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- PDB-7bpk: Zika virus envelope protein mutant bound to mAb -

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Basic information

Entry
Database: PDB / ID: 7bpk
TitleZika virus envelope protein mutant bound to mAb
Components
  • Envelope protein
  • IG c307_light_IGLV1-51_IGLJ2
  • Z3L1 Heavy chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Zika virus / envelop protein / monoclonal antibody / 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 / host cell surface / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...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 / host cell surface / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / immune response / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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 / GTP binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular space / extracellular region / ATP binding / metal ion binding / membrane
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 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulin-like fold / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / IG c307_light_IGLV1-51_IGLJ2
Similarity search - Component
Biological speciesZika virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 23, 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 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope protein
B: Envelope protein
C: Z3L1 Heavy chain
D: IG c307_light_IGLV1-51_IGLJ2
H: Z3L1 Heavy chain
L: IG c307_light_IGLV1-51_IGLJ2


Theoretical massNumber of molelcules
Total (without water)141,9876
Polymers141,9876
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10280 Å2
ΔGint-45 kcal/mol
Surface area54070 Å2
Unit cell
Length a, b, c (Å)78.462, 103.790, 205.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Envelope protein


Mass: 45671.723 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 Z3L1 Heavy chain


Mass: 14060.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293
Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
#3: Antibody IG c307_light_IGLV1-51_IGLJ2 / Z3L1 light chain


Mass: 11261.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293
Production host: Mammalian expression vector BsrGI-MCS-pcDNA3.1 (others)
References: UniProt: A0A5C2GK82
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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.12 M Ethylene Glycols, 0.1 M buffer system 3 at pH 8.5 and 30% V/V Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / 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: 3.1→50 Å / Num. obs: 30934 / % possible obs: 99.2 % / Redundancy: 9.3 % / Biso Wilson estimate: 69.81 Å2 / Rpim(I) all: 0.056 / Net I/σ(I): 12.4
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 3041 / CC1/2: 0.801

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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: 5JHM

5jhm


Resolution: 3.1→36.45 Å / SU ML: 0.4374 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.003
RfactorNum. reflection% reflection
Rfree0.268 1378 4.64 %
Rwork0.2323 --
obs0.2339 29728 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 69.82 Å2
Refinement stepCycle: LAST / Resolution: 3.1→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 0 0 9754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00179976
X-RAY DIFFRACTIONf_angle_d0.491113540
X-RAY DIFFRACTIONf_chiral_restr0.04071498
X-RAY DIFFRACTIONf_plane_restr0.00321734
X-RAY DIFFRACTIONf_dihedral_angle_d17.33823614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.21-3.340.37021400.32122646X-RAY DIFFRACTION90.4
3.34-3.50.3161550.29152825X-RAY DIFFRACTION97.13
3.5-3.680.31891490.26712910X-RAY DIFFRACTION99.32
3.68-3.910.29161450.25242930X-RAY DIFFRACTION99.84
3.91-4.210.29671240.23552947X-RAY DIFFRACTION99.48
4.21-4.630.2431350.19562904X-RAY DIFFRACTION97.59
4.63-5.30.21711420.19592976X-RAY DIFFRACTION99.9
5.3-6.670.25381400.22483012X-RAY DIFFRACTION99.53
Refinement TLS params.Method: refined / Origin x: 22.0928783361 Å / Origin y: 4.82720987627 Å / Origin z: -21.3735039542 Å
111213212223313233
T0.272848939192 Å20.0433108066395 Å2-0.0138377146552 Å2-0.291118783093 Å20.0163999914745 Å2--0.305466466274 Å2
L-0.0600970798101 °20.113471531115 °2-0.220085258347 °2--0.0387200151456 °20.165131523066 °2--1.01785558343 °2
S0.0184889082069 Å °-0.0264557476494 Å °0.0281505578337 Å °-0.0115237692199 Å °-0.000270562071524 Å °0.00280289812144 Å °-0.08099645922 Å °-0.0835031986493 Å °0.000730958564197 Å °
Refinement TLS groupSelection details: all

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