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- PDB-8sj4: 8F3-1H9-Ara h 6 -

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Basic information

Entry
Database: PDB / ID: 8sj4
Title8F3-1H9-Ara h 6
Components
  • 1H9 heavy chain
  • 1H9 light chain kappa
  • 8F3 heavy chain
  • 8F3 light chain kappa
  • Conglutin
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 / IgE binding / Conglutin
Function and homology information
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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
H: 1H9 heavy chain
L: 1H9 light chain kappa
D: 8F3 light chain kappa
F: 8F3 heavy chain
A: Conglutin


Theoretical massNumber of molelcules
Total (without water)108,5015
Polymers108,5015
Non-polymers00
Water2,936163
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)39.382, 85.450, 165.831
Angle α, β, γ (deg.)90.000, 96.170, 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 , 2 types, 2 molecules HA

#1: Protein 1H9 heavy chain


Mass: 23013.727 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 Conglutin


Mass: 14509.228 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arachis hypogaea (peanut) / Cell line (production host): expi293 / Production host: Homo sapiens (human) / References: UniProt: Q647G9

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Antibody , 3 types, 3 molecules LDF

#2: Antibody 1H9 light chain kappa


Mass: 23299.818 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 8F3 light chain kappa


Mass: 23412.021 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 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)

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Non-polymers , 1 types, 163 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 240 mM Sodium Malonate, pH 7.0, 20% PEG 3350

