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- PDB-5vic: Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Enve... -

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Basic information

Entry
Database: PDB / ID: 5vic
TitleCrystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII
Components
  • Dengue 1 Envelope DIII domain
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / Zika / Dengue / recurrent / neutralizing
Function / homology
Function and homology information


flavivirin / immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity ...flavivirin / immunoglobulin complex / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / 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 / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
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 ...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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa light chain / Genome polyprotein / Genome polyprotein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Dengue virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsKeeffe, J.R. / West Jr., A.P. / Gristick, H.B. / Bjorkman, P.J.
CitationJournal: Cell / Year: 2017
Title: Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico.
Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / ...Authors: Robbiani, D.F. / Bozzacco, L. / Keeffe, J.R. / Khouri, R. / Olsen, P.C. / Gazumyan, A. / Schaefer-Babajew, D. / Avila-Rios, S. / Nogueira, L. / Patel, R. / Azzopardi, S.A. / Uhl, L.F.K. / Saeed, M. / Sevilla-Reyes, E.E. / Agudelo, M. / Yao, K.H. / Golijanin, J. / Gristick, H.B. / Lee, Y.E. / Hurley, A. / Caskey, M. / Pai, J. / Oliveira, T. / Wunder, E.A. / Sacramento, G. / Nery, N. / Orge, C. / Costa, F. / Reis, M.G. / Thomas, N.M. / Eisenreich, T. / Weinberger, D.M. / de Almeida, A.R.P. / West, A.P. / Rice, C.M. / Bjorkman, P.J. / Reyes-Teran, G. / Ko, A.I. / MacDonald, M.R. / Nussenzweig, M.C.
History
DepositionApr 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references
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: Fab heavy chain
L: Fab light chain
E: Dengue 1 Envelope DIII domain


Theoretical massNumber of molelcules
Total (without water)59,3273
Polymers59,3273
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-31 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.225, 74.225, 190.758
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Fab heavy chain


Mass: 24984.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody Fab light chain / Immunoglobulin kappa light chain EU


Mass: 23552.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#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 type 1 (strain Nauru/West Pac/1974)
Strain: Nauru/West Pac/1974 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P17763, UniProt: Q8BE39*PLUS
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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2017
RadiationMonochromator: double crystal Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→74.23 Å / Num. obs: 15181 / % possible obs: 98.6 % / Redundancy: 10.9 % / Biso Wilson estimate: 58.66 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.235 / Rpim(I) all: 0.073 / Rrim(I) all: 0.247 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
2.7-2.8310.81.7670.5770.5541.85599.6
8.96-74.239.50.0580.9980.0190.06197.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.7 Å69.17 Å
Translation4.7 Å69.17 Å

