6IW2: 5A ScFv

Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state. Determined by X-ray diffraction at 2.9 Å resolution. Released 13 Feb 2019.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Yellow fever virus (strain 17D vaccine), Homo sapiens
Chains: 18
Atoms: 28,516
Mol. weight: 410.87 kDa
Released: 13 Feb 2019

Explore 6IW2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6IW2 contains 124 α-helices and 316 β-strands across 18 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, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	1
α-helix	14-15	2
β-strand	20-26	7	2
β-strand	27	1	1
β-strand	30-35	6	1
β-strand	38-50	13	1
α-helix	53-54	2
β-strand	55-72	18	1
α-helix	73-74	2
α-helix	83-85	3
β-strand	90-99	10	1
β-strand	109-129	21	1
α-helix	132-134	3
β-strand	135-143	9	1
α-helix	149-151	3
α-helix	152-155	4
α-helix	156	1
β-strand	157-161	5	1
β-strand	168-172	5	2
β-strand	176-185	10	2
α-helix	190-192	3
β-strand	193-197	5	1
β-strand	202-206	5	1
α-helix	207-211	5
β-strand	217-219	3	1
β-strand	226	1	1
α-helix	228-230	3
β-strand	232-234	3	3
α-helix	235-237	3
β-strand	244-246	3	3
α-helix	247-249	3
α-helix	251-257	7
β-strand	262-265	4	1
β-strand	274-276	3	1
β-strand	280-286	7	2
β-strand	290	1	2
β-strand	298-299	2	4
α-helix	300	1
β-strand	304-312	9	5
β-strand	318-324	7	5
β-strand	330-331	2	4
β-strand	334-337	4	6
β-strand	348-349	2	5
β-strand	355-356	2	4
β-strand	361-368	8	5
α-helix	369-370	2
β-strand	372-378	7	6
β-strand	385-391	7	6

Chain B: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	7
β-strand	19-26	8	7
β-strand	34-40	7	8
β-strand	47-52	6	8
β-strand	58-60	3	8
β-strand	68-73	6	7
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	92-102	11	8
β-strand	107-114	8	8
β-strand	118-120	3	8

Chains C, F, I, L and O: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	10-13	4	10
β-strand	19-25	7	9
β-strand	33-38	6	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-67	6	9
β-strand	70-75	6	9
α-helix	80-82	3
β-strand	85-90	6	10
α-helix	96	1
β-strand	97-98	2	10
β-strand	102-106	5	10

Chain D: 15 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	11
α-helix	14-15	2
β-strand	20-26	7	12
β-strand	30-35	6	11
β-strand	38-50	13	11
α-helix	53-54	2
β-strand	55-72	18	11
α-helix	73-74	2
α-helix	83-86	4
β-strand	90-99	10	11
β-strand	109-129	21	11
α-helix	132-134	3
β-strand	135-143	9	11
α-helix	149-155	7
β-strand	157-161	5	11
β-strand	168-172	5	12
β-strand	176-185	10	12
α-helix	190-192	3
β-strand	193-197	5	11
β-strand	201-206	6	11
α-helix	207-211	5
β-strand	217-218	2	11
β-strand	226	1	11
α-helix	228-230	3
β-strand	232-234	3	13
α-helix	235-237	3
β-strand	244-246	3	13
α-helix	247-249	3
α-helix	251-257	7
β-strand	262-266	5	11
β-strand	274-276	3	11
β-strand	280-286	7	12
β-strand	290	1	12
α-helix	297	1
β-strand	298-299	2	14
α-helix	300	1
β-strand	304-312	9	15
β-strand	318-324	7	15
β-strand	330-331	2	14
β-strand	334-337	4	16
β-strand	348-349	2	15
β-strand	355-356	2	14
β-strand	361-368	8	15
α-helix	369-370	2
β-strand	372-378	7	16
β-strand	385-391	7	16

Chains E, H, K and Q: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	17
β-strand	18-26	9	17
β-strand	34-40	7	18
β-strand	47-52	6	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	92-102	11	18
β-strand	107-114	8	18
β-strand	118-120	3	18

Chain G: 16 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	21
α-helix	14-15	2
β-strand	20-26	7	22
β-strand	30-35	6	21
β-strand	38-50	13	21
α-helix	53-54	2
β-strand	55-72	18	23
α-helix	73-74	2
α-helix	83-86	4
β-strand	90-99	10	23
β-strand	109-129	21	23
α-helix	132-134	3
β-strand	135-143	9	21
α-helix	149-151	3
α-helix	152-155	4
α-helix	156	1
β-strand	157-161	5	21
β-strand	168-172	5	22
β-strand	176-185	10	22
α-helix	190-192	3
β-strand	193-197	5	23
β-strand	202-206	5	23
α-helix	207-211	5
β-strand	217-219	3	23
β-strand	226	1	23
α-helix	228-231	4
β-strand	232-234	3	24
α-helix	235-237	3
β-strand	244-246	3	24
α-helix	247-249	3
α-helix	251-257	7
β-strand	262-264	3	23
β-strand	274-275	2	21
β-strand	280-286	7	22
β-strand	290	1	22
β-strand	298-299	2	25
α-helix	300	1
β-strand	304-312	9	26
β-strand	318-324	7	26
β-strand	330-331	2	25
β-strand	334-337	4	27
β-strand	348-349	2	26
β-strand	355-356	2	25
β-strand	361-368	8	26
α-helix	369-370	2
β-strand	372-378	7	27
β-strand	385-391	7	27

