8CXG: Zika Virus

Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy. Determined by electron microscopy at 3.2 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Zika virus
Chains: 12
Atoms: 18,381
Mol. weight: 1423.18 kDa
Released: 7 Jun 2023

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

Secondary structure: helices and β-sheets

8CXG contains 57 α-helices and 187 β-strands across 12 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 1: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	45
β-strand	11-12	2	46
β-strand	18-25	8	45
α-helix	29-31	3
β-strand	32-39	8	47
β-strand	45-51	7	47
β-strand	58-60	3	47
β-strand	65	1	45
β-strand	68-73	6	45
β-strand	78-83	6	45
α-helix	88-90	3
β-strand	92-100	9	47
β-strand	110-112	3	47
β-strand	116-118	3	47
β-strand	119-120	2	46

Chains 2, l and L: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	48
β-strand	10-13	4	49
β-strand	19-25	7	48
β-strand	33-38	6	49
β-strand	45-49	5	49
β-strand	53-54	2	49
α-helix	55	1
β-strand	62-67	6	48
β-strand	70-75	6	48
α-helix	80-82	3
β-strand	85-90	6	49
β-strand	99	1	49
β-strand	103-107	5	49

Chain A: 11 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	6
β-strand	21-26	6	7
β-strand	30-34	5	6
β-strand	41-50	10	6
β-strand	54-56	3	8
β-strand	59	1	9
β-strand	63-65	3	10
β-strand	69-72	4	11
α-helix	83-86	4
β-strand	87	1	12
β-strand	90-95	6	11
β-strand	98	1	13
β-strand	110	1	13
β-strand	113-118	6	11
β-strand	119-121	3	10
β-strand	126-129	4	8
β-strand	135-143	9	6
β-strand	164-169	6	6
β-strand	170	1	14
β-strand	173	1	14
β-strand	175-180	6	7
β-strand	184-191	8	7
β-strand	201-205	5	8
β-strand	210-214	5	8
β-strand	225	1	9
β-strand	243-248	6	15
β-strand	252-257	6	15
α-helix	262-268	7
α-helix	272	1
β-strand	273-275	3	8
β-strand	276-278	3	6
β-strand	281-284	4	6
β-strand	288-294	7	7
β-strand	298	1	7
α-helix	305-306	2
β-strand	307	1	16
α-helix	308	1
β-strand	312-320	9	17
β-strand	326-332	7	17
β-strand	339-340	2	16
α-helix	341-342	2
β-strand	343-347	5	18
β-strand	353-355	3	18
β-strand	357	1	19
β-strand	364-365	2	16
β-strand	372-378	7	17
β-strand	379	1	19
β-strand	384-389	6	18
β-strand	396-401	6	18
α-helix	406-424	19
α-helix	425-430	6
α-helix	438-456	19
α-helix	462-478	17
α-helix	484-498	15

Chain B: 11 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	26
β-strand	21-26	6	27
β-strand	30-33	4	26
β-strand	41-51	11	26
β-strand	54-65	12	26
β-strand	69-73	5	28
α-helix	83-86	4
β-strand	90-98	9	28
β-strand	110-118	9	28
β-strand	119-129	11	26
β-strand	135-143	9	26
β-strand	164-169	6	26
β-strand	170	1	29
β-strand	173	1	29
β-strand	175-180	6	27
β-strand	184-191	8	27
α-helix	192-195	4
β-strand	201-205	5	26
β-strand	210-214	5	26
β-strand	225	1	26
β-strand	243-247	5	30
β-strand	253-257	5	30
α-helix	264-268	5
β-strand	273-278	6	26
β-strand	281-284	4	26
β-strand	288-298	11	27
α-helix	306	1
β-strand	307	1	31
α-helix	308	1
β-strand	312-314	3	32
β-strand	319-320	2	32
β-strand	326-332	7	32
β-strand	339-340	2	31
α-helix	341-342	2
β-strand	343-346	4	33
β-strand	357	1	34
β-strand	364-365	2	31
β-strand	372-378	7	32
β-strand	379	1	34
β-strand	384-389	6	33
β-strand	396-401	6	33
α-helix	406-424	19
α-helix	426-429	4
α-helix	438-456	19
α-helix	464-478	15
α-helix	483-499	17

