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- PDB-9owf: X-ray crystal structure of Zika virus envelope glycoprotein in co... -

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Basic information

Entry
Database: PDB / ID: 9owf
TitleX-ray crystal structure of Zika virus envelope glycoprotein in complex with Fab of F25.S02
Components
  • F25.S02 heavy chain
  • F25.S02 light chain
  • Genome polyprotein
KeywordsIMMUNE SYSTEM / Orthoflavivirus / Zika
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / lipid binding / virion attachment to host cell / GTP binding / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Immunoglobulin E-set / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesZika virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHurlburt, N.K. / Pancera, M.
Funding support1items
OrganizationGrant numberCountry
Other privateFred Hutchinson Cancer Center
Citation
Journal: Commun Biol / Year: 2026
Title: Structural basis for antibody cross-neutralization of Dengue and Zika viruses.
Authors: Nicholas K Hurlburt / Jay Lubow / Leslie Goo / Marie Pancera /
Abstract: Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus (ZikV) and the four serotypes of Dengue virus (DenV1-4) must elicit broadly neutralizing ...Safe and effective vaccines against co-circulating mosquito-borne orthoflaviviruses such as Zika virus (ZikV) and the four serotypes of Dengue virus (DenV1-4) must elicit broadly neutralizing antibodies (bnAbs) to prevent the risk of enhancement of infection by non-neutralizing antibodies. We recently discovered new orthoflavivirus-directed bnAbs, including F25.S02, which neutralizes DenV1-4 and ZikV with comparable or superior potency to the previously characterized E dimer epitope (EDE) bnAbs. Here, we used cryoEM and X-ray crystallography to understand the basis of cross-neutralization of F25.S02 at the molecular level. We obtained a ~ 4.2 Å cryoEM structure of F25.S02 Fab bound to a stabilized DenV3 soluble E protein dimer and a 2.3 Å crystal structure of F25.S02 Fab bound to ZikV soluble E protein dimer. Like previously described EDE1 bnAbs, the structural epitope of F25.S02 is at the E dimer interface, encompassing predominantly conserved regions in domain II, including the fusion loop. However, unlike EDE1 bnAbs, F25.S02 binding is almost entirely dependent on the heavy chain and is shifted slightly away from the dimer symmetry axis. Our findings emphasize the importance of this cross-neutralizing site of vulnerability for DenV and ZikV that can facilitate rational design of vaccines and therapeutics.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 6, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein
B: Genome polyprotein
C: F25.S02 heavy chain
D: F25.S02 light chain
H: F25.S02 heavy chain
L: F25.S02 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,4328
Polymers185,4806
Non-polymers1,9522
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17780 Å2
ΔGint-31 kcal/mol
Surface area70440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.855, 117.855, 346.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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Antibody , 2 types, 4 molecules CHDL

#2: Antibody F25.S02 heavy chain


Mass: 25575.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK Expi293 / Production host: Homo sapiens (human)
#3: Antibody F25.S02 light chain


Mass: 23023.486 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK Expi293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 440 molecules AB

#1: Protein Genome polyprotein


Mass: 44141.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Cell (production host): HEK Expi293 / Production host: Homo sapiens (human) / References: UniProt: A0A0U3FSM8
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 62.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris, pH 8.0, 0.1 M NaCl, 5% w/v PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3→48.7 Å / Num. obs: 206051 / % possible obs: 99.9 % / Redundancy: 16.3 % / Biso Wilson estimate: 43.71 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.164 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.34 Å / Rmerge(I) obs: 1.878 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5312 / CC1/2: 0.615

