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- PDB-7lsf: Crystal structure of the human neutralizing antibody Fab fragment... -

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Basic information

Entry
Database: PDB / ID: 7lsf
TitleCrystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Western Subtype)
Components
  • Envelope protein E
  • T025 Fab Heavy Chain
  • T025 Fab Light Chain
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Tick-borne encephalitis virus / antibody / EDIII / TBEV / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


protein dimerization activity / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
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 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
Biological speciesHomo sapiens (human)
Tick-borne encephalitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKeeffe, J.R. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: J.Exp.Med. / Year: 2021
Title: Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease.
Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / ...Authors: Agudelo, M. / Palus, M. / Keeffe, J.R. / Bianchini, F. / Svoboda, P. / Salat, J. / Peace, A. / Gazumyan, A. / Cipolla, M. / Kapoor, T. / Guidetti, F. / Yao, K.H. / Elsterova, J. / Teislerova, D. / Chrdle, A. / Honig, V. / Oliveira, T. / West, A.P. / Lee, Y.E. / Rice, C.M. / MacDonald, M.R. / Bjorkman, P.J. / Ruzek, D. / Robbiani, D.F. / Nussenzweig, M.C.
History
DepositionFeb 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: T025 Fab Heavy Chain
L: T025 Fab Light Chain
E: Envelope protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9186
Polymers61,7803
Non-polymers1383
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-52 kcal/mol
Surface area23190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.542, 66.730, 91.210
Angle α, β, γ (deg.)90.000, 94.640, 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

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Protein , 1 types, 1 molecules E

#3: Protein Envelope protein E


Mass: 13520.290 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E3UMN9

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Antibody , 2 types, 2 molecules HL

#1: Antibody T025 Fab Heavy Chain


Mass: 24834.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#2: Antibody T025 Fab Light Chain


Mass: 23424.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 122 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium citrate tribasic dihydrate pH 5.0, 10% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.24→90.91 Å / Num. obs: 31036 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.994 / Χ2: 0.96 / Net I/σ(I): 8.8
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 6 % / Num. unique obs: 2897 / CC1/2: 0.838 / % possible all: 98

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX1.18.2_3874refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GHW, 4OGX, 6J5F