Chain J: 18 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	32
α-helix	14-15	2
β-strand	20-26	7	33
β-strand	30-35	6	32
β-strand	38-50	13	32
α-helix	53-54	2
β-strand	55-72	18	32
α-helix	73-74	2
α-helix	83-86	4
β-strand	90-99	10	32
β-strand	109-129	21	32
α-helix	132-134	3
β-strand	135-143	9	32
α-helix	149-151	3
α-helix	152-155	4
α-helix	156	1
β-strand	157-161	5	32
β-strand	168-172	5	33
β-strand	176-185	10	33
α-helix	190-192	3
β-strand	193-197	5	32
β-strand	202-206	5	32
α-helix	207-211	5
β-strand	217-219	3	32
β-strand	226	1	32
α-helix	228-230	3
β-strand	232-234	3	34
α-helix	235-237	3
β-strand	244-246	3	34
α-helix	247-249	3
α-helix	251-257	7
α-helix	262	1
β-strand	263-265	3	32
β-strand	274-276	3	32
β-strand	280-286	7	33
β-strand	290	1	33
α-helix	297	1
β-strand	298-299	2	35
α-helix	300	1
β-strand	304-312	9	36
β-strand	318-324	7	36
β-strand	330-331	2	35
β-strand	334-337	4	37
β-strand	348-349	2	36
β-strand	355-356	2	35
β-strand	361-368	8	36
α-helix	369-370	2
β-strand	372-378	7	37
β-strand	385-391	7	37

Chain M: 17 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	42
α-helix	14-15	2
β-strand	20-26	7	43
β-strand	27	1	42
β-strand	30-35	6	42
β-strand	38-50	13	42
α-helix	53-54	2
β-strand	55-72	18	42
α-helix	73-74	2
α-helix	83-86	4
β-strand	90-99	10	42
α-helix	101-103	3
β-strand	109-129	21	42
α-helix	132-134	3
β-strand	135-143	9	42
α-helix	149-151	3
α-helix	152-155	4
α-helix	156	1
β-strand	157-162	6	42
β-strand	168-172	5	43
β-strand	176-185	10	43
α-helix	190-192	3
β-strand	193-197	5	42
β-strand	202-206	5	42
α-helix	207-211	5
β-strand	217-219	3	42
β-strand	226	1	42
α-helix	228-230	3
β-strand	232-234	3	44
α-helix	235-237	3
β-strand	244-246	3	44
α-helix	247-249	3
α-helix	251-257	7
β-strand	262-266	5	42
β-strand	274-276	3	42
β-strand	280-286	7	43
β-strand	290	1	43
β-strand	298-299	2	45
α-helix	300	1
β-strand	304-312	9	46
β-strand	318-324	7	46
β-strand	330-331	2	45
β-strand	334-337	4	47
β-strand	348-349	2	46
β-strand	355-356	2	45
β-strand	361-368	8	46
α-helix	369-370	2
β-strand	372-378	7	47
β-strand	385-391	7	47

3 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
Envelope protein E	A, D, G, J, M, P	protein	395	Yellow fever virus (strain 17D vaccine)	P03314 (AlphaFold model)
Heavy chain of monoclonal antibody 5A	B, E, H, K, N, Q	protein	120	Homo sapiens
Light chain of monoclonal antibody 5A	C, F, I, L, O, R	protein	107	Homo sapiens

Sequence of entity 1 (A, D, G, J, M, P), FASTA

>6IW2_1 Envelope protein E (chains A, D, G, J, M, P)
AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVC
YNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFT
CAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATL
ECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAA
TIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKIC
TDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTND
DEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

Sequence of entity 2 (B, E, H, K, N, Q), FASTA

>6IW2_2 Heavy chain of monoclonal antibody 5A (chains B, E, H, K, N, Q)
EVQLVESGPRLVKPSETLSLTCTVSGGSTYNHHWSWIRQPPGRGLEWIGYISYSGKSNYN
PSLKSRVTISLEPSTTQFSLKLNSLTAADTAVYYCAREYRDDTNYYYYSLDVWGPGTMVT

Sequence of entity 3 (C, F, I, L, O, R), FASTA

>6IW2_3 Light chain of monoclonal antibody 5A (chains C, F, I, L, O, R)
QIVMTQSPSTLSASVGDRVTITCRASQSIGSWLAWYQQKPGKAPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISSLQPEDFATYYCQQYNNYSYTFGPGTKLEIK

Primary citation

Double Lock of a Human Neutralizing and Protective Monoclonal Antibody Targeting the Yellow Fever Virus Envelope. Lu, X., Xiao, H., Li, S. et al. Cell Rep (2019) 26:438-446.e5. DOI 10.1016/j.celrep.2018.12.065 · PubMed

Other PDB entries of the same protein (UniProt P03314 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EVF 1.45 Å, Crystal structure of Me7-GpppA complex of yellow fever virus methyltransferase and…
9SKO 1.49 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
3EVA 1.5 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
3EVD 1.5 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVC 1.6 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVE 1.7 Å, Crystal structure of GpppA complex of yellow fever virus methyltransferase and…
5N6B 1.71 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNPGMAV
1YKS 1.8 Å, Crystal structure of yellow fever virus NS3 helicase
3EVB 1.85 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
9SKP 1.89 Å, Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV
6SSA 2.11 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV
6SS8 2.24 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPIAV

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