Chain C: 9 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	35
β-strand	20-26	7	36
β-strand	31-34	4	35
β-strand	41-50	10	35
β-strand	54-65	12	35
β-strand	68	1	23
β-strand	69-73	5	37
α-helix	83-86	4
β-strand	87	1	12
β-strand	90-95	6	37
β-strand	98	1	38
β-strand	110	1	38
β-strand	112-118	7	37
β-strand	119-129	11	35
β-strand	135-143	9	35
β-strand	164-169	6	35
β-strand	170	1	39
β-strand	173	1	39
β-strand	175-180	6	36
β-strand	184-191	8	36
β-strand	201-205	5	35
β-strand	210-214	5	35
β-strand	225	1	35
β-strand	243-246	4	40
β-strand	254-257	4	40
α-helix	264-268	5
β-strand	273-278	6	35
β-strand	281-284	4	35
β-strand	288-298	11	36
α-helix	306-308	3
β-strand	312-314	3	41
β-strand	319-320	2	41
β-strand	326-332	7	41
β-strand	339-340	2	42
α-helix	341-342	2
β-strand	343-346	4	43
β-strand	357	1	44
β-strand	364-365	2	42
β-strand	372-378	7	41
β-strand	379	1	44
β-strand	384-389	6	43
β-strand	396-401	6	43
α-helix	406-424	19
α-helix	425-430	6
α-helix	438-456	19
α-helix	464-478	15
α-helix	484-499	16

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-10	4
α-helix	11-13	3
α-helix	24-38	15
α-helix	41-52	12
α-helix	57-70	14

Chain E: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	7-10	4
α-helix	11-13	3
α-helix	24-38	15
α-helix	41-52	12
α-helix	57-73	17

Chain F: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-10	4
α-helix	24-38	15
α-helix	41-52	12
α-helix	57-73	17

2 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
C8 scFv heavy chain	1, H, h	protein	122	Homo sapiens
C8 scFv light chain	2, L, l	protein	109	Homo sapiens
Ankyrin repeat family A protein 2,Envelope E protein	A, B, C	protein	639	Zika virus	A0A142DS37, Q9H9E1 (AlphaFold model)
Membrane M protein	D, E, F	protein	3423	Zika virus	A0A1S6LXE0

Sequence of entity 1 (1, H, h), FASTA

>8CXG_1 C8 scFv heavy chain (chains 1, H, h)
EVQLVESGGGLVQPGGSLRLSCSASGFTFSTYSMHWVRQAPGKGLEYVSAITGEGDSAFY
ADSVKGRFTISRDNSKNTLYFEMNSLRPEDTAVYYCVGGYSNFYYYYTMDVWGQGTTVTV
SS

Sequence of entity 2 (2, L, l), FASTA

>8CXG_2 C8 scFv light chain (chains 2, L, l)
SEIVLTQSPATLSLSPGERATLSCRASQSISTFLAWYQHKPGQAPRLLIYDASTRATGVP
ARFSGSRSGTDFTLTISTLEPEDFAVYYCQQRYNWPPYTFGQGTKVEIK

Sequence of entity 3 (A, B, C), FASTA

>8CXG_3 Ankyrin repeat family A protein 2,Envelope E protein (chains A, B, C)
MDTSTNLDIGAQLIVEECPSTYSLTGMPDIKIEHPLDPNSEEGSAQGVAMGMKFILPNRF
DMNVCSRFVKSLNEEDSKNIQDQVNSDLEVASVLFKAECNIHTSPSPGIQVRHVYTPSTT
KHFSPIKQSTTLTNKIRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIEL
VTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGC
GLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRA
KVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPW
HAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLS
SGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQM
AVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGS
TIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQ
ILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSA

