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- PDB-6jep: Structure of a neutralizing antibody bound to the Zika envelope p... -

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Basic information

Entry
Database: PDB / ID: 6jep
TitleStructure of a neutralizing antibody bound to the Zika envelope protein domain III
Components
  • Genome polyprotein
  • heavy chain of Fab ZK2B10
  • light chain of Fab ZK2B10
KeywordsANTIVIRAL PROTEIN / Antibody / complex
Function / homology
Function and homology information


: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / 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 endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding / membrane
Similarity search - Function
Immunoglobulin-like - #350 / 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 ...Immunoglobulin-like - #350 / 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, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / 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 / helicase superfamily c-terminal domain / Immunoglobulin E-set / 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Zika virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.316 Å
AuthorsWang, L. / Wang, R.K. / Wang, L. / Ben, H.J. / Yu, L. / Gao, F. / Shi, X.L. / Yin, C.B. / Zhang, F.C. / Xiang, Y. / Zhang, L.Q.
CitationJournal: Cell Rep / Year: 2019
Title: Structural Basis for Neutralization and Protection by a Zika Virus-Specific Human Antibody.
Authors: Lin Wang / Ruoke Wang / Lei Wang / Haijing Ben / Lei Yu / Fei Gao / Xuanling Shi / Chibiao Yin / Fuchun Zhang / Ye Xiang / Linqi Zhang /
Abstract: We previously reported a human monoclonal antibody, ZK2B10, capable of protection against Zika virus (ZIKV) infection and microcephaly in developing mouse embryos. Here, we report the structural ...We previously reported a human monoclonal antibody, ZK2B10, capable of protection against Zika virus (ZIKV) infection and microcephaly in developing mouse embryos. Here, we report the structural features and mechanism of action of ZK2B10. The crystal structure at a resolution of 2.32 Å revealed that the epitope is located on the lateral ridge of DIII of the envelope glycoprotein. Cryo-EM structure with mature ZIKV showed that the antibody binds to DIIIs around the icosahedral 2-fold, 3-fold, and 5-fold axes, a distinct feature compared to those reported for DIII-specific antibodies. The binding of ZK2B10 to ZIKV has no detectable effect on viral attachment to target cells or on conformational changes of the E glycoprotein in the acidic environment, suggesting that ZK2B10 functions at steps between the formation of the fusion intermediate and membrane fusion. These results provide structural and mechanistic insights into how ZK2B10 mediates protection against ZIKV infection.
History
DepositionFeb 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: heavy chain of Fab ZK2B10
L: light chain of Fab ZK2B10
E: Genome polyprotein
K: heavy chain of Fab ZK2B10
I: light chain of Fab ZK2B10
F: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)118,3106
Polymers118,3106
Non-polymers00
Water10,449580
1
H: heavy chain of Fab ZK2B10
L: light chain of Fab ZK2B10
E: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)59,1553
Polymers59,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-29 kcal/mol
Surface area24970 Å2
MethodPISA
2
K: heavy chain of Fab ZK2B10
I: light chain of Fab ZK2B10
F: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)59,1553
Polymers59,1553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-32 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.463, 126.984, 70.353
Angle α, β, γ (deg.)90.000, 96.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain E and (resid 303 through 398 or resid 400 through 403))
21(chain F and (resid 303 through 398 or resid 400 through 403))
12chain H
22chain K
13chain I
23chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALHISHIS(chain E and (resid 303 through 398 or resid 400 through 403))EC303 - 3981 - 96
121TRPTRPSERSER(chain E and (resid 303 through 398 or resid 400 through 403))EC400 - 40398 - 101
211VALVALHISHIS(chain F and (resid 303 through 398 or resid 400 through 403))FF303 - 3981 - 96
221TRPTRPSERSER(chain F and (resid 303 through 398 or resid 400 through 403))FF400 - 40398 - 101
112GLUGLULYSLYSchain HHA1 - 2351 - 235
212GLUGLULYSLYSchain KKD1 - 2351 - 235
113SERSERTHRTHRchain IIE1 - 2141 - 214
213SERSERTHRTHRchain LLB1 - 2141 - 214

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody heavy chain of Fab ZK2B10


Mass: 25383.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody light chain of Fab ZK2B10


Mass: 22782.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Genome polyprotein


Mass: 10989.564 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: A0A2Z2ESG6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 580 / Source method: isolated from a natural source / Formula: H2O
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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: MPD, PEG1500, Sodium acetate/Acetic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.316→35.646 Å / Num. obs: 50308 / % possible obs: 99.72 % / Redundancy: 3.7 % / Net I/σ(I): 16.15
Reflection shellResolution: 2.32→2.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3247refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.316→35.646 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2193 2434 4.84 %
Rwork0.1664 47874 -
obs0.1689 50308 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.88 Å2 / Biso mean: 36.8256 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 2.316→35.646 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 0 580 8892
Biso mean---40.29 -
Num. residues----1100
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11E592X-RAY DIFFRACTION6.23TORSIONAL
12F592X-RAY DIFFRACTION6.23TORSIONAL
21H1420X-RAY DIFFRACTION6.23TORSIONAL
22K1420X-RAY DIFFRACTION6.23TORSIONAL
31I1290X-RAY DIFFRACTION6.23TORSIONAL
32L1290X-RAY DIFFRACTION6.23TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3161-2.36340.27581740.20322726290098
2.3634-2.41480.3311400.206728132953100
2.4148-2.4710.31391370.201428172954100
2.471-2.53270.28121430.205828052948100
2.5327-2.60120.27871310.200128262957100
2.6012-2.67770.28141510.186127972948100
2.6777-2.76410.27521430.18628362979100
2.7641-2.86290.26641650.187427852950100
2.8629-2.97740.22681320.179328072939100
2.9774-3.11290.24711640.173927922956100
3.1129-3.27690.21031460.17328292975100
3.2769-3.4820.20991380.156728352973100
3.482-3.75060.19231380.150928082946100
3.7506-4.12750.18341340.143528522986100
4.1275-4.72360.1571220.129228272949100
4.7236-5.94680.18251400.149128472987100
5.9468-35.64970.19871360.178428723008100
Refinement TLS params.Method: refined / Origin x: -13.4998 Å / Origin y: 20.4834 Å / Origin z: -17.4096 Å
111213212223313233
T0.1836 Å20.0114 Å20.0032 Å2-0.1873 Å20.0029 Å2--0.1294 Å2
L0.2048 °20.1396 °20.0059 °2-0.2588 °2-0.0119 °2---0.0067 °2
S0.001 Å °0.0502 Å °-0.0041 Å °0.0132 Å °-0.0036 Å °-0.0227 Å °0.0034 Å °-0.0035 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allH1 - 235
2X-RAY DIFFRACTION1allL1 - 214
3X-RAY DIFFRACTION1allE303 - 403
4X-RAY DIFFRACTION1allK1 - 235
5X-RAY DIFFRACTION1allI1 - 214
6X-RAY DIFFRACTION1allF303 - 403
7X-RAY DIFFRACTION1allS1 - 580

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