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- PDB-8sj6: Ara h 2.01 38B7 8F3 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8sj6
TitleAra h 2.01 38B7 8F3
Components
  • 38B7 heavy chain
  • 38B7 light chain
  • 8F3 heavy chain
  • 8F3 light chain
  • Ara h 2 allergen
KeywordsIMMUNE SYSTEM / allergy / peanut / antibody
Function / homologyNapin/ 2S seed storage protein/Conglutin / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / nutrient reservoir activity / metal ion binding / Ara h 2 allergen
Function and homology information
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.97 Å
AuthorsSpiller, B.W. / Shrem, R.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)5R01AI155668 United States
CitationJournal: J.Allergy Clin.Immunol. / Year: 2025
Title: Structural determinants of peanut induced anaphylaxis.
Authors: Smith, S.A. / Shrem, R.A. / Lanca, B.B.C. / Zhang, J. / Wong, J.J.W. / Croote, D. / Peebles Jr., R.S. / Spiller, B.W.
History
DepositionApr 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 8F3 light chain
C: 8F3 heavy chain
A: 38B7 heavy chain
B: 38B7 light chain
Q: Ara h 2 allergen


Theoretical massNumber of molelcules
Total (without water)112,1925
Polymers112,1925
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.400, 182.892, 194.175
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

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Components

#1: Antibody 8F3 light chain


Mass: 23412.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 8F3 heavy chain


Mass: 24266.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 38B7 heavy chain


Mass: 23708.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody 38B7 light chain


Mass: 23771.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#5: Protein Ara h 2 allergen


Mass: 17033.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Gene: Ara h 2 / Cell line (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A445BYI5
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: 6.43 Å3/Da / Density meas: 83.4 Mg/m3 / Density % sol: 64.99 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 21% p8K, 200 mM NaCl, 50 mM NaPi, 50 mM Citrate, pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.97→97.1 Å / Num. obs: 57338 / % possible obs: 97.5 % / Redundancy: 4.1 % / Biso Wilson estimate: 119.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10.2
Reflection shellResolution: 3.97→4.11 Å / Rmerge(I) obs: 0.652 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5774 / CC1/2: 0.799

