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- PDB-8gkl: Crystal Structure of the Humanized MUC16 Specific Antibody huAR9.6 -

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Basic information

Entry
Database: PDB / ID: 8gkl
TitleCrystal Structure of the Humanized MUC16 Specific Antibody huAR9.6
Components
  • MUC16 antibody AR9.6 Fab heavy chain
  • MUC16 antibody AR9.6 Fab light chain
  • Mucin-16
KeywordsIMMUNE SYSTEM / CA125
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / Golgi lumen / vesicle / cell adhesion / external side of plasma membrane ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Dectin-2 family / Golgi lumen / vesicle / cell adhesion / external side of plasma membrane / extracellular exosome / plasma membrane
Similarity search - Function
Mucin-16 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBrooks, C.L. / Aguilar, E.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R15CA242349 United States
CitationJournal: Mol.Cancer Ther. / Year: 2024
Title: Structural Basis for Multivalent MUC16 Recognition and Robust Anti-Pancreatic Cancer Activity of Humanized Antibody AR9.6.
Authors: Aguilar, E.N. / Sagar, S. / Murray, B.R. / Rajesh, C. / Lei, E.K. / Michaud, S.A. / Goodlett, D.R. / Caffrey, T.C. / Grandgenett, P.M. / Swanson, B. / Brooks, T.M. / Black, A.R. / van ...Authors: Aguilar, E.N. / Sagar, S. / Murray, B.R. / Rajesh, C. / Lei, E.K. / Michaud, S.A. / Goodlett, D.R. / Caffrey, T.C. / Grandgenett, P.M. / Swanson, B. / Brooks, T.M. / Black, A.R. / van Faassen, H. / Hussack, G. / Henry, K.A. / Hollingsworth, M.A. / Brooks, C.L. / Radhakrishnan, P.
History
DepositionMar 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Mucin-16
L: MUC16 antibody AR9.6 Fab light chain
H: MUC16 antibody AR9.6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)63,3113
Polymers63,3113
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-36 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.470, 124.360, 235.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Mucin-16 / MUC-16 / Ovarian cancer-related tumor marker CA125 / CA-125 / Ovarian carcinoma antigen CA125


Mass: 14210.087 Da / Num. of mol.: 1 / Fragment: SEA5 domain, residues 12695-12821
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MUC16, CA125 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8WXI7
#2: Antibody MUC16 antibody AR9.6 Fab light chain


Mass: 23884.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody MUC16 antibody AR9.6 Fab heavy chain


Mass: 25216.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M PCTP pH 4.0 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.521 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.521 Å / Relative weight: 1
ReflectionResolution: 2.6→42.74 Å / Num. obs: 212625 / % possible obs: 99.21 % / Redundancy: 11.1 % / Biso Wilson estimate: 51.23 Å2 / CC1/2: 0.959 / Rpim(I) all: 0.06427 / Net I/σ(I): 8.6
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 17395 / CC1/2: 0.785 / Rpim(I) all: 0.3758