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Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.16phasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.113 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.9
RfactorNum. reflection% reflection
Rfree0.2858 520 4.66 %
Rwork0.2346 --
obs0.2369 11151 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 239.75 Å2 / Biso mean: 59.0363 Å2 / Biso min: 30.71 Å2
Refinement stepCycle: final / Resolution: 3→37.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 0 0 3904
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033995
X-RAY DIFFRACTIONf_angle_d0.6335426
X-RAY DIFFRACTIONf_chiral_restr0.044615
X-RAY DIFFRACTIONf_plane_restr0.004687
X-RAY DIFFRACTIONf_dihedral_angle_d12.6192395
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.30170.33121400.296226022742100
3.3017-3.77910.32271250.25542586271197
3.7791-4.75970.29171280.21062631275998
4.7597-37.11550.24051270.22222812293999
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)
11.1202-0.759-0.55645.7293.5735.6750.15690.04920.2434-0.81070.6195-0.5881-1.08130.9666-0.70470.5086-0.03090.21380.65490.11350.49841.434464.3723233.2686
26.64610.7107-0.1715.81020.6736.9824-0.21130.0197-0.3201-0.24640.3623-0.7448-0.73850.2033-0.06850.29840.01980.07230.25290.01190.34238.951362.0395245.5396
33.3841-1.8226-1.00362.19971.42516.42710.093-0.45060.09940.18560.1401-0.42890.38880.646-0.16740.3269-0.06230.07560.41690.03540.472439.16760.0937241.9885
42.7709-2.36361.20363.8484-2.21953.4141-0.4847-0.00530.17470.1060.24020.1912-0.13210.07270.23920.4558-0.1445-0.01460.34630.00570.393725.858773.4815218.9861
50.97450.5646-0.30726.00651.08026.7138-0.43270.51890.3798-1.2157-0.320.5218-2.4549-0.60780.10321.2622-0.1003-0.33380.39120.11390.908220.807686.2615215.6826
64.7818-4.92532.42746.1988-1.31922.7289-0.52730.20231.6292-0.02350.0461-0.7682-0.81530.32280.48160.6678-0.17290.0190.52360.03470.572630.962578.9795212.8074
73.78651.7832-0.01322.750.22374.37860.06690.09850.0407-0.3491-0.27950.1438-0.2329-1.04150.21950.47590.11030.07930.4935-0.09890.375120.245468.7251250.4377
81.28870.32651.48420.97510.19823.6298-0.3174-0.08430.33520.00460.09370.1603-0.7479-0.4330.19130.45420.1397-0.00620.3983-0.04410.504916.893472.1319235.1278
94.0424-1.02432.61652.2111.89389.0774-0.5230.007-0.13180.40130.04320.56450.7161-1.35740.54780.6598-0.2226-0.00710.5989-0.05030.55555.526669.0893216.9111
106.5644-1.0877-2.66923.0257-0.33836.14-0.42270.47850.5228-0.03980.00510.10240.1708-0.33280.32390.455-0.0263-0.08760.22180.04270.547911.397673.3575215.5617
113.91040.0021-0.17962.4136-0.84494.7417-1.15120.18980.9796-0.41550.49590.1515-0.5212-2.5983-0.01110.76070.0005-0.27921.11810.22350.66881.628977.8977214.9984
128.1065-7.3318-6.24829.83337.06815.8859-1.0574-1.7101-0.9396-0.71190.63320.75490.13492.07040.18650.5967-0.0485-0.01130.81270.10510.561737.631451.7435259.4402
135.7566-1.54841.55632.49861.19371.6221-0.5012-1.6001-0.0340.3138-0.50850.45320.7408-1.26280.77120.89720.19230.3961.20120.11250.926136.390752.2815275.034
142.84280.3765-0.70825.0198-1.11160.48850.21880.6428-0.4860.4448-0.1068-1.1386-0.0250.57760.07530.5741-0.0010.05550.82710.13030.634339.944653.0894261.7473
153.7078-0.3581-0.42691.16730.99453.129-0.5235-0.10671.0349-0.00270.1689-0.14281.09230.34870.19641.27410.2356-0.01220.76490.18451.147538.441845.8577265.9556
162.4264-3.2466-3.14335.31265.47757.40970.2547-1.27690.3595-0.42910.7413-1.61190.25541.5249-0.3480.7848-0.0342-0.10031.27070.16520.915944.862955.3708275.4748
178.1360.36572.2997.0353-4.53039.2344-0.8719-3.04170.96671.9670.63350.8417-2.1972-0.6260.34880.81070.26610.0910.9565-0.08610.811738.402662.0114269.0944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 23 )H1 - 23
2X-RAY DIFFRACTION2chain 'H' and (resid 24 through 60 )H24 - 60
3X-RAY DIFFRACTION3chain 'H' and (resid 61 through 111 )H61 - 111
4X-RAY DIFFRACTION4chain 'H' and (resid 112 through 184 )H112 - 184
5X-RAY DIFFRACTION5chain 'H' and (resid 185 through 203 )H185 - 203
6X-RAY DIFFRACTION6chain 'H' and (resid 204 through 214 )H204 - 214
7X-RAY DIFFRACTION7chain 'L' and (resid 1 through 61 )L1 - 61
8X-RAY DIFFRACTION8chain 'L' and (resid 62 through 139 )L62 - 139
9X-RAY DIFFRACTION9chain 'L' and (resid 140 through 160 )L140 - 160
10X-RAY DIFFRACTION10chain 'L' and (resid 161 through 197 )L161 - 197
11X-RAY DIFFRACTION11chain 'L' and (resid 198 through 211 )L198 - 211
12X-RAY DIFFRACTION12chain 'E' and (resid 298 through 307 )E298 - 307
13X-RAY DIFFRACTION13chain 'E' and (resid 308 through 327 )E308 - 327
14X-RAY DIFFRACTION14chain 'E' and (resid 328 through 340 )E328 - 340
15X-RAY DIFFRACTION15chain 'E' and (resid 351 through 364 )E351 - 364
16X-RAY DIFFRACTION16chain 'E' and (resid 365 through 376 )E365 - 376
17X-RAY DIFFRACTION17chain 'E' and (resid 377 through 391 )E377 - 391

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