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- PDB-6ute: Crystal structure of Z032 Fab in complex with WNV EDIII -

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Basic information

Entry
Database: PDB / ID: 6ute
TitleCrystal structure of Z032 Fab in complex with WNV EDIII
Components
  • Envelope domain III
  • Z032 Fab heavy chain
  • Z032 Fab light chain
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


immunoglobulin complex / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity ...immunoglobulin complex / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / adaptive immune response / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin-like - #350 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / Genome polyprotein, Flavivirus ...Immunoglobulin-like - #350 / : / : / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Flavivirus NS3 helicase, C-terminal helical domain / 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. / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / 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 superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set 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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa light chain / Envelope protein E / Genome polyprotein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
West Nile virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEsswein, S.R. / Gristick, H.B. / Keeffe, J.R. / Bjorkman, P.J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01-1-ROCKU.AI138938 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM007616-40 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F30AI147579 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008042 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Structural basis for Zika envelope domain III recognition by a germline version of a recurrent neutralizing antibody.
Authors: Esswein, S.R. / Gristick, H.B. / Jurado, A. / Peace, A. / Keeffe, J.R. / Lee, Y.E. / Voll, A.V. / Saeed, M. / Nussenzweig, M.C. / Rice, C.M. / Robbiani, D.F. / MacDonald, M.R. / Bjorkman, P.J.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Z032 Fab heavy chain
D: Z032 Fab light chain
S: Envelope domain III
A: Z032 Fab heavy chain
B: Z032 Fab light chain
E: Z032 Fab heavy chain
F: Z032 Fab light chain
G: Z032 Fab heavy chain
H: Z032 Fab light chain
I: Z032 Fab heavy chain
J: Z032 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,67916
Polymers253,21811
Non-polymers4605
Water0
1
C: Z032 Fab heavy chain
D: Z032 Fab light chain
S: Envelope domain III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1465
Polymers58,9623
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Z032 Fab heavy chain
B: Z032 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6563
Polymers48,5642
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-21 kcal/mol
Surface area19590 Å2
MethodPISA
3
E: Z032 Fab heavy chain
F: Z032 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6563
Polymers48,5642
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-23 kcal/mol
Surface area19110 Å2
MethodPISA
4
G: Z032 Fab heavy chain
H: Z032 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,5642
Polymers48,5642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area20140 Å2
MethodPISA
5
I: Z032 Fab heavy chain
J: Z032 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6563
Polymers48,5642
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-20 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.230, 114.020, 127.260
Angle α, β, γ (deg.)90.000, 109.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody
Z032 Fab heavy chain


Mass: 24844.746 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody
Z032 Fab light chain


Mass: 23719.354 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#3: Protein Envelope domain III


Mass: 10397.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) West Nile virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q06C97, UniProt: Q9Q6P4*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→39.99 Å / Num. obs: 57405 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 54.27 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.095 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 3.1 % / Num. unique obs: 5695 / CC1/2: 0.64 / Rpim(I) all: 0.504 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VIG, 1ZTX