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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: Nov 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.67→55 Å / Num. obs: 30930 / % possible obs: 99.3 % / Redundancy: 5.5 % / Biso Wilson estimate: 43.23 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Net I/σ(I): 12.95
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 4 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 2898 / CC1/2: 0.66 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.05data processing
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimless2.3.28data scaling
PHASER1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→54.96 Å / SU ML: 0.3481 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2316 1517 4.91 %
Rwork0.1902 29399 -
obs0.1923 30916 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.03 Å2
Refinement stepCycle: LAST / Resolution: 2.67→54.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7266 0 0 163 7429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00527425
X-RAY DIFFRACTIONf_angle_d0.65110091
X-RAY DIFFRACTIONf_chiral_restr0.04941138
X-RAY DIFFRACTIONf_plane_restr0.00551298
X-RAY DIFFRACTIONf_dihedral_angle_d21.44232694
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.760.35341120.28372508X-RAY DIFFRACTION93.01
2.76-2.860.30891140.23582692X-RAY DIFFRACTION99.93
2.86-2.970.31351430.23292666X-RAY DIFFRACTION99.96
2.97-3.110.27351450.24432649X-RAY DIFFRACTION100
3.11-3.270.24811530.20952702X-RAY DIFFRACTION100
3.27-3.480.25471370.19922648X-RAY DIFFRACTION100
3.48-3.740.25111300.192700X-RAY DIFFRACTION99.89
3.74-4.120.22051470.17882673X-RAY DIFFRACTION100
4.12-4.720.17831320.14572717X-RAY DIFFRACTION99.93
4.72-5.940.19131350.16172703X-RAY DIFFRACTION99.96
5.94-54.960.21081690.18322741X-RAY DIFFRACTION99.66
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)
12.71681192775-0.8118650943682.559808701872.300726841170.3650119453625.933644126050.147898787954-0.216342370734-0.7257271383760.104790228363-0.0244318195648-0.1966963584340.454120548895-0.00649903787497-0.1375374255120.2213131042390.006726686835080.04296509427320.2099217416830.0661132246080.50260235298422.716735187329.305076100313.3520702813
20.867012651093-0.3334505576870.108434230051.066721652861.023930178914.40064499639-0.0182708135771-0.140891413482-0.071995166372-0.1285451913920.01813511621440.1013774903060.0178809523339-0.0351331875410.002479523851780.1827459230260.00926280949878-0.03751886259220.120941133120.01810087732060.38259068650820.52245753232.18283927026.30340985032
35.558090998830.428346820415-1.467506996962.48478254181-0.890804619563.36292384285-0.039249167978-0.0806195277023-0.298001914995-0.207263052153-0.0320444448737-0.05342136846690.2885858594110.4400123866350.09323749846310.3568781483910.0305798136739-0.07422817412010.148288896672-0.03692261841180.34283137337532.508227900425.6378586048-15.4800485422
44.04012500496-2.29132343531-3.860442522572.345589093341.160220360918.295492448710.53328960998-0.2827259895580.217006822664-0.172288441417-0.3343201010580.317526622225-1.0821937844-0.121263792112-0.2570417443510.481461970533-0.0421441432684-0.06239236525090.174838640842-0.07012514914830.47062296501826.231471857254.90882414275.42791108775
52.242316316780.133836318154-1.485794518033.35443026114-0.05770573351233.5526140558-0.134142208321-0.05521450052790.133045394202-0.157924278727-9.55177006802E-5-0.31771149694-0.3662116895080.2355401924640.1318423144060.219493017144-0.0277208529707-0.0694542154420.168566260553-0.02077865076780.37096293608534.008915429350.034378949411.8450366435
67.097133615291.98558834155-2.592364704980.522179984549-0.5385576972516.79491652843-0.4096311490320.135924574831-0.626961485101-0.140397248092-0.0334662529777-0.475495905416-0.1111255204170.3723728811960.4493759545690.266048812889-0.05901435096820.04269869140660.1596386666970.0139410182940.48565966484935.20435295947.78492092054.23642038036
78.748456035262.72144869359-1.559707211944.9155091055-4.662528858584.512969182010.224479965377-0.5275700341550.5893137932360.3158458963470.4908905950640.384473781724-0.699705322738-0.930808628764-0.6960047948610.2500013699440.09939594381360.04604936665010.204284815696-0.001440467920570.42554135780322.219776300548.015144885315.2414928878
82.82968457683-0.253572277044-2.977639435770.01713682237430.2495174662393.156898924010.160047923930.263346387440.604179424579-0.3646753280390.407623658011-0.247652475214-0.810412264064-0.0576086030578-0.5212242100780.675156561004-0.1211435702890.09521069288620.3359291690880.004846291648860.47468373627537.99600940850.4023769574-11.4847399247
95.066918435235.90348032352.053056445337.165379047732.130803391528.033528667260.3220391667850.070846506746-0.344314069152-0.905437835754-0.25941130307-0.4511710375070.915851598264-0.566817113643-0.0429419375440.6710136848420.09640555773440.04597009766310.3356654507230.03494997869420.44152732571328.627140097927.0177999177-28.281711302
106.838199908333.288223753335.005429769996.610508225133.750830009228.103418468790.168298032435-0.1176137978140.602389860746-0.404357885898-0.500425647030.049821034275-0.691608013752-0.4160472619290.3302475616740.310100804530.03104473918070.05637046314780.2531424316170.03233442568310.4204550045929.73979214441.5395811404-23.6492220545
111.22485815554-1.064586010381.796933244593.09810379893-3.624565829837.130075322920.3684038060890.2255129466540.0237600742628-0.746994652583-0.116278194770.2389943610710.152330390367-0.83199360995-0.1143356710760.582468145280.182014208483-0.06565973025960.4475259107320.01178304802330.45617963233821.401525964140.2001120986-27.703485501
128.15381072239-4.513301202880.8873650306594.592127052443.581569352848.075995251350.165921002929-0.4586814806680.345404776041-0.5968512184360.33166910309-0.1649026181540.1596194673390.372612544523-0.4007098929050.523916581151-0.0312288433258-0.03423063007410.2094103715060.0594891256130.39472673208137.92244914742.7012084503-10.4890264095
133.036797827971.447070710681.311381763433.893180303072.180153446054.49863280032-0.02413070318470.330738128984-0.0744714243385-0.7990890041220.0268061861143-0.204256543253-0.327053899384-0.07558795110470.01040073387610.5648575316620.01049815116-0.01431352050650.3266923006470.06173094545170.32668881387927.46142476637.5080628703-31.9185257148
