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- PDB-5gzo: Structure of neutralizing antibody bound to Zika envelope protein -

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Basic information

Entry
Database: PDB / ID: 5gzo
TitleStructure of neutralizing antibody bound to Zika envelope protein
Components
  • Antibody heavy chain
  • Antibody light chain
  • Genome polyprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Zika virus / Human neutralizing antibodies / Envelope protein / Molecular determinants / 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 / ribonucleoside triphosphate phosphatase 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 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / ribonucleoside triphosphate phosphatase 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
Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / Immunoglobulin-like - #350 / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus ...Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / Viral Envelope Glycoprotein, domain 2 / Tick-borne Encephalitis virus Glycoprotein, domain 1 / Viral Envelope Glycoprotein; domain 2 / Tick-borne Encephalitis virus Glycoprotein; domain 1 / 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 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 / Immunoglobulins / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesZika virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.755 Å
AuthorsWang, Q. / Yang, H. / Liu, X. / Dai, L. / Ma, T. / Qi, J. / Wong, G. / Peng, R. / Liu, S. / Li, J. ...Wang, Q. / Yang, H. / Liu, X. / Dai, L. / Ma, T. / Qi, J. / Wong, G. / Peng, R. / Liu, S. / Li, J. / Li, S. / Song, J. / Liu, J. / He, J. / Yuan, H. / Xiong, Y. / Liao, Y. / Li, J. / Yang, J. / Tong, Z. / Griffin, B. / Bi, Y. / Liang, M. / Xu, X. / Cheng, G. / Wang, P. / Qiu, X. / Kobinger, G. / Shi, Y. / Yan, J. / Gao, G.F.
CitationJournal: Sci Transl Med / Year: 2016
Title: Molecular determinants of human neutralizing antibodies isolated from a patient infected with Zika virus.
Authors: Qihui Wang / Huabing Yang / Xiaoqing Liu / Lianpan Dai / Tong Ma / Jianxun Qi / Gary Wong / Ruchao Peng / Sheng Liu / Junfu Li / Shihua Li / Jian Song / Jianying Liu / Jianhua He / Hui Yuan ...Authors: Qihui Wang / Huabing Yang / Xiaoqing Liu / Lianpan Dai / Tong Ma / Jianxun Qi / Gary Wong / Ruchao Peng / Sheng Liu / Junfu Li / Shihua Li / Jian Song / Jianying Liu / Jianhua He / Hui Yuan / Ying Xiong / Yong Liao / Jianhua Li / Jianping Yang / Zhou Tong / Bryan D Griffin / Yuhai Bi / Mifang Liang / Xiaoning Xu / Chuan Qin / Gong Cheng / Xinzheng Zhang / Peiyi Wang / Xiangguo Qiu / Gary Kobinger / Yi Shi / Jinghua Yan / George F Gao /
Abstract: The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and ...The 2015-2016 outbreak of Zika virus (ZIKV) disease has affected many countries and is a major public health concern. ZIKV is associated with fetal microcephaly and neurological complications, and countermeasures are needed to treat and prevent ZIKV infection. We report the isolation of 13 specific human monoclonal antibodies from a single patient infected with ZIKV. Two of the isolated antibodies (Z23 and Z3L1) demonstrated potent ZIKV-specific neutralization in vitro without binding or neutralizing activity against strains 1 to 4 of dengue virus, the closest relative to ZIKV. These two antibodies provided postexposure protection to mice in vivo. Structural studies revealed that Z23 and Z3L1 bound to tertiary epitopes in envelope protein domain I, II, or III, indicating potential targets for ZIKV-specific therapy. Our results suggest the potential of antibody-based therapeutics and provide a structure-based rationale for the design of future ZIKV-specific vaccines.
History
DepositionSep 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: Genome polyprotein
H: Antibody heavy chain
L: Antibody light chain
B: Genome polyprotein
C: Antibody heavy chain
D: Antibody light chain


Theoretical massNumber of molelcules
Total (without water)182,7616
Polymers182,7616
Non-polymers00
Water00
1
A: Genome polyprotein
H: Antibody heavy chain
L: Antibody light chain

A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)135,9954
Polymers135,9954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
2
B: Genome polyprotein
C: Antibody heavy chain
D: Antibody light chain