2ghw

4ogx

6j5f


Resolution: 2.24→90.91 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.707
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 1539 4.96 %
Rwork0.1893 29460 -
obs0.1912 30999 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.97 Å2
Refinement stepCycle: LAST / Resolution: 2.24→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3995 0 8 119 4122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00754104
X-RAY DIFFRACTIONf_angle_d0.95185590
X-RAY DIFFRACTIONf_chiral_restr0.0535625
X-RAY DIFFRACTIONf_plane_restr0.0052721
X-RAY DIFFRACTIONf_dihedral_angle_d17.44551472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.320.26281390.23792713X-RAY DIFFRACTION97.87
2.32-2.40.31221450.24652677X-RAY DIFFRACTION97.88
2.4-2.50.30761470.25732627X-RAY DIFFRACTION96.89
2.5-2.610.32111170.23932616X-RAY DIFFRACTION94.18
2.61-2.750.26641430.22542688X-RAY DIFFRACTION97.92
2.75-2.920.26381270.21562716X-RAY DIFFRACTION97.5
2.92-3.140.26811590.21152609X-RAY DIFFRACTION95.22
3.14-3.460.24111350.18932705X-RAY DIFFRACTION97.86
3.46-3.960.2121590.16912698X-RAY DIFFRACTION97.51
3.96-4.990.16721310.14112678X-RAY DIFFRACTION96.63
4.99-90.910.16581370.16872733X-RAY DIFFRACTION95.48
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)
16.81198766909-0.664790785022-2.961779751120.710968131181-0.2348603245942.172568744760.219851814776-0.05082414435610.502111445562-0.124676701031-0.0039177834837-0.0410815235478-0.345673675507-0.17220834845-0.258098538310.3137669753450.03138269213220.02218739978730.18151426222-0.03128153146910.30990686453217.321310576612.253788757844.0400402899
23.445627441190.48121037662-2.123586140241.425355604670.5344137173433.07159060886-0.0851670458358-0.0998444325462-0.0212238923816-0.02726212473560.0577138407118-0.252272774917-0.05047494001580.1284173741780.04417925247980.2059707369340.00909247190370.009900217932790.1892665026775.09327127444E-50.2886042733219.34092433785.2599600048346.6893342487
32.139077663970.307915804577-0.8299399897462.90580716898-0.3367349308423.192157927850.227557219030.5674153629620.461281277916-0.44943827276-0.09815508042940.343625624091-0.216451865037-0.342012492204-0.1764134569770.2951842490320.08612112816820.0006183342767280.5128314774610.06834774393820.31642022942924.84798176111.4434118165912.926384817
45.058598724790.4519894819572.110980554165.402504157644.106167341948.64772622243-0.07427822386370.5027783602770.922622024415-0.882350449373-0.4360311852390.400597088131-1.475968790640.08145892561640.4110982005010.4521362681560.07221435107910.06363877623020.3605001311440.1363732974630.55356612449527.447008186910.172871100714.9581450299
52.06371762212-1.911513138651.875628267771.88412836837-2.499595885818.21984128543-0.02277354828470.0876265275576-0.304053585757-0.1766604359020.122650725603-0.00333150979655-0.05014841224920.0477891759978-0.1136685960850.209067394372-0.04059540422040.02175153796710.253524348526-0.02467796996870.4159043477067.95940196951-16.10949829836.4946844463
63.094101787120.665977976349-0.267753055833.642503419220.2111198186793.3134382175-0.02516655493080.33899160034-0.141607655785-0.3188465673740.03385601171760.289213448492-0.0107218387184-0.320222210734-0.02522330163410.2052958671016.08714725015E-5-0.006172370380030.26351031372-0.02708459308960.2682211548393.34985869553-8.9161551219240.1351913765
71.07349483096-0.406118776311-1.699951956660.4329822290392.378482334956.23586794738-0.1092987929090.312749610159-0.2211136835480.0632517518653-0.05453566953410.00275344973360.552798534233-0.228845430381-0.09950026514250.315245424253-0.00925150498347-0.001138173133450.263735778135-0.03731260091040.29621736175311.3114750549-11.625709761336.6348461383
86.35125181919-0.222707969387-1.439865816141.984603574750.4908014189872.848195747190.1141718985220.6041887584690.301112325493-0.1974371085190.03521230949010.0314225684243-0.112791441339-0.084288237806-0.170017367230.251731122520.0203066331808-0.014439681270.368858184256-0.00696978170130.19210578230729.4195333258-9.3855138247512.292002895
95.57805812803-0.027343415924-0.1657338999342.296348528540.8430633970862.697794061420.06802674776690.347520734690.482487994932-0.158115770027-0.06130081520460.159109786905-0.0628652913242-0.453288058586-0.01609704804980.244726085178-0.0197455270212-0.002598939482670.3242578660540.07439693460380.16945537154324.0636328669-11.78492050817.7733697485
102.8663317016-1.68335123813-0.5071648693021.579749178430.3657328899242.575216378020.130816039350.838560220736-0.125756267285-0.30639232572-0.133712907119-0.00162102244264-0.005899403313780.079617758687-0.003903971025970.2738500635840.04604835278060.01190424510550.522942677226-0.03816157726780.22857972711134.3035857044-13.77615339129.12039466209
112.03463849362-1.02832992134-1.727297448811.934973445670.1105735194016.324540255360.215662088366-0.422482350129-0.1164508010550.40003854545-0.1674688498180.2310210478470.814311569867-0.2190302453710.01133517371380.413800745117-0.149268643090.03000779254320.394973171221-0.0231915317880.2601298675890.5835812175140.071967847904871.0926695011
120.9472663933070.58702089327-0.7102714394344.567754568113.611402423124.920751031360.100809749847-0.1577958974640.05220139581480.586915459195-0.1014629995140.1891592153220.492620042659-0.147075711245-0.01626353942580.238367281746-0.01680204158720.008405485010480.3489002826830.0662586511630.244633437652.980720383955.2180244362671.7299888528
134.60720502485-0.510105775032-1.57259292882.611357936871.671867643374.644289663990.0247101208954-0.210913161662-0.06084502475460.521879560072-0.3561052202650.1677836677320.616670375732-0.7679477305740.3155306797560.315629616508-0.07909205389770.07283099734130.45252952043-0.01080353532880.240366582855-1.626393613994.3507516995974.8969083568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 33 )HA1 - 331 - 33
22chain 'H' and (resid 34 through 118 )HA34 - 11834 - 125
33chain 'H' and (resid 119 through 195 )HA119 - 195126 - 200
44chain 'H' and (resid 196 through 213 )HA - B196 - 301201
55chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
66chain 'L' and (resid 19 through 90 )LC19 - 9019 - 90
77chain 'L' and (resid 91 through 113 )LC91 - 11391 - 115
88chain 'L' and (resid 114 through 150 )LC114 - 150116 - 152
99chain 'L' and (resid 151 through 174 )LC151 - 174153 - 176
1010chain 'L' and (resid 175 through 213 )LC175 - 213177 - 215
1111chain 'E' and (resid 303 through 325 )ED303 - 3251 - 23
1212chain 'E' and (resid 326 through 361 )ED326 - 36124 - 59
1313chain 'E' and (resid 362 through 396 )ED362 - 39660 - 94

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