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→42.74 Å / SU ML: 0.451 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.0324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2692 959 5 %
Rwork0.2154 18214 -
obs0.2181 19173 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.54 Å2
Refinement stepCycle: LAST / Resolution: 2.6→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4100 0 0 124 4224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184204
X-RAY DIFFRACTIONf_angle_d0.4745734
X-RAY DIFFRACTIONf_chiral_restr0.0416645
X-RAY DIFFRACTIONf_plane_restr0.0037736
X-RAY DIFFRACTIONf_dihedral_angle_d3.7932579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.740.48651320.39122506X-RAY DIFFRACTION97.45
2.74-2.910.38611310.33362489X-RAY DIFFRACTION98.53
2.91-3.130.32361370.26242615X-RAY DIFFRACTION99.49
3.13-3.450.27331370.22652600X-RAY DIFFRACTION99.74
3.45-3.950.25831360.19362572X-RAY DIFFRACTION99.82
3.95-4.970.24221390.15822659X-RAY DIFFRACTION99.79
4.97-100.21441470.20462773X-RAY DIFFRACTION99.83
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)
14.57658001875-0.931595096341-3.689184109793.780420183433.902371075118.756638675140.3311869096260.4122002086540.333066747323-0.420441657856-0.2293184603660.256149341443-0.7932328872240.0753719702471-0.1519781994550.2285093781110.007941982984540.06680234881530.2412144143780.07035209940140.395196431054-14.464342172320.416934978751.4768757612
24.125977016760.553982522621-1.311450443085.55686806424-2.669523459657.244681003140.244648827451-0.04390226399020.3896581342440.1834252976070.1584713803570.3746041941170.1089242613910.0868670754647-0.3459515567780.194853052990.04123557655770.04409899253470.4525095820420.019410830140.418107075031-9.3429943322714.730774791954.2547943251
30.986759121418-1.3928468735-1.956102942244.602834463631.290225286084.637166664350.348140118739-0.01594105640670.5416361975180.0979370894998-0.1735810981730.071173174392-0.6562402257850.0206007741274-0.06161655842960.345683663651-0.0705740558840.1206778841220.319046801481-0.04920868981610.471767539539-13.268268565223.167335706353.0742396908
45.42426802328-2.18117194722-1.166539417827.483976720620.2810331924063.997523780660.6818651712550.8094304920981.00238052344-0.219517623932-0.213800922737-0.357626612494-0.890415670578-0.258113673176-0.4690911721690.4649418071160.0745006214090.1785833809420.4384513463350.1704492685120.528421178493-13.781030361128.704834400643.4703808166
52.59160902691-0.203636711821-1.26794047264.32684341299-0.05890798134452.349018073-0.210718290377-0.025130289346-0.157251282316-0.376842143110.09408905946540.1386905612010.6172439908670.1762541493010.1013649534190.3636688112180.02090033135850.02640550703690.3355054090340.04667708959360.2844753321836.53479375847-5.2537899068641.0882027114
63.919838609040.879313616279-2.639327563323.12062948508-0.9123778739665.7008378019-0.463200019145-0.187210964378-0.2738509965450.2783725848350.205787808672-0.1132689594310.7179643277510.3564389095940.291779761330.56695212250.07414243012740.1445616798730.611628069264-0.07593971543260.48655268139925.9146444281-18.970426630312.6266101174
75.779406355770.773373317216-0.802977878471.602019834790.1262195494193.0818662218-0.3996913253870.464133965413-0.0815370944197-0.5430664123420.233511767040.0555656227193-0.00430293208307-0.1109665664180.1146883455890.4545262511620.0603615532102-0.002081722170950.3777156321450.06623493719690.3449478269775.1381641013413.245893537824.6844103974
86.06833051640.594771379922-0.5435229796683.67041802272-0.01241073432256.214595905540.05099279016980.1247632452230.274679384713-0.401409110639-0.0584738382043-0.156361296999-0.2450330873250.3723919450780.008435093376180.3424588644590.0452191976310.06103337996980.2861895031210.04064983775970.2803761730617.5916773359117.346519883831.3971822249
91.42861052931-0.228933197661-1.839286365380.4087413482410.9499415302872.598190055770.08595471317080.228712195256-0.0854488672121-0.138255813921-0.09143471765110.170194025858-0.163983214633-0.0999207506063-0.02035373486150.3828782192240.0520478530543-0.02489302980960.4548693107410.09741918728020.38730502949410.01808959246.1250758721524.7964665413
101.20528951369-0.837518739329-1.737845820322.468140590441.031495257213.53787262056-0.1746459508010.11541262071-0.5682474548780.272993190246-0.00174487790228-0.07190233672590.237576577262-0.4717039650840.2043105150050.381878681654-0.03818175628420.09453681857650.623629023926-0.05212909837820.38188656477516.0441734899-7.6066979030511.8556011335
112.47393552942-0.844975192145-1.009108076031.27740101541.065344257185.001332616480.1507473016930.43203116761-0.2190120591-0.462650699232-0.117816500913-0.10717728180.306115821897-1.069421905530.03503879974970.481074211667-0.1235536160640.03794029414860.965173196277-0.1147414408540.42949816216111.0786879194-9.692702787482.07479155745
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'E' and (resid 36 through 53 )EA36 - 531 - 18
22chain 'E' and (resid 54 through 80 )EA54 - 8019 - 45
33chain 'E' and (resid 81 through 123 )EA81 - 12346 - 80
44chain 'E' and (resid 124 through 159 )EA124 - 15981 - 116
55chain 'H' and (resid 1 through 117 )HB1 - 1171 - 117
66chain 'H' and (resid 118 through 216 )HB118 - 216118 - 214
77chain 'L' and (resid 2 through 39 )LC2 - 391 - 38
88chain 'L' and (resid 40 through 83 )LC40 - 8339 - 82
99chain 'L' and (resid 84 through 136 )LC84 - 13683 - 135
1010chain 'L' and (resid 146 through 193 )LC146 - 193136 - 183
1111chain 'L' and (resid 194 through 223 )LC194 - 223184 - 213

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