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- PDB-6uta: Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII -

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Basic information

Entry
Database: PDB / ID: 6uta
TitleCrystal structure of Z004 iGL Fab in complex with ZIKV EDIII
Components
  • Env
  • Z004 iGL Fab heavy chain
  • Z004 iGL 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 / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell surface / mRNA (nucleoside-2'-O-)-methyltransferase activity ...immunoglobulin complex / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell surface / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / adaptive immune response / RNA helicase activity / 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 / virion attachment to host cell / GTP binding / virion membrane / structural molecule activity / 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 NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2B / 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 NS3 helicase, C-terminal helical domain / 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 / Envelope glycoprotein M, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Helicase superfamily 1/2, ATP-binding domain / 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
Genome polyprotein / Env / Immunoglobulin kappa light chain / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Z004 iGL Fab heavy chain
L: Z004 iGL Fab light chain
E: Env
A: Z004 iGL Fab heavy chain
B: Z004 iGL Fab light chain
C: Env


Theoretical massNumber of molelcules
Total (without water)120,5416
Polymers120,5416
Non-polymers00
Water0
1
H: Z004 iGL Fab heavy chain
L: Z004 iGL Fab light chain
E: Env


Theoretical massNumber of molelcules
Total (without water)60,2703
Polymers60,2703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Z004 iGL Fab heavy chain
B: Z004 iGL Fab light chain
C: Env


Theoretical massNumber of molelcules
Total (without water)60,2703
Polymers60,2703
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-27 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.907, 85.907, 327.458
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULYSLYSchain 'A'AD1 - 1291 - 138
121THRTHRLYSLYSchain 'A'AD135 - 214144 - 223
231GLUGLULYSLYS(chain 'H' and (resid 1 through 129 or resid 135 through 214))HA1 - 1291 - 138
241THRTHRLYSLYS(chain 'H' and (resid 1 through 129 or resid 135 through 214))HA135 - 214144 - 223
152ASPASPARGARGchain 'B'BE1 - 2111 - 211
262ASPASPARGARGchain 'L'LB1 - 2111 - 211
173SERSERPROPRO(chain 'C' and (resid 304 through 318 or resid 321 through 403))CF304 - 3187 - 21
183THRTHRVALVAL(chain 'C' and (resid 304 through 318 or resid 321 through 403))CF321 - 34724 - 50
193METMETSERSER(chain 'C' and (resid 304 through 318 or resid 321 through 403))CF349 - 40352 - 106
2103SERSERPROPRO(chain 'E' and (resid 304 through 347 or resid 349 through 403))EC304 - 3187 - 21
2113THRTHRVALVAL(chain 'E' and (resid 304 through 347 or resid 349 through 403))EC321 - 34724 - 50
2123METMETSERSER(chain 'E' and (resid 304 through 347 or resid 349 through 403))EC349 - 40352 - 106

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody Z004 iGL Fab heavy chain


Mass: 24819.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6C4S0
#2: Antibody Z004 iGL Fab light chain


Mass: 23515.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0DOX7
#3: Protein Env


Mass: 11935.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1X9PPI0, UniProt: A0A142I5B9*PLUS

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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: 2.63 Å3/Da / Density % sol: 53.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: % w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 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: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.1→38.42 Å / Num. obs: 21992 / % possible obs: 93.6 % / Redundancy: 12.4 % / Biso Wilson estimate: 67.73 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.088 / Net I/σ(I): 9.1
Reflection shellResolution: 3.1→3.21 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1620 / CC1/2: 0.76 / Rpim(I) all: 0.491 / % possible all: 71.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VIC

5vic


Resolution: 3.1→38.42 Å / SU ML: 0.4232 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.3493
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2912 1071 4.91 %
Rwork0.2743 20746 -
obs0.2751 21817 93.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.19 Å2
Refinement stepCycle: LAST / Resolution: 3.1→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8038 0 0 0 8038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01338222
X-RAY DIFFRACTIONf_angle_d1.571511177
X-RAY DIFFRACTIONf_chiral_restr0.10081268
X-RAY DIFFRACTIONf_plane_restr0.00761421
X-RAY DIFFRACTIONf_dihedral_angle_d20.91932971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.240.43391000.36441944X-RAY DIFFRACTION72.64
3.24-3.410.35351070.35462306X-RAY DIFFRACTION84.61
3.41-3.630.35911380.31122654X-RAY DIFFRACTION97.62
3.63-3.910.37571350.32132658X-RAY DIFFRACTION97.42
3.91-4.30.26381560.27192676X-RAY DIFFRACTION98.27
4.3-4.920.2541280.22682752X-RAY DIFFRACTION99.45
4.92-6.190.24551550.24852794X-RAY DIFFRACTION99.49
6.19-38.420.25491520.25172962X-RAY DIFFRACTION98.89
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)
11.417636216831.766287784820.6801311317874.517739472420.8098015008671.08100428404-0.1142613905970.215996066457-0.187329501111-0.1734932877060.183045202126-0.135466675057-0.00503944721660.204574108986-0.08068083696130.3677582202480.02695097432150.09104741732680.318547438191-0.009968698866570.458741436595-32.21763883440.159151909711.4721472788
20.8565233803790.5117869642280.9144093645164.598791652681.837028142631.563116501380.0951803902675-0.0080761022545-0.1217529670690.276705959275-0.0871225119668-0.005392128672930.260050975633-0.0723273256133-0.02648390537980.3337839942080.02977609104730.07901432821520.3136655709090.0380458528980.484637972863-35.995087359932.186204862227.6514376285
31.882123808690.2885117015990.07564182354636.85832276960.2361269071491.34652279154-0.4265033468860.150505156170.3745484855550.2983507382410.288870280268-0.548637744321-0.4721011880950.1458002992370.1170815521290.621683120103-0.0339068122647-0.04039275421430.440593237503-0.00635096003190.815477421135-17.521594384177.212872348529.2910351613
41.344073855540.943849243899-0.4614516932773.08717315472-0.1128709895911.15019380285-0.1027742403010.146937348201-0.142937175003-0.123609993370.1684205129690.3728627357620.298249079015-0.104699567158-0.04464867253610.3812735007220.0570307147054-0.02015570758070.4009023255380.0331921932630.66790138370111.665282580938.455436454511.1679092106
50.3110794730.7951290276010.1707202000752.85543457430.8509801746451.60138624432-0.0351788798441-0.123415291382-0.2482604719850.2420650642440.0956731919826-0.001875496974230.293612099828-0.0116965030627-0.05742530533540.3681219131010.05653834785120.03212647390790.4328439478080.07299085239250.855970737367.4626547079633.342357502827.8203012932
62.94834618172-0.6453727569620.8479568823293.94535847035-0.7118734462132.037937753050.2551320605920.2980132528430.69808985247-0.0290688409218-0.226380142868-0.0272605144905-0.6438575473950.278156815493-0.06432806345620.528861491366-0.06026917542520.1875792227530.448348370241-0.002536240747620.65619028022828.519074321875.518747453929.6244666862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'H' and resid 1 through 214)
2X-RAY DIFFRACTION2(chain 'L' and resid 1 through 212)
3X-RAY DIFFRACTION3(chain 'E' and resid 304 through 404)
4X-RAY DIFFRACTION4(chain 'A' and resid 1 through 214)
5X-RAY DIFFRACTION5(chain 'B' and resid 1 through 212)
6X-RAY DIFFRACTION6(chain 'C' and resid 304 through 403)

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