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.0.5data processing
XDSVERSION Feb 5, 2021 BUILT=20210205data reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.97→97.09 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2938
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3018 672 4.76 %
Rwork0.2515 13441 -
obs0.2538 14113 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 144.92 Å2
Refinement stepCycle: LAST / Resolution: 3.97→97.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7501 0 0 0 7501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00157672
X-RAY DIFFRACTIONf_angle_d0.445410426
X-RAY DIFFRACTIONf_chiral_restr0.04091149
X-RAY DIFFRACTIONf_plane_restr0.00391357
X-RAY DIFFRACTIONf_dihedral_angle_d3.64231054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.97-4.280.36181570.32112608X-RAY DIFFRACTION98.61
4.28-4.710.30831220.26452683X-RAY DIFFRACTION98.49
4.71-5.390.30181200.24542684X-RAY DIFFRACTION98.18
5.39-6.790.3351400.27622681X-RAY DIFFRACTION97.68
6.79-97.090.25851330.21532785X-RAY DIFFRACTION94.62
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)
10.572851442111-1.248582098430.3076813041434.89110281393-0.2606817869233.519802057561.37425369362-0.6355289418051.35480541134-0.9027654579610.250431341197-1.66559538532-0.780544885118-0.485290311103-1.11451119281.63587404779-0.1647516695380.6151274377641.73619680301-0.02401535143681.6106439359310.946095931353.4698037949106.337741632
22.86473988133-3.75460169111.230368370017.057279543030.8900234170483.34543639680.149137105040.467146409778-0.648875668839-0.982120073206-0.543575329442-0.285557559825-0.870533010748-1.4998378287-0.5909839784631.427042801220.178758976250.02993045008861.515155012610.06839909287071.215947887364.9328108379843.2800849528105.768290804
37.1264097731-0.234068796545.341967080873.398294665913.753488437528.512909051440.734979776801-4.317768466233.1276442955-0.808241374458-0.50024179632-1.044831871790.0219130501734-0.0375942684826-0.07827297107881.38509626360.06472405053710.1678849477681.4630913766-0.04038157630441.988187097436.6669715857946.426432306198.7204332323
44.82947790864-1.32910196392.907712813995.259087078592.505350238197.39597462604-0.797171489410.165674486442-0.30560416242-0.4105846913470.3769476955310.598304057094-1.14645172003-0.822388456533-0.08870372896041.041078616880.1141644073130.2175977670351.179539797750.03947672305911.457047526398.4224601773145.3713823281109.035274597
58.59293582221-0.82251219222-0.8533997285490.07039611133870.07750582320870.08539131885430.838869135431.18064539001-2.324196641220.4136344084690.363441176755-0.1933997042170.7801174235170.1070019154013.898637747851.628106889250.7501806661780.09314259940931.098372456170.01857622645611.24996443912-6.0511332883863.0826034737114.76369116
66.87427768379-2.390254695372.462235298417.24483339719-1.437119008797.355676629030.701649404495-0.7121566940450.2293855431790.08509627816751.52183959195-0.575758601194-0.2051667620111.231842837550.04766746189021.927696147350.2605960213470.3536337898032.01047803227-0.5563573999031.94934275021.6450738942469.6390577808143.791103689
71.006722470180.70052522416-0.08819552708872.90588523320.7047427661190.2458713670390.966010391559-0.6454071550712.04812213697-2.06006852957-0.632577491505-0.401321828062-1.066420374051.428853365830.467191567061.826944420940.3925353147330.3661918115541.61972788721-0.1475951678431.8143550723-1.5046326010567.1970774444123.880841297
84.17250978962-3.09880481286-0.6493017671813.16988493844-1.514233454164.60053515096-0.22517222388-0.735435036868-0.226578729727-2.1935545894-0.2464714038770.8819972060740.3003816993041.451559835390.1496975636591.54338680281-0.4806804916720.4638331573181.53995503261-0.5548032881681.827855136868.771361762174.4318821122130.497223757
91.32049497918-2.09439417249-0.2835284692344.09420764885-1.138080850843.78076222993-0.0863097846261-0.4089218775040.620752006246-0.251314338169-0.240112938973-1.97989942009-1.18785447780.830797013426-6.319414689781.352906427290.01385226801890.8113917341661.23041674214-0.5821633361741.989829158052.411638887667.9737906024132.929074204
103.41076951425-2.04950108614-0.7485380123555.66750981633-1.820646845131.302955614671.256378135081.026520665270.185487841802-0.06990121210530.0498145044866-2.30064783546-1.453361541280.0241903050654-1.004197130892.12317818601-0.06870969387180.4692762614271.08301078727-0.0444993069791.78546417418-1.119669745678.5894180999130.780397441
114.424938606160.4313720901465.562675637158.012101657140.8788652898077.029101366070.3026839106410.2804400442321.13823440062-0.4669804747530.3889796974370.03246302657880.314535997157-2.145371211211.830095242940.7564787985330.1208456629150.07703314014951.89610557301-0.2476216035250.84987705970315.107605367836.8859749751130.526359053