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.7 Å / SU ML: 0.3278 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.0814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2736 10226 4.96 %
Rwork0.2254 195825 -
obs0.2277 206051 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.64 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12582 0 131 438 13151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004413005
X-RAY DIFFRACTIONf_angle_d0.746117672
X-RAY DIFFRACTIONf_chiral_restr0.04822019
X-RAY DIFFRACTIONf_plane_restr0.00942241
X-RAY DIFFRACTIONf_dihedral_angle_d6.37691874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.320.33593260.30696510X-RAY DIFFRACTION98.79
2.32-2.350.32633300.29596636X-RAY DIFFRACTION99.69
2.35-2.380.3243410.29066438X-RAY DIFFRACTION99.09
2.38-2.410.32573120.29486587X-RAY DIFFRACTION99.61
2.41-2.440.32033210.29056612X-RAY DIFFRACTION99.54
2.44-2.480.31993250.2886496X-RAY DIFFRACTION99.63
2.48-2.510.33483490.28616618X-RAY DIFFRACTION99.9
2.51-2.550.38083660.31516460X-RAY DIFFRACTION99.52
2.55-2.590.3273640.29676546X-RAY DIFFRACTION99.65
2.59-2.630.34683530.28416555X-RAY DIFFRACTION99.84
2.63-2.680.39473350.31526456X-RAY DIFFRACTION98.24
2.68-2.720.34794020.30786445X-RAY DIFFRACTION98.93
2.72-2.780.31083460.26746571X-RAY DIFFRACTION99.67
2.78-2.830.31613240.25846522X-RAY DIFFRACTION99.58
2.83-2.90.30963350.25966565X-RAY DIFFRACTION99.48
2.9-2.960.30963380.27126544X-RAY DIFFRACTION99.41
2.96-3.040.34893440.28286519X-RAY DIFFRACTION99.26
3.04-3.120.35723100.29456517X-RAY DIFFRACTION99.58
3.12-3.210.37622920.28666621X-RAY DIFFRACTION99.54
3.21-3.310.3573510.26756450X-RAY DIFFRACTION99.13
3.31-3.430.26763780.24326413X-RAY DIFFRACTION97.67
3.43-3.570.28083280.2286440X-RAY DIFFRACTION97.61
3.57-3.730.29783080.22146558X-RAY DIFFRACTION99.41
3.73-3.930.24363500.19856540X-RAY DIFFRACTION99.47
3.93-4.170.18883150.17596553X-RAY DIFFRACTION99.52
4.18-4.50.21533070.15486606X-RAY DIFFRACTION99.75
4.5-4.950.1943700.15346514X-RAY DIFFRACTION99.75
4.95-5.660.22123670.1696516X-RAY DIFFRACTION99.88
5.67-7.130.25153790.20816461X-RAY DIFFRACTION98.83
7.14-48.70.23133600.196556X-RAY DIFFRACTION99.83
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1049780229070.84014516965-0.4019037888632.39344622211-1.263572197710.6537580658740.04807961328870.06216598321290.1083775127340.3264947084190.2331206431870.439995897221-0.203270476053-0.193114276496-0.2701988914550.5029526474730.1028942830460.1467366566680.4191712058150.1627734842410.5530440916777.1542016082939.8334463093-48.6918868466
20.06231138514460.434678632067-0.04305460258062.57424847487-1.337966863170.873546628772-0.06263813680930.0677588185969-0.0421266257547-0.3807170046990.0414450412302-0.23253581140.326656722965-0.0293585681960.01596537429420.5274837989450.01124461691250.1235088858980.2935919292110.01869645147460.41805283249415.3752957193-12.7755427993-37.5809843539
31.57188348720.1984407223590.802880648091.140372460790.9654869012941.70042561663-0.0416290500577-0.6444449681860.1570799061610.528584238466-0.0860447222639-0.01101775966970.0829226596024-0.4386265220240.1048341606540.723675000616-0.0081519323996-0.006214292027160.5857190950060.09256340326850.42356954485234.985110530353.1010699838-27.635981788
40.550901914089-0.2030275691980.8561932921070.02291621427310.0283310689223.02169005234-0.204697252456-0.4099675252630.1678893482650.3709425187290.0450970470149-0.145159609572-0.5314620608110.1007835397780.1559345757220.863467825359-0.052543260649-0.08775368426880.541758665910.01076258224760.4427036348747.42923037866.3526190631-28.678013622
52.41091413648-0.1990029458840.926448399910.830169225881-1.020714531372.21032670729-0.1267486794650.1831478112680.239089179657-0.00627952089911-0.271819766085-0.477316239289-0.3718833076530.703966029420.2609037678620.420799263768-0.1015473197660.03649747174730.4550527389820.1542526938170.57084151756329.6841157108-9.97651306893-3.79093216117
61.06363986022-0.346905334898-0.06883534026041.81003001094-1.085604405631.72221591260.0397183636529-0.1052159349760.184821645520.210033322017-0.373320665619-0.634352962205-0.2361557657260.6079234834280.02880250479030.278899552732-0.0809616843059-0.05900224013710.4328465033020.1370081247650.4571340948729.4974702611-20.437654185711.9616444224
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 1 through 404)AA1 - 4041 - 404
22(chain 'B' and resid 1 through 404)BB1 - 4041 - 404
33(chain 'C' and resid 1 through 226)CC1 - 2131 - 220
44(chain 'D' and resid 3 through 213)DD3 - 2081 - 211
55(chain 'H' and resid 1 through 226)HE1 - 2131 - 212
66(chain 'L' and resid 2 through 213)LF2 - 2081 - 212

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