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- PDB-7bq5: ZIKV sE bound to mAb Z6 -

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Basic information

Entry
Database: PDB / ID: 7bq5
TitleZIKV sE bound to mAb Z6
Components
  • Z6 Light Chain
  • Z6 heavy chain
  • envelope protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Zika virus / antibody / fusion loop / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell surface ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / host cell surface / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / GTP binding / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / 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 capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / 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 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 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 / : / Flavivirus NS3 helicase, C-terminal helical domain / 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 / 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: 2.99 Å
AuthorsDai, L. / Qi, J. / Gao, G.F.
CitationJournal: Nat.Immunol. / Year: 2021
Title: Protective Zika vaccines engineered to eliminate enhancement of dengue infection via immunodominance switch.
Authors: Dai, L. / Xu, K. / Li, J. / Huang, Q. / Song, J. / Han, Y. / Zheng, T. / Gao, P. / Lu, X. / Yang, H. / Liu, K. / Xia, Q. / Wang, Q. / Chai, Y. / Qi, J. / Yan, J. / Gao, G.F.
History
DepositionMar 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 20, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: envelope protein
H: Z6 heavy chain
L: Z6 Light Chain
B: envelope protein
C: Z6 heavy chain
D: Z6 Light Chain


Theoretical massNumber of molelcules
Total (without water)184,7436
Polymers184,7436
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-70 kcal/mol
Surface area76570 Å2
Unit cell
Length a, b, c (Å)158.245, 153.672, 115.201
Angle α, β, γ (deg.)90.000, 125.489, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein envelope protein


Mass: 45443.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A142I5B9
#2: Antibody Z6 heavy chain


Mass: 23449.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
#3: Antibody Z6 Light Chain


Mass: 23479.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Amino Acids, 0.1 M Buffer system 3 at pH 8.5 and 30% v/v Precipitant Mix 3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.99→50 Å / Num. obs: 44965 / % possible obs: 99.8 % / Redundancy: 11.7 % / Biso Wilson estimate: 69.28 Å2 / Rpim(I) all: 0.094 / Net I/σ(I): 7.8
Reflection shellResolution: 3→3.11 Å / Num. unique obs: 4462 / CC1/2: 0.555

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JHL

5jhl


Resolution: 2.99→39.23 Å / SU ML: 0.4668 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7684
RfactorNum. reflection% reflection
Rfree0.2754 2261 5.03 %
Rwork0.2609 --
obs0.2617 44922 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 86.29 Å2
Refinement stepCycle: LAST / Resolution: 2.99→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12474 0 0 0 12474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002812760
X-RAY DIFFRACTIONf_angle_d0.732917338
X-RAY DIFFRACTIONf_chiral_restr0.04541956
X-RAY DIFFRACTIONf_plane_restr0.0052212
X-RAY DIFFRACTIONf_dihedral_angle_d11.8114632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.050.39721230.38812315X-RAY DIFFRACTION85.85
3.05-3.120.40441540.36782664X-RAY DIFFRACTION99.89
3.12-3.20.35711432682X-RAY DIFFRACTION99.75
3.29-3.380.33311290.32052706X-RAY DIFFRACTION99.75
3.38-3.490.3281310.31582690X-RAY DIFFRACTION99.82
3.49-3.620.35341520.30632664X-RAY DIFFRACTION99.68
3.76-3.930.28641240.282730X-RAY DIFFRACTION99.96
3.93-4.140.26851490.24892662X-RAY DIFFRACTION99.93
4.14-4.40.23921420.22532708X-RAY DIFFRACTION99.93
4.4-4.740.22791430.20912684X-RAY DIFFRACTION99.93
4.74-5.220.23721410.20752698X-RAY DIFFRACTION99.89
5.22-5.970.27121450.23092700X-RAY DIFFRACTION99.72
5.97-7.510.25421510.2482705X-RAY DIFFRACTION99.9
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)
12.172942784050.5780994851-0.0818882245972-0.7506317046460.232242807816-0.559485791119-0.06826394066050.0729167720835-0.4597524597130.0267824918440.1377164925590.0808098036467-0.0392319399199-0.0827598094562-0.06421587420360.515885358131-0.08023791749720.01060978197480.9172990286740.121348476331.33987762523-2.016821794541.0303100944389.081465231
22.166564965150.89562244919-0.263609235564-0.736314650884-0.010333644027-0.56732336723-0.0235010924950.3762925563950.606127750070.04621167850080.111002357157-0.1069668694690.02049642548370.115229036667-0.08094022350860.539798594349-0.0598125087423-0.03059043281060.9941078262970.09992436109141.46606751637-125.456873125-34.0942216867389.138541688
31.51368021776-0.6954963497750.1511589597532.027626410750.1183354824481.3089588931-0.125218532458-0.02593694174620.1130639174350.299394238690.096540601512-0.3479482719420.2121135274720.128270891994-0.09575760971780.4372985627210.0628393856563-0.01462940396840.3017849124-0.08159808532740.228139983624-28.6178918733-38.4581502569405.348147408
42.20590540534-0.277674136494-0.3314118251862.238318273110.3884447877471.46934839858-0.214504962798-0.10665327860.3782828063180.7746785808150.383010869404-0.4402883080630.03892018785140.4781659886480.09776265934430.5861812716890.127969106888-0.1894643939750.386156657448-0.2432597133640.256251292101-29.5250567435-27.3307870006419.621093373
51.80457481499-1.00030566086-0.3826486861212.08368090917-0.0736960837791.45865177602-0.04571830971510.0643945942908-0.09055240566740.3346291215250.001478353932650.344244002979-0.172297426257-0.206761250774-0.05685499707050.4324821000540.04345868137330.022120760510.2677494608990.01780322451710.256299684197-98.74573311255.43292185817405.482124999
62.1415715528-0.503050740346-0.1176402688131.99233833386-0.3134446207251.8077653308-0.121994992905-0.178878176697-0.6830920935170.639769480260.2299538390060.416301970372-0.0107632128922-0.3247057521110.0538260855850.5274948596030.02976622514320.1326283361530.335844654980.1895997726440.280353569597-97.6920031944-5.57551342336419.76687934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain H
6X-RAY DIFFRACTION6chain L

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