122.426390175662.844044795624.959721210125.309098015226.452811010471.997195707891.11804036989-0.2778800199070.04308719496340.596320893803-1.396874067150.0056040247021.31721213776-0.819222693782-1.256724526840.554034132238-0.05843001256870.02362965005351.49834230438-0.2148452891390.86379231831515.294843076126.7154626629121.837275652
133.47985093611-2.210039879821.597993082847.86241042633-0.1726442732973.73646812134-0.405081313453-0.3255826196120.260465799837-0.1633671201430.939328232596-0.559744199624-0.1917391803730.288621417529-0.3662003557920.939820575725-0.02963821538860.2072845642361.69458919914-0.2918611117081.2528131465221.114853507135.2131082937120.351863878
143.68222423002-1.221822859750.09767308124382.48689419816-1.128735839450.5800469008720.125743396785-1.385221562120.8727742848390.879448048813-0.391380448556-0.429830523465-0.358727174818-0.860064961795-1.895067544340.4516108002520.1541681034330.1752695304171.45462553083-0.3667954619331.0083806612517.52347786241.4225393375123.101633938
154.98511473502-4.731278028033.166567089468.978759161351.963571229847.406472261280.824740964924-0.122789482527-1.47852693791-0.219623990026-0.175857614688-0.390033621484-0.764770833832.36927481407-0.7646685207651.23182056972-0.2725698498840.3280581766771.25291064769-0.07639587295671.1530721177311.513162123333.1725219505110.658461557
160.3001524708150.433100640543-0.3731303951692.35863604049-1.910870770732.31066159621-0.0369956225844-0.889765995403-0.9421819429230.5680152867390.605732177208-0.22185593499-1.128032313290.361194278473-0.7140510878140.9800286751210.13053915128-0.1673492065631.16314611352-0.4830622081361.232596301054.1891359895257.2299241586139.736667058
173.361276228310.606478502783-1.311045776861.059189443621.181781456722.604363931510.7113681770850.334400203210.01544574819150.494759747437-0.13142766073-0.711984985751-0.268373040092-0.121459081096-0.6733981091631.51709484448-0.0058522030329-0.1346317180941.30584248646-0.1848949466081.79491803818-5.0749463884953.682086681135.911549152
180.2259484526410.710017471316-0.2896704044443.199222172751.672686150686.157022063441.121154453250.9003386371150.420793902957-0.193813738684-0.403282677477-0.3548429880870.293693214240.0441810094109-0.2359883074340.8047086996760.1391289223580.07285791439681.43750111066-0.3926686793681.4810644784-3.6540050228558.4615012929140.484509306
192.72077719525-1.981476558621.998035682755.805776833831.339196319393.162081730420.0265003575104-0.377748505438-0.3173402903380.815604422203-0.172611554063-0.4624797023150.007982599435490.4794467588110.3978793556620.914751906542-0.2412855747-0.1399370890371.54691306285-0.02230142290931.1575203212558.56463176250.496239612887121.689648106
204.495024914840.333026654077-0.5305637430919.83353766921-8.158412099956.77670571203-0.26931761842-0.03865994854130.5919496334080.476341477224-1.46047258343-1.057609685050.1962272856391.42257254598-0.6397190702931.89875581185-0.165886139605-0.3703221354991.29001177925-0.3669456580431.2375495915151.55558480569.07648867924127.835499853
212.154941736950.6777972448552.650561717399.17062171557-0.7785618767743.53011769005-0.265473582756-0.409395536673-0.476872883651.86520703120.161458680426-2.13298566657-1.16556606041-0.2454774125110.6041803475890.9987202799940.0111021461451-0.04785996443421.343173533580.03837691784461.0767544356159.46079477592.30058920278126.433892203
220.9214240291142.201042804312.530175368125.269281858756.088532761297.04300001524-0.725499559165-0.0202100504392-0.911061181383-0.753038593502-0.3619484641990.69164315496-1.0369214463-1.89201197307-1.519260522480.956133862516-0.3171525642430.1351913999711.518921427520.2102018154990.99665418228549.62435191682.12506646535114.107921001
233.54706608821-1.6219385476-1.155311039950.8148400236850.8837297143082.194106492760.125059403742-2.29997088055-1.483884671920.8614952776620.109676346696-0.2558971670590.46215712910.7021723635180.7840941674920.601877308569-0.353746453239-0.1111715570021.747789731640.6462070033811.3983518578668.0527612399-14.9626766204131.197401087
240.01865269166990.06261062462470.1392424513530.09061685912510.2128234374890.654892881778-0.321269277022-0.2379170548420.5686244691370.171862188663-0.270568345418-0.889971238767-0.4591670120861.32351771855-5.859890804840.537064519699-0.0366270224867-0.5270131349261.892146432170.2761998269061.2844960204266.5750949272-35.9078120063124.744650868
251.52039259672-0.8309421586221.624055159952.61818035599-0.7741344423721.62334436228-0.01059144095660.760343442367-0.0917355900321-0.247844110864-0.568228146561-0.3114014924040.03511387465940.0987537922858-0.0438041513890.777133382855-0.09525065786060.007444235294361.655359420730.1364854679381.2690530578465.4006759978-31.7599058221119.675409052
