8CXI: Zika Virus

Structures of Zika Virus in Complex with Antibodies Targeting E Dimer Epitopes and Basis for Neutralization Efficacy. Determined by electron microscopy at 3.4 Å resolution. Released 7 Jun 2023.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Zika virus, Homo sapiens
Chains: 10
Atoms: 16,832
Mol. weight: 1401.23 kDa
Released: 7 Jun 2023

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

Secondary structure: helices and β-sheets

8CXI contains 52 α-helices and 168 β-strands across 10 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: 8 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
β-strand	21-26	6	2
β-strand	30-34	5	1
β-strand	41-50	10	1
β-strand	54-59	6	3
β-strand	63-65	3	4
β-strand	69-73	5	5
β-strand	87	1	6
β-strand	90-95	6	5
β-strand	98	1	7
β-strand	110	1	7
β-strand	112-118	7	5
β-strand	119-121	3	4
β-strand	125-129	5	3
β-strand	135-143	9	1
β-strand	164-169	6	1
β-strand	170	1	8
β-strand	173	1	8
β-strand	175-180	6	2
β-strand	184-191	8	2
β-strand	201-205	5	3
β-strand	210-214	5	3
β-strand	225	1	3
β-strand	243-247	5	9
β-strand	253-257	5	9
α-helix	264-268	5
β-strand	274-275	2	3
β-strand	276-278	3	1
β-strand	281-284	4	1
β-strand	288-294	7	2
β-strand	298	1	2
α-helix	305-306	2
β-strand	307	1	10
α-helix	308	1
β-strand	312-314	3	11
β-strand	319-320	2	11
β-strand	326-332	7	11
β-strand	339	1	12
β-strand	340	1	10
β-strand	343-346	4	13
β-strand	357	1	14
β-strand	365	1	12
β-strand	372-378	7	11
β-strand	379	1	14
β-strand	384-389	6	13
β-strand	396-401	6	13
α-helix	406-424	19
α-helix	425-430	6
α-helix	438-456	19
α-helix	462-477	16
α-helix	484-498	15

Chain B: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	10-11	2	21
β-strand	21-26	6	22
β-strand	31-33	3	21
β-strand	41-50	10	21
β-strand	54-55	2	21
β-strand	58-59	2	23
β-strand	63-72	10	24
α-helix	83-86	4
β-strand	90-98	9	24
β-strand	110-121	12	24
β-strand	125	1	23
β-strand	126-129	4	21
β-strand	135-143	9	21
α-helix	150-152	3
α-helix	158-161	4
β-strand	164-169	6	21
β-strand	170	1	25
β-strand	173	1	25
β-strand	175-180	6	22
β-strand	184-190	7	22
β-strand	201-205	5	21
β-strand	210-214	5	21
α-helix	215-219	5
β-strand	225-226	2	23
β-strand	237	1	23
β-strand	243-247	5	26
β-strand	253-257	5	26
α-helix	262-268	7
β-strand	274-278	5	21
β-strand	281-284	4	21
β-strand	288-298	11	22
α-helix	306	1
β-strand	307	1	27
α-helix	308	1
β-strand	312-320	9	28
β-strand	326-332	7	28
β-strand	339-340	2	27
β-strand	343-346	4	29
β-strand	357	1	30
β-strand	364-365	2	27
β-strand	372-378	7	28
β-strand	379	1	30
β-strand	384-389	6	29
β-strand	396-401	6	29
α-helix	406-424	19
α-helix	425-428	4
α-helix	438-456	19
α-helix	464-477	14
α-helix	483-499	17

