
β-strand	45-48	4	45
β-strand	54	1	45
β-strand	62-67	6	44
β-strand	70-75	6	44
α-helix	80-82	3
β-strand	84-90	7	45
α-helix	96	1
β-strand	97-98	2	45
β-strand	102-107	6	45
β-strand	111	1	47
β-strand	118	1	48
α-helix	122-125	4
β-strand	129-139	11	48
β-strand	140	1	47
β-strand	145-150	6	49
β-strand	153-154	2	49
α-helix	155	1
β-strand	159-163	5	48
β-strand	173-182	10	48
α-helix	183-187	5
β-strand	192-197	6	49
β-strand	205-209	5	49

8 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
Fab KZ52 heavy chain	A, C, E, G	protein	226	Homo sapiens	P01857 (AlphaFold model)
Fab KZ52 light chain	B, D, F, H	protein	217	Homo sapiens	P01834 (AlphaFold model)
Envelope glycoprotein GP1	I, K, M, O	protein	334	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)
Envelope glycoprotein GP2	J, L, N, P	protein	131	Ebola virus - Mayinga, Zaire, 1976	Q05320 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>3CSY_1 Fab KZ52 heavy chain (chains A, C, E, G)
EVQLLESGGGLVKPGGSLRLSCAASGFTLINYRMNWVRQAPGKGLEWVSSISSSSSYIHY
ADSVKGRFTISRDNAENSLYLQMNSLRAEDTAVYYCVREGPRATGYSMADVFDIWGQGTM
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

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

>3CSY_2 Fab KZ52 light chain (chains B, D, F, H)
ELVMTQSPDSLAVSLGERATINCKSSQSVLYSSNNKSYLAWYQQKPGQPPKLLIYWASTR
ESGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYSAPLTFGGGTKVEIKRTVAAPS
VFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYS
LSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNR

Sequence of entity 3 (I, K, M, O), FASTA

>3CSY_3 Envelope glycoprotein GP1 (chains I, K, M, O)
YPYDVPDYAIEGRGARSIPLGVIHNSVLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGV
ATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRC
RYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFS
SHPLREPVNATEDPSSGYYSTTIRYQATGFGTNEVEYLFEVDNLTYVQLESRFTPQFLLQ
LNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVTHHQ
DTGEESASSGKLGLITNTIAGVAGLITGGRRTRR

Sequence of entity 4 (J, L, N, P), FASTA

>3CSY_4 Envelope glycoprotein GP2 (chains J, L, N, P)
EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQL
ANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITD
KIDQIIHDFVD

Primary citation

Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor. Lee, J.E., Fusco, M.L., Hessell, A.J. et al. Nature (2008) 454:177-182. DOI 10.1038/nature07082 · PubMed

Other PDB entries of the same protein (UniProt P01857 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLD 1.19 Å, Structure of wild-type IgG1 antibody heavy chain constant domain 1 and light chain…
3TV3 1.29 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT128 in complex with…
4LLQ 1.42 Å, Structure of redesigned IgG1 first constant and lambda domains (CH1:Clambda constant…
5HSF 1.52 Å, 1.52 Angstrom Crystal Structure of Fc fragment of Human IgG1.
6YT7 1.55 Å, Glycosylated knob/dummy-hole fc fragment
4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
1L6X 1.65 Å, Fc fragment of rituximab bound to a minimized version of the B-domain from protein A…
3TWC 1.65 Å, Crystal structure of broad and potent HIV-1 neutralizing antibody PGT127 in complex with…
5JIH 1.66 Å, Crystal structure of HER2 binding IgG1-Fc (Fcab STAB19)
3MCL 1.7 Å, Anti-beta-amyloid antibody c706 fab in space group P21
5U66 1.7 Å, Modified single helix from the B-domain of protein A bound to IgG1 Fc
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement

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3CSY is part of these collections:

Viruses

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