261.420371939581.565647524331.291111937669.778868735380.0541538386321.54767743929-0.3973307422930.3505223200780.445468255119-2.23859761826-0.32525975176-0.320744249137-0.09694009002851.676362148270.1183888649080.9174876752410.044891482272-0.08071384037391.809609024820.09792691237661.3829999923574.1463744124-33.0599170485121.230989524
274.75204291443-1.267721309760.4229051758995.68087795504-2.185452080950.7456878476740.0305741267488-0.3230638393570.231020747938-0.6025019199150.3267809001440.436815339532-0.03651605830620.0195820395745-0.2010063245840.767066915658-0.312440258339-0.1944780155811.692805292060.02973902664031.2139854873840.1617189245-7.99020581349114.264617672
284.018154953571.955398915150.789274093493.44408024268-0.6613173571122.8012860910.1387600819710.28547119849-1.28727899602-0.169352795933-0.209610539592-0.5132807129030.972554475780.6638054606480.1510115168010.7816226518570.02043166180590.1409571270641.338307437280.1743102968391.196189980254.2001976247-38.0819040653127.939935622
294.9581584858-4.459136359920.5630211693215.65310540159-0.07141401922556.83722048475-0.658473460342-0.2640124838571.12921081241-0.419041998187-0.147033284101-0.626880398236-1.32743673984-1.71813199287-1.61290243020.7730655209960.00170152437230.2763927389761.739635773470.3591229156971.0779224554927.670841167921.593411649197.6587757842
300.105305797321-0.9591346626290.8528661466918.54884376419-7.731982575266.99869854781-0.815725988071-2.440495582891.11005602983.82365552755-0.4129657231491.16397157334-1.7882157933-1.756182438350.2714332657181.50432081543-0.1294435068320.30737342262.43289562933-0.8825832780132.1054444067243.089108123517.5185434811120.071744601
312.961776543111.950644816220.6477010014145.450525630551.814495491531.71613783138-0.549547460030.5492368708720.5071734767-1.276188269970.5053823736530.144043589402-0.285618582518-0.030236987291.157954578631.66398635432-0.823464947874-0.2234212246581.00653187046-0.1499264295571.6091909711750.056525583623.3223669468106.173551714
324.65670233380.4493362541534.375790400753.325090290344.393288841468.92023784938-1.298867825311.297009357441.87423680964-0.165318946316-1.06563305463-1.071774687510.165696723402-2.3627697208-2.872632358091.30354042065-0.4408258103970.3918314045151.989123902160.2905749634121.9183931635832.440256734831.9311237069100.212201469
335.880618915640.122230104116-2.37126518237.42631222952-0.4860825602794.11221883470.1027293444170.117794829982-0.6512354543550.01972894284160.00758049234376-0.956874984301-0.03449044570551.1431397458-0.02340257792841.206219278890.122838267182-0.0168966741321.64036214575-0.0571574952831.1558151783721.905726998416.67467757998.8507704877
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 1 through 13 )DA1 - 131 - 13
22chain 'D' and (resid 14 through 61 )DA14 - 6114 - 61
33chain 'D' and (resid 62 through 75 )DA62 - 7562 - 75
44chain 'D' and (resid 76 through 102 )DA76 - 10276 - 102
55chain 'D' and (resid 103 through 114 )DA103 - 114103 - 114
66chain 'D' and (resid 115 through 131 )DA115 - 131115 - 131
77chain 'D' and (resid 132 through 144 )DA132 - 144132 - 144
88chain 'D' and (resid 145 through 163 )DA145 - 163145 - 163
99chain 'D' and (resid 164 through 190 )DA164 - 190164 - 190
1010chain 'D' and (resid 191 through 214 )DA191 - 214191 - 214
1111chain 'C' and (resid 1 through 17 )CB1 - 171 - 17
1212chain 'C' and (resid 18 through 33 )CB18 - 3318 - 33
1313chain 'C' and (resid 34 through 84 )CB34 - 8434 - 84
1414chain 'C' and (resid 85 through 101 )CB85 - 10185 - 101
1515chain 'C' and (resid 102 through 115 )CB102 - 115102 - 115
1616chain 'C' and (resid 116 through 154 )CB116 - 154116 - 147
1717chain 'C' and (resid 155 through 174 )CB155 - 174148 - 167
1818chain 'C' and (resid 175 through 223 )CB175 - 223168 - 216
1919chain 'A' and (resid 2 through 51 )AC2 - 511 - 50
2020chain 'A' and (resid 52 through 64 )AC52 - 6451 - 63
2121chain 'A' and (resid 65 through 99 )AC65 - 9964 - 98
2222chain 'A' and (resid 100 through 111 )AC100 - 11199 - 110
2323chain 'A' and (resid 112 through 124 )AC112 - 124111 - 123
2424chain 'A' and (resid 125 through 150 )AC125 - 150124 - 142
2525chain 'A' and (resid 151 through 198 )AC151 - 198143 - 190
2626chain 'A' and (resid 199 through 220 )AC199 - 220191 - 212
2727chain 'B' and (resid 1 through 107 )BD1 - 1071 - 107
2828chain 'B' and (resid 108 through 213 )BD108 - 213108 - 213
2929chain 'Q' and (resid 11 through 37 )QE11 - 371 - 27
3030chain 'Q' and (resid 38 through 47 )QE38 - 4728 - 37
3131chain 'Q' and (resid 48 through 52 )QE48 - 5238 - 42
3232chain 'Q' and (resid 53 through 66 )QE53 - 6643 - 49
3333chain 'Q' and (resid 67 through 130 )QE67 - 13050 - 113

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