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- PDB-5jhl: Crystal structure of zika virus envelope protein in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5jhl
TitleCrystal structure of zika virus envelope protein in complex with a flavivirus broadly-protective antibody
Components
  • Antibody Heavy chain
  • antibody Light chain
  • envelope protein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / zika virus / envelope protein / flavivirus / broadly-protective antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


: / 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 ...: / 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 / 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
Viral Envelope Glycoprotein, domain 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / 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 2 / Viral Envelope Glycoprotein; domain 3 / Viral Envelope Glycoprotein, domain 3 / 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 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 envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical 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 / 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
Biological speciesZika virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDai, L. / Shi, Y. / Qi, J. / Gao, G.F.
CitationJournal: Cell Host Microbe / Year: 2016
Title: Structures of the Zika Virus Envelope Protein and Its Complex with a Flavivirus Broadly Protective Antibody.
Authors: Dai, L. / Song, J. / Lu, X. / Deng, Y.Q. / Musyoki, A.M. / Cheng, H. / Zhang, Y. / Yuan, Y. / Song, H. / Haywood, J. / Xiao, H. / Yan, J. / Shi, Y. / Qin, C.F. / Qi, J. / Gao, G.F.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Aug 10, 2016Group: Source and taxonomy
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 6, 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: Antibody Heavy chain
L: antibody Light chain


Theoretical massNumber of molelcules
Total (without water)94,3923
Polymers94,3923
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 104.856, 81.862
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein envelope protein


Mass: 45574.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus / Strain: BeH818995 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: A0A0X9QZM7*PLUS
#2: Antibody Antibody Heavy chain


Mass: 24976.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Antibody antibody Light chain


Mass: 23840.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm)
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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium chloride, 0.1 Na/K phosphate, pH 6.5, 25 % PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16275 / % possible obs: 98.6 % / Redundancy: 4.6 % / Net I/σ(I): 9
Reflection shellResolution: 3→3.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GMS

4gms


Resolution: 3→30.693 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.07
RfactorNum. reflection% reflection
Rfree0.2686 820 5.05 %
Rwork0.2277 --
obs0.2298 16253 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→30.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6087 0 0 0 6087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056237
X-RAY DIFFRACTIONf_angle_d0.9288488
X-RAY DIFFRACTIONf_dihedral_angle_d15.9892177
X-RAY DIFFRACTIONf_chiral_restr0.037970
X-RAY DIFFRACTIONf_plane_restr0.0051091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.17560.41451180.3362321X-RAY DIFFRACTION89
3.1756-3.42050.3491310.29882586X-RAY DIFFRACTION98
3.4205-3.76420.3021550.25892595X-RAY DIFFRACTION100
3.7642-4.30760.25771480.22752616X-RAY DIFFRACTION100
4.3076-5.42230.22151220.19692655X-RAY DIFFRACTION100
5.4223-30.69480.24121460.1922660X-RAY DIFFRACTION100
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)
10.24810.3827-0.74270.6907-1.03622.03160.05350.028-0.01210.1066-0.0057-0.0471-0.3022-0.08-00.5124-0.0164-0.03580.43330.0560.4231-19.717816.8595-8.4401
20.73040.5502-0.96310.4495-1.09792.24990.0599-0.00050.1043-0.11310.0430.07410.02540.046100.5082-0.025-0.01190.43630.01650.4413-21.746813.5961-0.4922
30.3483-0.02130.34650.404-0.82591.3314-0.0514-0.10260.04320.20710.0577-0.02940.07390.114-00.5357-0.0237-0.00050.5311-0.03060.5198-21.968-0.976641.526
40.3250.1932-0.09620.0089-0.33020.3178-0.05670.00460.20330.02580.13860.0283-0.01430.0479-00.5510.00960.01480.42430.02360.5371-2.583147.0192-70.1024
50.183-0.23090.23260.4395-0.50720.5779-0.44140.5961-0.2513-0.29410.3342-0.342-0.1074-0.5037-00.47520.0817-0.0340.4441-0.03880.3884-4.308235.4763-64.2842
60.0053-0.0671-0.71990.3583-0.45781.6211-0.1066-0.03620.091-0.04420.03770.0928-0.174-0.064800.3160.0388-0.02250.3398-00.3031-1.390143.0186-62.8577
70.21660.07780.32380.02470.02010.11110.05630.2030.1916-1.16630.2818-0.3315-0.3222-0.0475-00.6965-0.23250.14830.7254-0.0460.69618.973841.8077-101.348
81.0403-0.9986-0.42731.4724-1.38180.35880.07160.0171-0.2643-0.0553-0.05480.1264-0.1338-0.288-00.3801-0.0282-0.00580.5588-0.03360.569910.798342.6236-91.2808
90.84650.115-1.13860.31060.39621.0575-0.1006-0.03610.09910.3480.0774-0.18450.14530.088800.39710.0674-0.04830.29820.03020.372612.081725.1681-61.6658
100.40540.5198-0.2271.46540.2195-0.0758-0.04920.0652-0.11730.270.1348-0.1976-0.24520.045900.3271-0.00860.06240.3987-0.0880.437726.86942.3502-90.6921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 128 )
2X-RAY DIFFRACTION2chain 'A' and (resid 129 through 275 )
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 403 )
4X-RAY DIFFRACTION4chain 'H' and (resid 7 through 28 )
5X-RAY DIFFRACTION5chain 'H' and (resid 29 through 48 )
6X-RAY DIFFRACTION6chain 'H' and (resid 49 through 128 )
7X-RAY DIFFRACTION7chain 'H' and (resid 129 through 143 )
8X-RAY DIFFRACTION8chain 'H' and (resid 144 through 222 )
9X-RAY DIFFRACTION9chain 'L' and (resid 2 through 103 )
10X-RAY DIFFRACTION10chain 'L' and (resid 104 through 212 )

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