5vig

1ztx


Resolution: 2.9→39.99 Å / SU ML: 0.4274 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2641 2848 4.96 %
Rwork0.2232 54542 -
obs0.2252 57390 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.41 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17225 0 30 0 17255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001817663
X-RAY DIFFRACTIONf_angle_d0.539324019
X-RAY DIFFRACTIONf_chiral_restr0.04122701
X-RAY DIFFRACTIONf_plane_restr0.00443058
X-RAY DIFFRACTIONf_dihedral_angle_d11.343110499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.950.33361720.29832679X-RAY DIFFRACTION99.51
2.95-30.33871620.29122681X-RAY DIFFRACTION99.51
3-3.060.331390.28842706X-RAY DIFFRACTION98.96
3.06-3.120.32091520.28962649X-RAY DIFFRACTION99.26
3.12-3.190.30431170.27472742X-RAY DIFFRACTION99.41
3.19-3.270.33111270.2682706X-RAY DIFFRACTION99.06
3.27-3.350.29531500.27822745X-RAY DIFFRACTION99.93
3.35-3.440.3091610.24982701X-RAY DIFFRACTION99.86
3.44-3.540.29661430.23512719X-RAY DIFFRACTION99.9
3.54-3.650.29291150.23292738X-RAY DIFFRACTION99.96
3.65-3.780.29071430.23762733X-RAY DIFFRACTION99.93
3.78-3.940.27641570.23812689X-RAY DIFFRACTION99.86
3.94-4.110.25681550.22322717X-RAY DIFFRACTION99.86
4.11-4.330.25441370.2042728X-RAY DIFFRACTION99.93
4.33-4.60.21611500.17572737X-RAY DIFFRACTION99.93
4.6-4.960.20261130.18372786X-RAY DIFFRACTION100
4.96-5.450.24391300.19252753X-RAY DIFFRACTION99.97
5.45-6.240.26821180.22132771X-RAY DIFFRACTION99.93
6.24-7.850.24111620.22352749X-RAY DIFFRACTION99.9
7.85-39.990.20241450.17572813X-RAY DIFFRACTION99.63
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)
11.841876966731.33415290957-0.3717168907693.53736159506-1.288364798661.507069684770.0878420614621-0.4562591856950.01005525625980.578247526728-0.269173257188-0.322043018296-0.2059805537790.1235897870950.1815950196880.5568704958160.0204177596645-0.06304021801380.4792359539270.02039425325820.279752185078-25.470898559414.3204940713-11.1497323434
22.139164028721.3733233616-0.03601559547793.01547016754-0.5010812092671.35650976972-0.0295419231577-0.0004365772956980.2048707080420.0148256989937-0.149927185046-0.220981863305-0.178901763154-0.1237282385840.1755079449490.4602871024980.06464155609870.04631495608620.3062951138730.00933600178650.319540562866-30.287769348121.0243301554-27.5076845634
33.69121680162-2.00864028863-1.264035399482.43806123475-0.09816881483353.02421904826-0.126347002409-0.453095002454-0.4693771499240.3518702235950.329801521846-0.2171098755870.796306189958-0.406990211812-0.1835833379420.829205854517-0.226343584668-0.1947574846340.7407501944330.2311091446110.73667561903-50.9459252556-21.9858791321-13.2973134487
42.57196226314-1.74818245414-2.352540063082.815892206822.133042541163.044923550040.122915968846-0.2624485617030.154465403986-0.2537480412430.138800074289-0.306888824124-0.2693710695290.550204334754-0.2556972967410.450471805641-0.0442457114753-0.05196119057090.362776841561-0.03918652548660.309719312747-8.16128015151-2.94433398151-50.6055506967
51.23438792081-0.348868217208-0.8244023762571.770777611480.7769174571591.13591379159-0.0573001815646-0.115666710294-0.00671494050439-0.2159919368810.0675191592814-0.04514922804310.1227257411220.208073608336-0.004582549955670.545683394330.006635662915330.01009352734670.2372039634090.002141591575750.267533485563-18.2802314319-12.7292738818-62.1246276411
61.191149039750.348938155413-0.9665769573462.52924245575-2.096110557932.63609193341-0.1432683637860.0390124872807-0.0413675802525-0.190653083601-0.0838491146657-0.2534089307460.187897627142-0.08903047224050.2111673385360.466507246967-0.03102018588360.02871006825890.258467886023-0.0463584210810.366366046494-32.3641886966-40.2395946481-37.2407744308
70.4894731105960.111236784857-0.5506739241242.53785654467-2.320385468183.62884251967-0.0346564421754-0.04130078263270.117988113037-0.09324930901920.1574689386230.2465417754260.248034069019-0.311415620512-0.1326651027070.417742523164-0.04097021189420.00380055834620.26802875692-0.009079509905910.397429144824-50.4518081304-39.9346413775-33.4134516224
82.17881853090.292230421214-0.8848806242141.183438478520.1106282653671.808116343830.0729819650519-0.6228786160820.0939723649570.216249663205-0.182858842433-0.192741150021-0.04899089278790.3174730313490.07547187821560.559701265456-0.0888604654102-0.06550520875780.3765394086190.01421049174610.471657965191-5.90333324882-44.017084995-33.0356361879
93.11881848476-0.338403433441-0.7066768108721.102223224010.3517408011583.76259262731-0.118353091005-1.03112901553-0.4502847174360.444468386439-0.062270274517-0.4045767584440.2234665035810.2396703164250.2670270509240.60385869419-0.0452068317711-0.1167004499610.6939866403370.2282117344620.71303120531810.1168580587-49.211691183-26.3657400969
102.68817635043-0.417919932544-0.1394672483582.61304182162-1.048964564011.104995028960.159844293186-0.3053421602840.232249520247-0.0001729879526160.02479363873790.175162425258-0.0854849696942-0.00504329773929-0.1804808435030.42719582045-0.02448397977960.03610116944870.767913408536-0.09860614848530.38045507724110.89807911925.02774944608-34.5161948736
112.03445062927-1.617842086060.1363495717164.35985172618-0.08329008571041.10224229417-0.112591928986-0.6141299292010.543727244620.4412910540940.138390449331-0.295547653361-0.297656804679-0.0356493721411-0.01752877677440.479862618374-0.03936455539250.009014267115070.726772700359-0.1549897621480.58230660879325.72141879976.92169722168-24.6696356199
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and resid 1 through 213)
2X-RAY DIFFRACTION2(chain 'D' and resid 1 through 213)
3X-RAY DIFFRACTION3(chain 'S' and resid 303 through 400)
4X-RAY DIFFRACTION4(chain 'A' and resid 1 through 214)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 213)
6X-RAY DIFFRACTION6(chain 'E' and resid 1 through 213)
7X-RAY DIFFRACTION7(chain 'F' and resid 1 through 213)
8X-RAY DIFFRACTION8(chain 'G' and resid 1 through 214)
9X-RAY DIFFRACTION9(chain 'H' and resid 1 through 213)
10X-RAY DIFFRACTION10(chain 'I' and resid 1 through 215)
11X-RAY DIFFRACTION11(chain 'J' and resid 1 through 213)

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