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- PDB-8shw: 38B7 with hydroxy-proline peptide -

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Open data


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Basic information

Entry
Database: PDB / ID: 8shw
Title38B7 with hydroxy-proline peptide
Components
  • 38B7 heavy chain
  • 38B7 light chain
  • Conglutin-7
KeywordsIMMUNE SYSTEM / allergy / peanut / antibody
Function / homology
Function and homology information


negative regulation of peptidase activity / nutrient reservoir activity / IgE binding / serine-type endopeptidase inhibitor activity
Similarity search - Function
Napin/ 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Arachis hypogaea (peanut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 14, 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
L: 38B7 light chain
H: 38B7 heavy chain
A: 38B7 light chain
C: 38B7 heavy chain
Q: Conglutin-7
B: Conglutin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3398
Polymers98,3696
Non-polymers9702
Water11,728651
1
L: 38B7 light chain
H: 38B7 heavy chain
Q: Conglutin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9334
Polymers49,1843
Non-polymers7491
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 38B7 light chain
C: 38B7 heavy chain
B: Conglutin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4064
Polymers49,1843
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.021, 91.784, 82.946
Angle α, β, γ (deg.)90.000, 93.220, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 41 or resid 43 through 66 or resid 68 through 214 or resid 215))
d_2ens_1(chain "L" and (resid 1 through 41 or resid 43 through 66 or resid 68 through 215))
d_1ens_2chain "B"
d_2ens_2chain "Q"
d_1ens_3(chain "C" and (resid 1 through 95 or resid 97...
d_2ens_3(chain "H" and (resid 1 through 95 or resid 97...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLUGLUGLYGLYAC1 - 411 - 41
d_12ens_1SERSERGLYGLYAC43 - 6643 - 66
d_13ens_1GLYGLYGLUGLUAC68 - 21468 - 214
d_14ens_1NAGNAGNAGNAGAH301
d_21ens_1GLUGLUGLYGLYLA1 - 411 - 41
d_22ens_1SERSERGLYGLYLA43 - 6643 - 66
d_23ens_1GLYGLYGLUGLULA68 - 21468 - 214
d_24ens_1NAGNAGNAGNAGDG1
d_11ens_2ARGARGGLNGLNBF37 - 446 - 13
d_21ens_2ARGARGGLNGLNQE37 - 446 - 13
d_11ens_3GLNGLNTYRTYRCD1 - 951 - 95
d_12ens_3ALAALAVALVALCD97 - 18697 - 186
d_13ens_3THRTHRPROPROCD188 - 190188 - 190
d_14ens_3SERSERSERSERCD192 - 220192 - 220
d_21ens_3GLNGLNTYRTYRHB1 - 951 - 95
d_22ens_3ALAALASERSERHB97 - 13297 - 132
d_23ens_3GLYGLYVALVALHB138 - 186138 - 186
d_24ens_3THRTHRPROPROHB188 - 190188 - 190
d_25ens_3SERSERSERSERHB192 - 220192 - 220

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.986587062515, 0.0537350184757, -0.154137976722), (0.0517196656278, -0.792715163976, -0.607394225351), (-0.154825851413, -0.607219249194, 0.77930336785)118.39768156, -8.88417708114, -3.24857770308
2given(-0.889612454517, 0.169698257121, -0.424019082469), (0.0470826583676, -0.889385942406, -0.454726146963), (-0.454282845867, -0.424493989334, 0.783218966171)116.069516974, -12.5357756343, 27.5625237382
3given(-0.985784522424, 0.0538723905169, -0.159143460089), (0.0552889212085, -0.79043185996, -0.610049678266), (-0.158656895661, -0.61017640097, 0.776216947224)118.293835465, -8.95925788313, -2.97245077257

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Components

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Antibody , 2 types, 4 molecules LAHC

#1: Antibody 38B7 light chain


Mass: 23771.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: expi293 / Cell line (production host): expi293 / Production host: Homo sapiens (human)
#2: Antibody 38B7 heavy chain


Mass: 23708.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): expi293 / Production host: Homo sapiens (human)

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Protein/peptide / Non-polymers , 2 types, 653 molecules QB

#3: Protein/peptide Conglutin-7 / 2S protein 1 / Seed storage protein SSP1 / Seed storage protein SSP2