Chain C: 10 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	37
β-strand	20-26	7	38
β-strand	31-34	4	37
β-strand	41-50	10	37
β-strand	54-56	3	37
β-strand	59	1	39
β-strand	63-65	3	40
β-strand	69-72	4	41
α-helix	83-85	3
β-strand	87	1	6
β-strand	90-95	6	41
β-strand	98	1	42
β-strand	110	1	42
β-strand	113-118	6	41
β-strand	119-121	3	40
β-strand	126-129	4	37
β-strand	135-143	9	37
β-strand	164-169	6	37
β-strand	170	1	43
β-strand	173	1	43
β-strand	175-180	6	38
β-strand	184-190	7	38
β-strand	201-205	5	37
β-strand	210-214	5	37
β-strand	225	1	39
β-strand	243-246	4	44
β-strand	254-257	4	44
α-helix	262-268	7
β-strand	274-278	5	37
β-strand	281-284	4	37
β-strand	288-294	7	38
β-strand	298	1	38
α-helix	306	1
β-strand	307	1	45
α-helix	308	1
β-strand	312-314	3	46
β-strand	319-320	2	46
β-strand	326-332	7	46
β-strand	339-340	2	45
α-helix	341-342	2
β-strand	343-346	4	47
β-strand	357	1	48
β-strand	364-365	2	45
β-strand	372-378	7	46
β-strand	379	1	48
β-strand	385-389	5	47
β-strand	396-400	5	47
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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-10	3
α-helix	24-38	15
α-helix	42-52	11
α-helix	57-70	14

Chain E: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	7-10	4
α-helix	24-38	15
α-helix	41-51	11
α-helix	57-70	14

Chain F: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-10	3
α-helix	11-13	3
α-helix	24-38	15
α-helix	41-51	11
α-helix	57-73	17

Chain h: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	31
β-strand	11-12	2	32
β-strand	18-25	8	31
α-helix	29-31	3
β-strand	33-39	7	33
β-strand	45-51	7	33
β-strand	57-59	3	33
β-strand	67-72	6	31
β-strand	77-82	6	31
α-helix	84-86	3
β-strand	88-95	8	33
β-strand	102-103	2	33
β-strand	107-109	3	33
β-strand	110-111	2	32

Chain H: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	15
β-strand	12	1	16
β-strand	18-23	6	15
α-helix	29-31	3
β-strand	34-39	6	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	88-94	7	17
α-helix	98-100A	4
β-strand	102-103	2	17
β-strand	107-109	3	17
β-strand	111	1	16

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
Ankyrin repeat family A protein 2,Envelope E protein	A, B, C	protein	639	Zika virus	A0A024B7W1 (AlphaFold model), Q9H9E1 (AlphaFold model)
Membrane M protein	D, E, F	protein	3423	Zika virus	A0A024B7W1 (AlphaFold model)
A11 heavy chain	H, h	protein	133	Homo sapiens
A11 light chain	L, l	protein	111	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>8CXI_1 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 2 (D, E, F), FASTA

>8CXI_2 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

Sequence of entity 3 (H, h), FASTA

>8CXI_3 A11 heavy chain (chains H, h)
EVQLVESGGGLVRPGGSLRLSCAASGFSYSNHWMHWVRQAPGKGLVWVSRINSDGSTRNY
ADFVKGRFTISRDNAENTLYLEMNSLTADDTAVYYCVRDGVRFYYDSTGYYPDSFFKYGM
DVWGQGTTVTVSS

Sequence of entity 4 (L, l), FASTA

>8CXI_4 A11 light chain (chains L, l)
QSVLTQPVSVSGSPGQSITISCTGTSSNADTYNLVSWYQQRPGKAPKLMIYEGTKRPSGV
SNRFSASKSATAASLTISGLQPEDEADYYCCSYATSRTLVFGGGTKLTVVG

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 A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KQR 1.33 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine
6LD1 1.4 Å, Zika NS5 polymerase domain
6LD2 1.4 Å, Zika NS5 polymerase domain
5KQS 1.5 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and…
6LD4 1.5 Å, Zika NS5 polymerase domain
6S0J 1.5 Å, Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-
5ULP 1.55 Å, Structure of the NS5 methyltransferase from Zika bound to MS2042
5Y6N 1.57 Å, Zika virus helicase in complex with ADP
7M1V 1.6 Å, Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the…
5KVE 1.7 Å, Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
6RWZ 1.7 Å, Structure of Zika virus NS3 helicase in complex with ADP-BeF3
5JMT 1.8 Å, Crystal structure of Zika virus NS3 helicase

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