Sequence of entity 4 (D, E, F), FASTA

>8CXG_4 Membrane M protein (chains D, E, F)
MKNPKKKSGGFRIVNMLKRGVARVSPFGGLKRLPAGLLLGHGPIRMVLAILAFLRFTAIK
PSLGLINRWGSVGKKEAMEIIKKFKKDLAAMLRIINARKEKKRRGADTSVGIVGLLLTTA
MAAEVTRRGSAYYMYLDRNDAGEAISFPTTLGMNKCYIQIMDLGHMCDATMSYECPMLDE
GVEPDDVDCWCNTTSTWVVYGTCHHKKGEARRSRRAVTLPSHSTRKLQTRSQTWLESREY
TKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKVIYLVMILLIAPAYSIRCIGVSNRD
FVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMAS
DSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSI
QPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDC
EPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHA
KRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTA
AFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTE
NSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWD
FGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLA
LGGVLIFLSTAVSADVGCSVDFSKKETRCGTGVFVYNDVEAWRDRYKYHPDSPRRLAAAV
KQAWEDGICGISSVSRMENIMWRSVEGELNAILEENGVQLTVVVGSVKNPMWRGPQRLPV
PVNELPHGWKAWGKSYFVRAAKTNNSFVVDGDTLKECPLKHRAWNSFLVEDHGFGVFHTS
VWLKVREDYSLECDPAVIGTAVKGKEAVHSDLGYWIESEKNDTWRLKRAHLIEMKTCEWP
KSHTLWTDGIEESDLIIPKSLAGPLSHHNTREGYRTQMKGPWHSEELEIRFEECPGTKVH
VEETCGTRGPSLRSTTASGRVIEEWCCRECTMPPLSFRAKDGCWYGMEIRPRKEPESNLV
RSMVTAGSTDHMDHFSLGVLVILLMVQEGLKKRMTTKIIISTSMAVLVAMILGGFSMSDL
AKLAILMGATFAEMNTGGDVAHLALIAAFKVRPALLVSFIFRANWTPRESMLLALASCLL
QTAISALEGDLMVLINGFALAWLAIRAMVVPRTDNITLAILAALTPLARGTLLVAWRAGL
ATCGGFMLLSLKGKGSVKKNLPFVMALGLTAVRLVDPINVVGLLLLTRSGKRSWPPSEVL
TAVGLICALAGGFAKADIEMAGPMAAVGLLIVSYVVSGKSVDMYIERAGDITWEKDAEVT
GNSPRLDVALDESGDFSLVEDDGPPMREIILKVVLMTICGMNPIAIPFAAGAWYVYVKTG
KRSGALWDVPAPKEVKKGETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGSAL
RSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGHSEVQLLAVPPGERARNIQTLPGIFKT
KDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGRREEETPVEC
FEPSMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEMEEALRG
LPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDPSSIAAR
GYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWVTDHSGK
TVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDISEMGANF
KADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYLYGGGCA
ETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTFVELMKR
GDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKPRWMDAR
VCSDHAALKSFKEFAAGKRGAAFGVMEALGTLPGHMTERFQEAIDNLAVLMRAETGSRPY
KAAAAQLPETLETIMLLGLLGTVSLGIFFVLMRNKGIGKMGFGMVTLGASAWLMWLSEIE
PARIACVLIVVFLLLVVLIPEPEKQRSPQDNQMAIIIMVAVGLLGLITANELGWLERTKS
DLSHLMGRREEGATIGFSMDIDLRPASAWAIYAALTTFITPAVQHAVTTSYNNYSLMAMA
TQAGVLFGMGKGMPFYAWDFGVPLLMMGCYSQLTPLTLIVAIILLVAHYMYLIPGLQAAA
ARAAQKRTAAGIMKNPVVDGIVVTDIDTMTIDPQVEKKMGQVLLIAVAVSSAILSRTAWG
WGEAGALITAATSTLWEGSPNKYWNSSTATSLCNIFRGSYLAGASLIYTVTRNAGLVKRR
GGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSA
KLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYG
WNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFC
IKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLL
LGRMDGPRRPVKYEEDVNLGSGTRAVVSCAEAPNMKIIGNRIERIRSEHAETWFFDENHP
YRTWAYHGSYEAPTQGSASSLINGVVRLLSKPWDVVTGVTGIAMTDTTPYGQQRVFKEKV
DTRVPDPQEGTRQVMSMVSSWLWKELGKHKRPRVCTKEEFINKVRSNAALGAIFEEEKEW
KTAVEAVNDPRFWALVDKEREHHLRGECQSCVYNMMGKREKKQGEFGKAKGSRAIWYMWL
GARFLEFEALGFLNEDHWMGRENSGGGVEGLGLQRLGYVLEEMSRIPGGRMYADDTAGWD
TRISRFDLENEALITNQMEKGHRALALAIIKYTYQNKVVKVLRPAEKGKTVMDIISRQDQ
RGSGQVVTYALNTFTNLVVQLIRNMEAEEVLEMQDLWLLRRSEKVTNWLQSNGWDRLKRM
AVSGDDCVVKPIDDRFAHALRFLNDMGKVRKDTQEWKPSTGWDNWEEVPFCSHHFNKLHL
KDGRSIVVPCRHQDELIGRARVSPGAGWSIRETACLAKSYAQMWQLLYFHRRDLRLMANA
ICSSVPVDWVPTGRTTWSIHGKGEWMTTEDMLVVWNRVWIEENDHMEDKTLVTKWTDIPY
LGKREDLWCGSLIGHRPRTTWAENIKNTVNMVRRIIGDEEKYMDYLSTQVRYLGEEGSTP
GVL

Primary citation

Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy. Liu, W., Zhang, X.K., Gong, D.Y. et al. To be published.

Other PDB entries of the same protein (UniProt A0A142DS37), best resolution first:

8CXH 3.2 Å, Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis…

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