142.18617546777-0.253136827024-1.954343750711.77694425356-2.337164592525.63247197006-0.315354394289-0.843321172906-0.1364173923491.02043941308-0.493115159655-0.6472141078080.6738463017790.5264657408030.3715569624281.30361985754-0.0174406456329-0.01985649592921.236561383410.03628153186450.43391178743327.185393268524.672028653872.6893782604
152.530868160221.21073694508-0.8645684615384.32131429306-1.985998389752.78594196494-0.0189172123693-0.616690946086-0.1063391381831.19772113088-0.189167455158-0.377997213702-0.8431893232760.4916079149450.4474957425320.940789237582-0.191557505083-0.009131926329630.871844066225-0.04634050004090.1567152597127.385165807531.115716664162.2079414544
162.18174942817-1.67473223022-1.021417600251.321725127380.4982580588593.715207303950.47277293876-0.2348261738640.2966487229050.709176929063-0.589452257640.892604786144-0.550684729654-0.08395214687850.02868314095390.927856846788-0.1245870878520.258340878741.051286727-0.1004442821720.45709686935915.724533084629.207635344263.5757485883
172.23899563012-0.60424490797-1.284394670142.45825756504-3.164293254066.703285225410.0651054516863-0.4562099990940.2119454281911.19315215376-0.518279446085-0.234055020365-0.06293830063710.3402802400670.2708896657590.929934181819-0.2758923571990.102954083621.05944587956-0.1127837053280.34277079026324.406020779327.308197987966.1468918295
182.096732108690.199104950874-0.7335956563280.875959939642-0.4198420431382.71151060170.599248167215-1.09841506748-0.5471544581660.748706555921-0.52427238991-0.4601127007260.2149435869560.0617575879446-0.136240334551.07885723595-0.135085921875-0.04772912089551.149522469250.342269857270.69140137916912.7084982713-4.3685116931572.88084296
192.117934614271.14104807420.1529747164170.7159385119030.6358069912192.385255007320.542047054249-1.39185620792-0.9201710573120.536240306392-0.476716451233-0.7977199578940.09139609418420.586783637095-0.04002973795511.47703157982-0.217607397655-0.08640582081481.289975670110.434109741970.77591449581711.4688062195-8.4456508532674.5441425691
202.04692948620.7725323309390.5082949911376.64881082353-1.591430434373.193358399420.07515384332-0.22680726392-0.2295985993690.0652025091184-0.0679563068648-0.01355047357240.3407751384530.16986536795-0.0009803419186350.3538430573110.05463246338170.04183813319280.4962813436150.04940518325680.2209561944923.782575223719.88901848346.1588919962
212.04330280654-0.2144289797380.6133673892225.269763495110.1809225637742.316689208840.283204726226-0.94294082487-0.4202139062290.193112666718-0.1115214720290.5374449874770.170503274825-0.479445986016-0.1096532612410.712129326118-0.0319140838786-0.0320121959370.8346316975130.2354493428730.5264445558065.51546302357-2.085916331260.2693902295
224.8473823294-1.082214350245.505909077917.9896301039-2.951258088857.56674760642-0.133415433163-1.17801080982.244429541070.912315535139-0.6035718657660.574761124964-1.81120941775-0.7417463640761.146316890071.2376128602-0.2463396301610.03980094404560.853853850163-0.4049864361261.0734202250830.093015166361.493162604545.0160289716
233.235060068045.218660951731.787467197029.047503051031.863492732195.350001560520.473936734279-0.01341378783050.3728818627920.283189114792-0.429472652687-0.749727746766-0.5087231931320.545022478851-0.04436174248010.471023107603-0.04691758268450.02738717315470.538532293253-0.05489509286220.53783171830731.775552668743.19769646541.4244688598
246.71571262361.962420314651.634142560082.28106550671-1.008109296551.70474458380.739595378786-1.279878993751.149407561110.457344356672-1.094528391770.108599391995-1.46168593125-0.344795435730.2154415289381.5084946764-0.06846570028660.03192526857040.885879908571-0.3108357848250.72696528738228.697546412250.472522112949.9600788038
254.33624690675-0.1770962378170.6659603137334.955563310422.561700110577.55951867730.0203420910184-0.3604270665360.5134225660830.257646628715-0.04922657175250.0074120062291-0.886405174697-0.325129364107-0.05139320548570.4155555987810.04610108782790.02550786231030.286175953755-0.05017101173090.46822249017425.378385600846.978535518936.0526525669
260.584185879428-0.4020409027910.4970135538150.933919522835-1.461869948642.173355195820.4724161983920.1959431546320.09599633878590.565806777942-0.4617299857830.825181615026-0.759321861091-1.09118832761-0.07283370607841.259551976310.3273667492440.1756995184950.859685998694-0.1283245771650.89548407541618.610644144652.306720033739.5591345832
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 40 )HA1 - 401 - 40
22chain 'H' and (resid 41 through 132 )HA41 - 13241 - 136
33chain 'H' and (resid 133 through 211 )HA133 - 211137 - 215
44chain 'L' and (resid 2 through 15 )LB2 - 151 - 14
55chain 'L' and (resid 16 through 76 )LB16 - 7615 - 75
66chain 'L' and (resid 77 through 91 )LB77 - 9176 - 90
77chain 'L' and (resid 92 through 103 )LB92 - 10391 - 102
88chain 'L' and (resid 104 through 114 )LB104 - 114103 - 113
99chain 'L' and (resid 115 through 129 )LB115 - 129114 - 128
1010chain 'L' and (resid 130 through 151 )LB130 - 151129 - 150
1111chain 'L' and (resid 152 through 164 )LB152 - 164151 - 163
1212chain 'L' and (resid 165 through 175 )LB165 - 175164 - 174
1313chain 'L' and (resid 176 through 213 )LB176 - 213175 - 212
1414chain 'D' and (resid 2 through 26 )DC2 - 261 - 25
1515chain 'D' and (resid 27 through 39 )DC27 - 3926 - 38
1616chain 'D' and (resid 40 through 62 )DC40 - 6239 - 61
1717chain 'D' and (resid 63 through 105 )DC63 - 10562 - 104
1818chain 'D' and (resid 106 through 165 )DC106 - 165105 - 156
1919chain 'D' and (resid 166 through 212 )DC166 - 212157 - 203
2020chain 'F' and (resid 3 through 128 )FD3 - 1281 - 128
2121chain 'F' and (resid 129 through 222 )FD129 - 222129 - 222
2222chain 'A' and (resid 12 through 23 )AE12 - 231 - 12
2323chain 'A' and (resid 24 through 34 )AE24 - 3413 - 23
2424chain 'A' and (resid 35 through 71 )AE35 - 7124 - 45
2525chain 'A' and (resid 72 through 106 )AE72 - 10646 - 80
2626chain 'A' and (resid 107 through 124 )AE107 - 12481 - 98

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