B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)135,9954
Polymers135,9954
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_757-x+2,y,-z+21
Unit cell
Length a, b, c (Å)128.668, 97.504, 165.753
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Genome polyprotein


Mass: 44614.547 Da / Num. of mol.: 2 / Fragment: Envelope protein, UNP residues 291-699
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: Mr 766 / Production host: Escherichia coli (E. coli) / References: UniProt: H9A910, UniProt: A0A1B0XTC8*PLUS
#2: Antibody Antibody heavy chain


Mass: 23294.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody Antibody light chain


Mass: 23471.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Alcohols, 0.1 M Buffer System 2, 50%(v/v) Precipitant Mix 2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.76→50 Å / Num. obs: 53031 / % possible obs: 99.9 % / Redundancy: 5.5 % / Net I/σ(I): 9.903
Reflection shellResolution: 2.76→2.86 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JHM, 5JHL

5jhm

5jhl


Resolution: 2.755→44.68 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 2593 4.89 %
Rwork0.2311 --
obs0.2334 53004 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.755→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12422 0 0 0 12422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512720
X-RAY DIFFRACTIONf_angle_d1.07417246
X-RAY DIFFRACTIONf_dihedral_angle_d15.5084588
X-RAY DIFFRACTIONf_chiral_restr0.0751946
X-RAY DIFFRACTIONf_plane_restr0.0042212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.755-2.80510.44451090.35732607X-RAY DIFFRACTION98
2.8051-2.85910.38791420.34162645X-RAY DIFFRACTION100
2.8591-2.91740.3451400.31452593X-RAY DIFFRACTION100
2.9174-2.98080.37231430.29852659X-RAY DIFFRACTION100
2.9808-3.05020.36071320.30252646X-RAY DIFFRACTION100
3.0502-3.12640.3431410.29032634X-RAY DIFFRACTION100
3.1264-3.21090.36331630.27192628X-RAY DIFFRACTION100
3.2109-3.30540.3431210.27192621X-RAY DIFFRACTION100
3.3054-3.4120.32481210.26662659X-RAY DIFFRACTION100
3.412-3.53390.26931790.24482625X-RAY DIFFRACTION100
3.5339-3.67540.26391530.23622634X-RAY DIFFRACTION100
3.6754-3.84250.29471290.22982678X-RAY DIFFRACTION100
3.8425-4.0450.24991300.22292663X-RAY DIFFRACTION100
4.045-4.29830.2638900.20062694X-RAY DIFFRACTION100
4.2983-4.62980.22971340.18342661X-RAY DIFFRACTION100
4.6298-5.09510.20641440.1842680X-RAY DIFFRACTION100
5.0951-5.8310.23641230.2042691X-RAY DIFFRACTION100
5.831-7.34120.25341570.21842668X-RAY DIFFRACTION100
7.3412-44.68560.25751420.20362725X-RAY DIFFRACTION99
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)
11.4061-0.12350.93820.1917-0.06781.1954-0.00710.22630.0731-0.0815-0.0113-0-0.11290.0854-0.00190.24410.0068-0.00540.08320.04020.2096109.8119-57.0249225.368
2-0.0620.08370.01551.2905-0.12160.2640.0278-0.01370.00320.01270.018-0.03820.0088-0.04560.00130.11670.00880.01720.1056-0.00890.2303141.4462-101.9007252.5749
30.37830.2039-0.00840.89420.04150.48510.0091-0.0942-0.02910.23980.00270.1060.0306-0.0387-0.00050.23580.00560.07910.14410.02870.2199133.0279-103.3466269.0994
40.2973-0.01930.61290.3350.16291.81290.0983-0.2686-0.0739-0.0342-0.00880.09010.3135-0.42550.00010.4201-0.1221-0.06460.59220.0090.3866104.9427-60.1692147.8957
50.4545-0.05560.32330.82010.13350.2049-0.1493-0.03510.0236-0.0975-0.00260.2217-0.2093-0.0495-0.01190.49620.0937-0.08040.6478-0.04530.292122.3523-15.3651185.6202
60.399-0.32770.13581.11510.11320.5282-0.064-0.06270.0747-0.2324-0.049-0.1718-0.1487-0.0123-0.0010.34450.00840.00590.48630.00710.2641140.6671-13.8055182.3164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain L
4X-RAY DIFFRACTION4chain B
5X-RAY DIFFRACTION5chain C
6X-RAY DIFFRACTION6chain D

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