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

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Basic information

Entry
Database: PDB / ID: 7lse
TitleCrystal structure of the human neutralizing antibody Fab fragment T025 bound to TBEV EDIII (Far Eastern 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


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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 / 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 / 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 / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
: / Flavivirus envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / 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 envelope glycoprotein E, stem/anchor domain / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / : / 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 / 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 / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Tick-borne encephalitis virus Far Eastern subtype
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 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

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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)61,6424
Polymers61,5503
Non-polymers921
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-27 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.960, 69.720, 180.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11E-506-

HOH

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Components

#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)
#3: Protein Envelope protein E /


Mass: 13290.007 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tick-borne encephalitis virus Far Eastern subtype
Strain: Sofjin / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07720
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
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: 2.91 Å3/Da / Density % sol: 57.68 %
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: 2.35→90.1 Å / Num. obs: 30383 / % possible obs: 99.2 % / Redundancy: 11.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.058 / Rrim(I) all: 0.205 / Net I/σ(I): 8.6 / Num. measured all: 362021 / Scaling rejects: 39
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.891 / Num. unique obs: 2950 / CC1/2: 0.853 / Rpim(I) all: 0.261 / Rrim(I) all: 0.929 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OGX, 6J5F

4ogx

6j5f


Resolution: 2.35→90.1 Å / SU ML: 0.2406 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3269
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2105 1586 5.23 %
Rwork0.1726 28740 -
obs0.1745 30326 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.9 Å2
Refinement stepCycle: LAST / Resolution: 2.35→90.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3961 0 6 202 4169
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00774064
X-RAY DIFFRACTIONf_angle_d0.94645535
X-RAY DIFFRACTIONf_chiral_restr0.0542619
X-RAY DIFFRACTIONf_plane_restr0.006713
X-RAY DIFFRACTIONf_dihedral_angle_d18.59081457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.430.26581580.21732574X-RAY DIFFRACTION99.45
2.43-2.510.25621410.21192579X-RAY DIFFRACTION99.74
2.51-2.620.28021650.20912560X-RAY DIFFRACTION99.49
2.62-2.730.22561390.19642552X-RAY DIFFRACTION97.22
2.73-2.880.22411390.19622596X-RAY DIFFRACTION99.82
2.88-3.060.22691520.18892596X-RAY DIFFRACTION99.75
3.06-3.30.24311310.18272582X-RAY DIFFRACTION98.15
3.3-3.630.19411320.16382637X-RAY DIFFRACTION98.93
3.63-4.150.19041490.15892640X-RAY DIFFRACTION99.61
4.15-5.230.18121430.13472639X-RAY DIFFRACTION97.65
5.23-90.10.1791370.17182785X-RAY DIFFRACTION97.66
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)
11.031285854770.4333165239620.01600800860281.003282626670.1506301452712.11897234925-0.0200677167601-0.1047810641360.3301937467420.1833854892170.0169613047263-0.00712609635773-0.2669559655820.262348216879-0.09612620504190.32172485161-0.00834127334006-0.02213553498020.213300313392-0.013127103630.335924748438-23.0415794007-18.315410508740.8096244376
24.431584348010.0002364224916271.106634289682.06586763030.2841241072635.41195081545-0.0212074743969-0.2925074436240.1346474436650.2222355538560.02755521312230.1608416821920.45204166097-0.337791378899-0.02777265700440.1939379049720.002615353221180.006853786195770.169833874801-0.04417036113170.188524228422-27.3172435758-27.581070286237.1326972072
37.994227446911.18763406167-2.50005924832.7992464952-4.308229686656.76795399559-0.08161244697770.1204564787490.0461187991292-0.2196882269940.1153589927150.6078311004030.343239022474-0.706250934430.04820920784630.323239450723-0.04050189985530.05814707067120.325377640077-0.03725602021330.294444462847-33.8839751482-25.026105859339.8192150815
43.97443194612-1.21731445547-1.114919231190.424488455980.9938094543438.56670813959-0.3614749459310.03493818023650.09344014687150.3427469417430.1873675643950.213616425853-0.0124748986183-0.6395171803590.2040419732380.292540641617-0.00705342280327-0.01867820223720.21239592004-0.0579775729980.372772140235-29.9527382807-20.993449204543.658662328