Mass: 1704.639 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Arachis hypogaea (peanut) / References: UniProt: Q6PSU2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM NaCitrate pH 5.6, 20% Isopropyl alcohol, 20% PEG 4000, 10 mM CdCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 67997 / % possible obs: 97.6 % / Redundancy: 4.3 % / Biso Wilson estimate: 33.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6725 / CC1/2: 0.837 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
pointless1.12.12data scaling
XDS20220820data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30.74 Å / SU ML: 0.2155 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.5453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 3336 4.91 %
Rwork0.1778 64636 -
obs0.1791 67972 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.41 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6737 0 64 651 7452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276984
X-RAY DIFFRACTIONf_angle_d0.58889503
X-RAY DIFFRACTIONf_chiral_restr0.04531069
X-RAY DIFFRACTIONf_plane_restr0.00451218
X-RAY DIFFRACTIONf_dihedral_angle_d12.84032530
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS0.711780512234
ens_2d_2FBX-RAY DIFFRACTIONTorsion NCS2.60621105485
ens_3d_2DCX-RAY DIFFRACTIONTorsion NCS0.628207157577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.980.2921380.26112642X-RAY DIFFRACTION96.59
1.98-2.010.32021660.25262628X-RAY DIFFRACTION96.51
2.01-2.040.27871520.24452628X-RAY DIFFRACTION96.76
2.04-2.070.2581300.23242711X-RAY DIFFRACTION96.7
2.07-2.110.28281280.23072628X-RAY DIFFRACTION97.04
2.11-2.150.2571360.21752666X-RAY DIFFRACTION97.02
2.15-2.190.23821560.20772684X-RAY DIFFRACTION97.13
2.19-2.230.22541360.20372645X-RAY DIFFRACTION97.07
2.23-2.280.26321370.19822684X-RAY DIFFRACTION97.18
2.28-2.340.23051410.20422668X-RAY DIFFRACTION97.23
2.34-2.390.27991370.20682692X-RAY DIFFRACTION97.48
2.39-2.460.23971300.20482694X-RAY DIFFRACTION97.38
2.46-2.530.25631250.20852694X-RAY DIFFRACTION97.68
2.53-2.610.29531280.22192694X-RAY DIFFRACTION97.65
2.61-2.710.24061340.2112703X-RAY DIFFRACTION97.83
2.71-2.810.25091480.20092687X-RAY DIFFRACTION98
2.81-2.940.25181480.2012702X-RAY DIFFRACTION98.01
2.94-3.10.21811340.19782698X-RAY DIFFRACTION98.2
3.1-3.290.21091250.19382759X-RAY DIFFRACTION98.3
3.29-3.540.21211160.16712720X-RAY DIFFRACTION98.23
3.54-3.90.17091420.15832741X-RAY DIFFRACTION98.7
3.9-4.460.14891480.14172736X-RAY DIFFRACTION98.94
4.46-5.620.14491290.12322780X-RAY DIFFRACTION98.81
5.62-30.740.16361720.15282752X-RAY DIFFRACTION98.32
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)
12.359302104340.4497806243040.1907487387023.061175019121.095966598142.59235913842-0.03390090335540.0333290220556-0.06149978586740.066841635395-0.150352717220.1733286726070.131233759674-0.07060820999970.1720772129540.2945127437060.02738014511880.03032387370350.311256200227-0.05689005857640.29456286525226.3483972365-3.6001971676224.9849030841
23.787174023770.9604053784230.2678473231322.130598520960.3615693626323.37584175198-0.0335441378954-0.3129122943490.676865505456-0.0445012634166-0.0139047154418-0.0761055266758-0.585188250430.16783545429-0.2600893190410.3287300702160.0278024326529-0.1136747440150.129823335793-0.08936831058620.53112553094455.581773680516.931204718626.9454826273
34.925630957920.676958106139-0.3227589325890.7595363448930.4458024971991.75654227207-0.420139754940.832795776724-0.185550791718-0.3579247077470.1031829992560.09776746601030.0317074407142-0.1105832364890.1498528280470.485433011308-0.03961320691210.02374760272810.469041958085-0.08398771657120.3192743898733.7045748345-7.080275435684.80872383367
44.50984658917-0.5927903970650.3416460555933.62999713505-0.6901458621383.70919373141-0.163483082094-0.220625765240.3385406157930.08545660997840.0491339405279-0.37464903814-0.06360397194360.4450208194290.01313267024980.380266095440.030872581654-0.02546018614720.384486616881-0.0004652281392080.4056112825263.6081572714.2921793124121.6689133036
