6UTA: Z004 iGL Fab

Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII. Determined by X-ray diffraction at 3.1 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Homo sapiens, Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Chains: 6
Atoms: 8,038
Mol. weight: 120.54 kDa
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6UTA contains 25 α-helices and 114 β-strands across 6 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: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	17
β-strand	11-12	2	18
β-strand	18-23	6	17
α-helix	29-31	3
β-strand	32-39	8	19
β-strand	45-51	7	19
β-strand	57-59	3	19
β-strand	67-72	6	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-98	11	19
β-strand	102-103	2	19
β-strand	107-109	3	19
β-strand	110-111	2	18
β-strand	117	1	20
β-strand	120	1	21
β-strand	123-124	2	21
β-strand	138-145	8	21
β-strand	146	1	20
β-strand	151-154	4	22
β-strand	159	1	22
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-182	7	21
α-helix	183-185	3
β-strand	195-200	6	22
β-strand	205-210	6	22

Chain B: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-7	3	23
β-strand	10-13	4	24
β-strand	19-24	6	23
β-strand	33-38	6	24
β-strand	44-49	6	24
β-strand	53-54	2	24
α-helix	55	1
β-strand	62-67	6	23
β-strand	70-75	6	23
β-strand	85-90	6	24
β-strand	97-98	2	24
β-strand	103-106	4	24
β-strand	111	1	25
α-helix	112-113	2
β-strand	114-118	5	26
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	26
β-strand	140	1	25
β-strand	144-150	7	27
β-strand	154	1	27
β-strand	159-163	5	26
α-helix	164-167	4
β-strand	173-182	10	26
α-helix	183-186	4
β-strand	191-198	8	27
β-strand	205-210	6	27

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	306	1
β-strand	307	1	28
α-helix	308	1
β-strand	311-316	6	29
β-strand	326-333	8	29
β-strand	339-340	2	28
β-strand	343-346	4	30
β-strand	355	1	30
β-strand	357-358	2	29
β-strand	364-365	2	28
β-strand	372-379	8	29
β-strand	385-389	5	30
β-strand	396-400	5	30

Chain E: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	306	1
β-strand	307	1	12
α-helix	308	1
β-strand	311-314	4	13
β-strand	322-323	2	14
β-strand	325	1	14
β-strand	326-333	8	13
β-strand	340	1	12
β-strand	343-346	4	15
β-strand	355	1	15
β-strand	364	1	12
β-strand	372-378	7	13
α-helix	380-381	2
β-strand	383-385	3	16
β-strand	386-389	4	15
β-strand	396	1	15
β-strand	400-402	3	16

Chain H: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
α-helix	29-31	3
β-strand	32-39	8	3
β-strand	45-51	7	3
β-strand	57-59	3	3
β-strand	67-72	6	1
β-strand	77-82	6	1
β-strand	88-98	11	3
β-strand	100E-102	3	3
β-strand	107-109	3	3
β-strand	110-111	2	2
β-strand	117	1	4
β-strand	120-123	4	5
β-strand	138-145	8	5
β-strand	146	1	4
β-strand	151-154	4	6
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-182	7	5
β-strand	194-199	6	6
β-strand	207-211	5	6

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-7	3	7
β-strand	10-13	4	8
β-strand	19-24	6	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	62-67	6	7
β-strand	70-75	6	7
β-strand	85-90	6	8
β-strand	98	1	8
β-strand	102-106	5	8
β-strand	111	1	9
α-helix	112-113	2
β-strand	114-118	5	10
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	10
β-strand	140	1	9
β-strand	145-150	6	11
β-strand	153-154	2	11
β-strand	159-160	2	10
α-helix	163-167	5
β-strand	173-182	10	10
α-helix	183-186	4
β-strand	191-197	7	11
β-strand	205-210	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Z004 iGL Fab heavy chain	A, H	protein	234	Homo sapiens	S6C4S0 (AlphaFold model)
Z004 iGL Fab light chain	B, L	protein	214	Homo sapiens	P0DOX7 (AlphaFold model)
Env	C, E	protein	110	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013	A0A142I5B9

Sequence of entity 1 (A, H), FASTA

>6UTA_1 Z004 iGL Fab heavy chain (chains A, H)
EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGPRGVGELFDYWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 2 (B, L), FASTA

>6UTA_2 Z004 iGL Fab light chain (chains B, L)
DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPS
RFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYPWTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (C, E), FASTA

>6UTA_3 Env (chains C, E)
MRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGR
LITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTI

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 S6C4S0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W08 2.6 Å, A/Texas/50/2012(H3N2) Influenza hemagglutinin in complex with K03.12 Fab
4NM4 2.65 Å, Crystal structure of broadly neutralizing antibody CR8043
4O58 2.75 Å, Crystal structure of broadly neutralizing antibody F045-092 in complex with…
5UGY 2.8 Å, Influenza hemagglutinin in complex with a neutralizing antibody
6CBJ 2.85 Å, Crystal Structure of DH270.3 Fab in complex with Man9
6MYY 3.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 3 Fabs…
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
4NM8 4.0 Å, Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza…
6MZJ 4.8 Å, Germline VRC01 antibody recognition of a modified clade C HIV-1 envelope trimer, 2 Fabs…
4O5I 6.5 Å, Crystal structure of broadly neutralizing antibody F045-092 in complex with…

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