50.828227158839-0.06795870772450.6988700701990.581732224032-1.320235644033.29879299037-0.135550384409-0.081027519340.1047213682040.2453545003450.0733139130702-0.143499623878-0.5790611746210.1485421520470.06907119137560.3395961707450.0319704903422-0.04216883026920.258085677991-0.03888110758050.31837031754-18.2178073348-26.191488474248.5454549844
64.16471630867-1.22316239989-0.6022385505522.804315257611.32475134645.603478648840.1785362044990.374390630560.50853192-0.0525570814843-0.305013711058-0.442653650399-0.723519787712-0.02475284153740.1467957476720.3457118598850.00348094707831-0.07728589515320.2465745278610.04678000743170.395387986685-6.14254690353-29.483465520364.4099554042
73.69301403882-2.127617960730.1922076347652.4758882985-0.255356398273.388588227640.0642563529286-0.5532575795871.589371525770.099026170557-0.221006900737-0.69623769249-1.041557296820.07267135404240.2536114658270.733557165472-0.0208999165693-0.08466236268730.386268008532-0.03223246683350.637662847862-2.62817974403-21.494879302668.5972736903
88.459321980941.00200904993.578527712482.36050148125-0.3917015845035.15706150501-0.236803436134-0.286238645751-0.2216803530470.02655795530240.161689642601-0.2038553813150.6408487632120.4120338983550.03282613922110.4815077208670.1481889201110.06770030898360.2589291926520.045281903280.33482297178-11.7285148582-47.014065337738.3564319838
92.826335001-0.8207686580360.7128576866483.446462916670.2249518000685.21792237659-0.24275202799-0.03320634698020.072839822390.1835919683040.233990425194-0.436009150890.1712712781980.441703492976-0.01070271897080.1881464650140.0332614057841-0.01407343424760.196774823825-0.01968453222340.26116609795-13.2180265079-38.179119892831.8504408597
103.56058452563-2.07539634623-1.088562066242.995806712170.00245603202665.44138741874-0.1013201618133.57506843713E-50.2818201333150.4137130976690.195789478813-0.7140143416060.5892238419460.604608148159-0.1349321855260.3651362298730.0696527052941-0.0545684961260.198583964232-0.03102261969430.420046733674-9.71843486927-41.840771579733.5262110865
113.84882314788-2.394577358634.014594215651.59757830131-2.960310137575.991750216030.211871790529-0.240186598875-0.301005502511-0.1899594747310.0901672976410.02109395374680.599118598484-0.00376582613059-0.2264955033320.2699713307620.0414114385710.005012149396970.202986614471-0.01336491596390.304163623614-13.4684761226-42.171125296341.1403450081
122.65123138868-0.22276408924-1.612381836941.79647891154-0.3361662345366.56847669850.0587766402451-0.02027851297480.08882796119430.175102593593-0.117982068459-0.170257488483-0.01055772652840.09466289696770.05791722360360.2269436064920.0398832069127-0.07708881644920.242601183525-0.006342845184870.288589359755-6.47473734452-42.801854275770.5308560125
131.4155597223-0.5391239392850.7749204847791.796706850860.1175446090683.668881350040.05745587129090.223350987408-0.132076664517-0.106791565097-0.1356037215480.1615936334690.0587644072385-0.312691095820.03539785486010.164859129031-0.0237841884314-0.006371804554190.278327240825-0.03564712990820.205260526732-33.7882984246-31.231447562212.633624869
144.69262419765-0.2761441278952.791531655665.016760382451.54469304352.99747921398-0.06492470777980.2201517407060.219545640534-0.3116320754770.04815053224950.266099294563-0.470726633744-0.059609470730.1142264669520.3002417346260.02020125385680.02651964566060.428218769459-0.005592694167850.205163615271-38.7570050938-19.18225274479.42649107378
153.84780599818-0.1050768879992.470193843152.34957050751-0.8030110217899.063661556960.300475182631-0.0512834718566-0.203503426998-0.2183847308320.0174103231623-0.02327747459960.610846088157-0.87060209694-0.4257997951770.206112392302-0.04035931877560.0003596266026480.38986186794-0.01878894595470.238912034174-38.9543089662-31.293641655211.2834879896
164.309997973110.257876049753.15380524695.09419152044-0.1367111347119.180882302380.03264539299090.6235237170420.364535103776-0.636021886161-0.334991076437-0.240516328743-0.558833372170.2443522128130.2447525407010.2802451597990.02601422891410.02237084963890.3596380201850.02781745562630.204951619941-32.6094207541-21.86958966753.21700294175
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 59 )HA34 - 5934 - 60
33chain 'H' and (resid 60 through 72 )HA60 - 7261 - 73
44chain 'H' and (resid 73 through 87 )HA73 - 8774 - 91
55chain 'H' and (resid 88 through 134 )HA88 - 13492 - 134
66chain 'H' and (resid 135 through 188 )HA135 - 188135 - 188
77chain 'H' and (resid 189 through 213 )HA189 - 213189 - 213
88chain 'L' and (resid 1 through 18 )LC1 - 181 - 18
99chain 'L' and (resid 19 through 61 )LC19 - 6119 - 61
1010chain 'L' and (resid 62 through 90 )LC62 - 9062 - 90
1111chain 'L' and (resid 91 through 113 )LC91 - 11391 - 113
1212chain 'L' and (resid 114 through 213 )LC114 - 213114 - 213
1313chain 'E' and (resid 303 through 341 )ED303 - 3411 - 39
1414chain 'E' and (resid 342 through 361 )ED342 - 36140 - 59
1515chain 'E' and (resid 362 through 378 )ED362 - 37860 - 76
1616chain 'E' and (resid 379 through 395 )ED379 - 39577 - 93

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