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- PDB-6dfj: Crystal structure of anti-Zika antibody Z021 bound to DENV-1 enve... -

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Basic information

Entry
Database: PDB / ID: 6dfj
TitleCrystal structure of anti-Zika antibody Z021 bound to DENV-1 envelope protein DIII
Components
  • Dengue 1 Envelope DIII domain
  • anti-Zika antibody Z021, Heavy Chain
  • anti-Zika antibody Z021, Light Chain
KeywordsIMMUNE SYSTEM / antibody / Fab / Zika / Dengue / recurrent / neutralizing
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Immunoglobulin-like - #350 / 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 ...Immunoglobulin-like - #350 / 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/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Dengue virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.07 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J.
CitationJournal: Cell Rep / Year: 2018
Title: A Combination of Two Human Monoclonal Antibodies Prevents Zika Virus Escape Mutations in Non-human Primates.
Authors: Keeffe, J.R. / Van Rompay, K.K.A. / Olsen, P.C. / Wang, Q. / Gazumyan, A. / Azzopardi, S.A. / Schaefer-Babajew, D. / Lee, Y.E. / Stuart, J.B. / Singapuri, A. / Watanabe, J. / Usachenko, J. / ...Authors: Keeffe, J.R. / Van Rompay, K.K.A. / Olsen, P.C. / Wang, Q. / Gazumyan, A. / Azzopardi, S.A. / Schaefer-Babajew, D. / Lee, Y.E. / Stuart, J.B. / Singapuri, A. / Watanabe, J. / Usachenko, J. / Ardeshir, A. / Saeed, M. / Agudelo, M. / Eisenreich, T. / Bournazos, S. / Oliveira, T.Y. / Rice, C.M. / Coffey, L.L. / MacDonald, M.R. / Bjorkman, P.J. / Nussenzweig, M.C. / Robbiani, D.F.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-Zika antibody Z021, Heavy Chain
L: anti-Zika antibody Z021, Light Chain
E: Dengue 1 Envelope DIII domain


Theoretical massNumber of molelcules
Total (without water)59,3933
Polymers59,3933
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-27 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.540, 91.600, 187.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody anti-Zika antibody Z021, Heavy Chain


Mass: 24787.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human)
#2: Antibody anti-Zika antibody Z021, Light Chain


Mass: 23815.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293-6E / Production host: Homo sapiens (human)
#3: Protein Dengue 1 Envelope DIII domain


Mass: 10790.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus 1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8BE58, UniProt: Q8BE39*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium citrate pH 4.8, 28% Jeffamine ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.07→93.57 Å / Num. obs: 31907 / % possible obs: 99.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 50.34 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.022 / Net I/σ(I): 15
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 14638 / CC1/2: 0.724 / Rpim(I) all: 0.339 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.07→50.51 Å / SU ML: 0.2929 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7063
RfactorNum. reflection% reflection
Rfree0.2315 1566 4.92 %
Rwork0.1838 --
obs0.1862 31846 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.96 Å2
Refinement stepCycle: LAST / Resolution: 2.07→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4065 0 0 126 4191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00474168
X-RAY DIFFRACTIONf_angle_d0.75185677
X-RAY DIFFRACTIONf_chiral_restr0.0505640
X-RAY DIFFRACTIONf_plane_restr0.0042724
X-RAY DIFFRACTIONf_dihedral_angle_d11.50512498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.140.33341370.27332708X-RAY DIFFRACTION99.61
2.14-2.220.27461190.2522744X-RAY DIFFRACTION99.44
2.22-2.310.31021450.23992712X-RAY DIFFRACTION99.27
2.31-2.410.29241470.22662718X-RAY DIFFRACTION99.76
2.41-2.540.26531400.23142743X-RAY DIFFRACTION99.86
2.54-2.70.28861270.22542730X-RAY DIFFRACTION99.86
2.7-2.910.28831510.23212739X-RAY DIFFRACTION99.24
2.91-3.20.28621350.23092758X-RAY DIFFRACTION99.66
3.2-3.660.26821410.19352776X-RAY DIFFRACTION99.29
3.66-4.610.19661570.1512787X-RAY DIFFRACTION99.8
4.61-50.520.18171670.14482865X-RAY DIFFRACTION98.99
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)
15.506143131732.629568719054.73736815097.297184789695.325786543648.070824757150.2488132568990.191099077825-0.488617090963-0.696079381210.0681969727627-0.0665077209886-0.5239020770420.245760845753-0.3278636161380.795654886087-0.025957482931-0.01322333534710.7696035816640.001908514092590.5273555235638.6582716858753.256379320137.8460786449
23.24711686572-0.0840801642411.419503230063.801533898290.3807769646746.60041424845-0.008596649125360.376185009445-0.529473933624-0.2499011846980.458705798328-0.3036757613840.599834735320.349174204547-0.3955456631560.350698000638-0.0391361224235-0.01727495367850.346421925879-0.07872556183940.39857637727620.319860075752.780078251667.3238579036
31.481481128970.1885263541910.620037849454.02522795291.329072094144.44190640984-0.085216983230.3824885030580.340108158253-0.6497774832170.268351925073-0.0885495083209-0.6686227740150.124226309495-0.1880729003090.415502702681-0.1161267782680.02675711627310.4169575043360.1341737288710.41267780033118.321984139574.677647742164.5428849343
47.75778299165-2.68441816752-0.7894965328163.859845966621.008183340022.53324176642-0.32991595211-0.644887706179-0.4639193460480.8109082687520.1615918651830.6476864593140.733192227487-0.1415571017670.180655981810.6390765022650.0003763024631120.1063820914770.4004064476140.04999549127290.51732693184411.495587503761.473105475395.8739381097
54.64913141399-1.72990187540.1606953310083.496354322950.07072151219234.16622905988-0.582355979771-1.064656743660.7647135261781.242272482680.331559301708-0.6192286499040.077017758544-0.04421104502170.1854712553240.7876906175630.119085949957-0.1444650129780.567504894052-0.1384235253760.60407838087518.769547566773.4588275154102.711863407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'E' and resid 298 through 396)
2X-RAY DIFFRACTION2(chain 'H' and resid 1 through 113)
3X-RAY DIFFRACTION3(chain 'L' and resid 2 through 107)
4X-RAY DIFFRACTION4(chain 'H' and resid 114 through 214)
5X-RAY DIFFRACTION5(chain 'L' and resid 108 through 212)

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