6UTE: Z032 Fab

Crystal structure of Z032 Fab in complex with WNV EDIII. Determined by X-ray diffraction at 2.9 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, West Nile virus
Chains: 11
Atoms: 17,255
Mol. weight: 253.68 kDa
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6UTE contains 72 α-helices and 228 β-strands across 11 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	15
β-strand	11-12	2	16
β-strand	18-25	8	15
α-helix	29-31	3
β-strand	32-39	8	17
β-strand	45-51	7	17
β-strand	57-59	3	17
β-strand	67-72	6	15
β-strand	77-82	6	15
α-helix	84-86	3
β-strand	88-98	11	17
β-strand	102-103	2	17
β-strand	108-109	2	17
β-strand	110-111	2	16
α-helix	114-116	3
β-strand	117	1	18
α-helix	118-119	2
β-strand	120-124	5	19
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	176-185	10	19
α-helix	186-188	3
β-strand	194-200	7	20
β-strand	205-211	7	20

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	21
β-strand	10-13	4	22
β-strand	19-25	7	21
β-strand	33-38	6	22
β-strand	45-49	5	22
β-strand	53-54	2	22
α-helix	55	1
β-strand	62-67	6	21
β-strand	70-75	6	21
α-helix	80-82	3
β-strand	85-90	6	22
β-strand	98	1	22
β-strand	102-106	5	22
β-strand	111	1	23
β-strand	114-118	5	24
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	24
β-strand	140	1	23
β-strand	144-150	7	25
β-strand	154	1	25
β-strand	156	1	26
β-strand	160-163	4	24
α-helix	164-167	4
β-strand	173-182	10	24
α-helix	183-187	5
β-strand	191-198	8	25
β-strand	205-210	6	25

Chain C: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	32-39	8	3
β-strand	45-51	7	3
β-strand	57-59	3	3
α-helix	61-63	3
β-strand	67-72	6	1
α-helix	73-75	3
β-strand	77-82A	7	1
α-helix	84-86	3
β-strand	88-98	11	3
β-strand	102-103	2	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
β-strand	120-124	5	5
β-strand	136-145	10	5
β-strand	146	1	4
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-184	9	5
α-helix	186-190	5
β-strand	194-200	7	6
α-helix	201-203	3
β-strand	205-211	7	6

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-29	11	7
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-75	14	7
α-helix	80-82	3
β-strand	85-90	6	8
β-strand	97-98	2	8
β-strand	102-106	5	8
β-strand	111	1	9
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	144-150	7	11
β-strand	154	1	11
β-strand	159-163	5	10
α-helix	164-167	4
β-strand	173-182	10	10
α-helix	183-187	5
β-strand	191-198	8	11
β-strand	205-210	6	11

Chain E: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	27
β-strand	11-12	2	28
β-strand	18-25	8	27
α-helix	29-31	3
β-strand	34-39	6	29
β-strand	45-51	7	29
β-strand	57-59	3	29
β-strand	67-72	6	27
β-strand	77-82	6	27
α-helix	84-86	3
β-strand	88-94	7	29
β-strand	102-103	2	29
β-strand	107-109	3	29
β-strand	110-111	2	28
β-strand	117	1	30
β-strand	120-124	5	31
β-strand	136-145	10	31
β-strand	146	1	30
β-strand	151-154	4	32
α-helix	155-157	3
β-strand	163-165	3	31
α-helix	166-168	3
β-strand	169-170	2	31
β-strand	176-184	9	31
α-helix	186-188	3
β-strand	194-200	7	32
α-helix	201-203	3
β-strand	205-211	7	32

Chain F: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	33
β-strand	10-13	4	34
β-strand	19-25	7	33
β-strand	33-38	6	34
β-strand	45-49	5	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-67	6	33
β-strand	70-75	6	33
α-helix	80-82	3
β-strand	85-90	6	34
β-strand	98	1	34
α-helix	100-101	2
β-strand	102-106	5	34
β-strand	111	1	35
α-helix	112-113	2
β-strand	114-118	5	36
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	36
β-strand	140	1	35
β-strand	145-150	6	37
β-strand	153-154	2	37
α-helix	155	1
β-strand	159-163	5	36
α-helix	165-167	3
β-strand	173-182	10	36
α-helix	183-187	5
β-strand	191-197	7	37
β-strand	205-210	6	37