53.371168339640.512750950853-1.297234402993.71553176321-1.107149790442.513963839590.02534078839580.122841114873-0.362893704828-0.0404896186081-0.0730411429899-0.1373268338950.0766685119520.2374976870790.009463433577680.1787468008540.00658754794789-0.02368870292670.16653272066-0.06169905853260.21539120964184.1044988379-33.833661345132.1406085217
61.035843281070.1848925372640.4569112343883.492557022680.2056540848922.019272574480.0886485335730.0499303907690.03073159771440.0264745262394-0.0650024830970.118979345812-0.114113289485-0.0692540217468-0.02820917589810.2327164565520.0310298699083-0.00378700411480.239143280676-0.02020973525120.21454203166587.7560476347-23.507570792634.2378221871
71.197038701430.1584132527270.02852968508451.83487759021-0.2560877657431.507534276290.1372907335730.0504168249785-0.09822077579330.0554824529175-0.069772322881-0.03382640165560.01876391712290.0234516878707-0.02259875037460.2243318255280.04923634275090.007566362649080.244437181228-0.03707894153040.24534544640286.9774659124-26.543079871231.9373096883
81.937420293141.5564020608-0.4376649633272.87143719446-0.5622118382632.03638527681-0.04422474717471.11482901793-1.00309940859-0.5344267676190.2784657453680.02803752542950.365846321207-0.00704333636206-0.1759709181670.457018439587-0.0276122638295-0.05283365063140.841360039202-0.4393359177930.69008483245358.6823867949-42.098769860117.6107440914
93.9867438250.7414343656040.1504987303573.135795431870.9715001786992.57405207661-0.05273564635050.03734084775070.413189692882-0.128794803156-0.04001885883960.179679195493-0.477263195162-0.485531191750.04393083414930.4514430256850.112084084513-0.03399869970160.3897199446310.04251129885540.37466268682779.9657016943-5.7921650318520.7090223819
102.60338902876-0.0725800506554-0.4244698065051.2067621072-0.7262413685351.68939920663-0.08397659394680.4168396601430.224074349271-0.3039604690830.055530988809-0.0245176547689-0.189955636927-0.2242587714160.2918171664970.3072328097580.03221522805840.001820890290840.2879875785530.01094441137220.17295784213782.9672219909-12.523984473917.4675013487
110.840592581062-0.0738353894353-9.96176914468E-53.118981244210.5327306774713.02724836702-0.06944420195770.981368961414-0.0180878916605-0.200907377211-0.02869624477230.8644066986420.0201945265861-0.4123020524080.03257483886030.235805884846-0.0308441981997-0.05261996468230.661367098716-0.08261891205190.4068471230951.0140798379-27.867756376419.6841836608
123.578304450690.928956635511.731623598231.725187233490.3703704494762.83961984376-0.07553353202770.270055578238-0.151370424104-0.4244454190350.0303315476080.9606739611660.306905053984-1.105723410120.1554673458350.49944478116-0.141263545836-0.1102893338110.94837981009-0.5618279885780.68959218608614.8499961397-12.87036281825.0956163045
138.23286245786-1.444462753370.1764807498163.27269898203-0.7536501710587.32899829819-0.6137618622170.3092979842080.1252780984790.002771638790460.397422545941-0.4950301548760.2628772960231.131990102110.3890375437270.433455605609-0.00643410492717-0.008709800178810.5180303652940.07004109604610.47931680032100.248908177-7.3444152652325.4747221841
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 1 through 107 )LA1 - 1071 - 107
22chain 'L' and (resid 108 through 214 )LA108 - 214108 - 214
33chain 'H' and (resid 1 through 124 )HF1 - 1241 - 124
44chain 'H' and (resid 125 through 220 )HF125 - 220125 - 217
55chain 'A' and (resid 1 through 18 )AG1 - 181 - 18
66chain 'A' and (resid 19 through 61 )AG19 - 6119 - 61
77chain 'A' and (resid 62 through 107 )AG62 - 10762 - 107
88chain 'A' and (resid 108 through 214 )AG108 - 214108 - 214
99chain 'C' and (resid 1 through 33 )CI1 - 331 - 33
1010chain 'C' and (resid 34 through 124 )CI34 - 12434 - 124
1111chain 'C' and (resid 125 through 220 )CI125 - 220125 - 215
1212chain 'Q' and (resid 37 through 44 )QJ37 - 441 - 8
1313chain 'B' and (resid 37 through 44 )BK37 - 441 - 8

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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