Chain G: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	38
β-strand	11-12	2	39
β-strand	18-25	8	38
β-strand	27	1	26
α-helix	29-31	3
β-strand	32-39	8	40
β-strand	45-51	7	40
β-strand	57-59	3	40
β-strand	67-72	6	38
β-strand	77-82	6	38
α-helix	84-86	3
β-strand	88-98	11	40
β-strand	102-103	2	40
β-strand	107-109	3	40
β-strand	110-111	2	39
α-helix	114-116	3
β-strand	117	1	41
β-strand	120-124	5	42
α-helix	125	1
β-strand	132	1	42
β-strand	136-145	10	42
β-strand	146	1	41
β-strand	151-154	4	43
α-helix	155-157	3
β-strand	163-165	3	42
α-helix	166-168	3
β-strand	169-170	2	42
β-strand	176-184	9	42
α-helix	186-189	4
β-strand	194-200	7	43
α-helix	201-203	3
β-strand	205-211	7	43

Chain H: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	44
β-strand	10-13	4	45
β-strand	19-25	7	44
β-strand	33-38	6	45
β-strand	45-49	5	45
β-strand	53-54	2	45
α-helix	55	1
β-strand	62-67	6	44
β-strand	70-75	6	44
α-helix	80-82	3
β-strand	85-90	6	45
β-strand	97-98	2	45
β-strand	102-106	5	45
β-strand	111	1	46
β-strand	114-118	5	47
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	47
β-strand	140	1	46
β-strand	145-148	4	48
β-strand	159-163	5	47
α-helix	165-167	3
β-strand	173-182	10	47
α-helix	183-188	6
β-strand	194-197	4	48
β-strand	205-206	2	48

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
Z032 Fab heavy chain	A, C, E, G, I	protein	234	Homo sapiens	S6B291 (AlphaFold model)
Z032 Fab light chain	B, D, F, H, J	protein	214	Homo sapiens	P0DOX7 (AlphaFold model)
Envelope domain III	S	protein	98	West Nile virus	Q9Q6P4

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

>6UTE_1 Z032 Fab heavy chain (chains A, C, E, G, I)
EVQLLESGGRLVQPGGSLTLSCAASGFPFSTYAMSWLRQAPGKGLEWVSGITGDSGSTYY
AASVKGRFTISRDNSKNTLYLQMNSLTADDTAVYYCAKDRLHSGLGELFSYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

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

>6UTE_2 Z032 Fab light chain (chains B, D, F, H, J)
DIQMTQSPSTLSASVGDRVNITCRASQSINQWLAWYQQKPGKAPKFLMYKASTLETGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQHYFSYPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (S), FASTA

>6UTE_3 Envelope domain III (chains S)
GVCSKAFKFLGTPADTGHGTVVLELQYTGTDGPCKVPISSVASLNDLTPVGRLVTVNPFV
SVATANAKVLIELEPPFGDSYIVVGRGEQQINHHWHKS

Primary citation

Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody. Esswein, S.R., Gristick, H.B., Jurado, A. et al. Proc Natl Acad Sci U S A (2020) 117:9865-9875. DOI 10.1073/pnas.1919269117 · PubMed

Other PDB entries of the same protein (UniProt S6B291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4LLY 1.6 Å, Crystal structure of Pertuzumab Clambda Fab with variable and constant domain redesigns…
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6B9Z 1.82 Å, Trastuzumab Fab v3
4LLW 1.95 Å, Crystal structure of Pertuzumab Clambda Fab with variable domain redesign (VRD2) at 1.95A
6BAE 2.14 Å, Trastuzumab Fab v3 in complex with CQFDLSTRRLKC
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
5VEB 2.34 Å, Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6
6AZK 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine…
6AYN 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine…
6AZL 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope…
6AU5 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant
6AXP 2.48 Å, Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant

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