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- PDB-7u8c: Crystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB... -

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Basic information

Entry
Database: PDB / ID: 7u8c
TitleCrystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB complex
Components
  • MORab 15B6 Fab heavy chain
  • MORab 15B6 Fab light chain
  • Mesothelin, cleaved form
KeywordsIMMUNE SYSTEM / Mesothelin
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region ...Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Mesothelin / Stereocilin-related / Mesothelin
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsZhan, J. / Esser, L. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Highly active CAR T cells that bind to a juxtamembrane region of mesothelin and are not blocked by shed mesothelin.
Authors: Liu, X. / Onda, M. / Watson, N. / Hassan, R. / Ho, M. / Bera, T.K. / Wei, J. / Chakraborty, A. / Beers, R. / Zhou, Q. / Shajahan, A. / Azadi, P. / Zhan, J. / Xia, D. / Pastan, I.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
BA2: Mesothelin, cleaved form
H: MORab 15B6 Fab heavy chain
L: MORab 15B6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,5273
Polymers47,5273
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-33 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.832, 64.832, 250.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11H-301-

HOH

21H-431-

HOH

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Components

#1: Protein/peptide Mesothelin, cleaved form


Mass: 1863.138 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (UNP residues 590-606) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13421
#2: Antibody MORab 15B6 Fab heavy chain


Mass: 22799.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody MORab 15B6 Fab light chain


Mass: 22864.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.5, 26% PEG550 MME, 6% 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 53658 / % possible obs: 95.3 % / Redundancy: 27.4 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 35
Reflection shellResolution: 1.74→1.8 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 3899

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RIF

3rif


Resolution: 1.74→24.01 Å / SU ML: 0.2218 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 26.3108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 2770 5.17 %
Rwork0.2043 50761 -
obs0.2061 53531 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 1.74→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 311 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293405
X-RAY DIFFRACTIONf_angle_d0.53434651
X-RAY DIFFRACTIONf_chiral_restr0.0442539
X-RAY DIFFRACTIONf_plane_restr0.0031586
X-RAY DIFFRACTIONf_dihedral_angle_d11.83651189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.3716880.36911661X-RAY DIFFRACTION63.37
1.77-1.80.37231320.3491995X-RAY DIFFRACTION76.9
1.8-1.840.3841160.34592188X-RAY DIFFRACTION83.97
1.84-1.870.32681250.33932282X-RAY DIFFRACTION88.59
1.87-1.910.33371530.31672483X-RAY DIFFRACTION94.11
1.91-1.960.35421250.30672615X-RAY DIFFRACTION99.6
1.96-2.010.30161510.29472578X-RAY DIFFRACTION99.89
2.01-2.060.32151340.26882617X-RAY DIFFRACTION99.89
2.06-2.120.29111480.25582630X-RAY DIFFRACTION99.96
2.12-2.190.30241400.23252653X-RAY DIFFRACTION99.79
2.19-2.270.26381520.21252609X-RAY DIFFRACTION99.93
2.27-2.360.24641500.2092627X-RAY DIFFRACTION99.96
2.36-2.470.24951440.20382659X-RAY DIFFRACTION99.86
2.47-2.60.23111490.1942658X-RAY DIFFRACTION99.86
2.6-2.760.23881480.20142651X-RAY DIFFRACTION99.96
2.76-2.970.23881420.21742697X-RAY DIFFRACTION99.96
2.97-3.270.22091190.20662723X-RAY DIFFRACTION99.93
3.27-3.740.23721270.19132725X-RAY DIFFRACTION100
3.74-4.710.19281620.15342768X-RAY DIFFRACTION100
4.71-24.010.20751650.17792942X-RAY DIFFRACTION99.84
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)
12.23364589296-0.852472134457-2.783374497484.375068073092.713752414247.01797819961-0.460952823265-0.4796005827590.1850692517651.323961786350.212365189401-0.2653479123450.4160204924080.673688924870.2040872551950.5246060693190.101873907919-0.03997462836320.8285711910650.06539627370620.31238712480912.1635830533-8.7891071713258.3586865499
25.17055258045-4.6098381572-1.313264395985.937092882291.60215884174.39679953566-0.662256042233-0.504959720310.1486607196331.131562954410.27041496397-0.5356630543140.2387625669330.779152913180.191628250610.3359193245420.0859930760663-0.01760323556580.973163770930.02184332435630.33587957991920.8723997214-18.106300814151.0457557672
31.274297816930.1939879240.6746320439691.55449913119-0.3184438183133.96051711686-0.13780040459-0.1540237641950.132880341041-0.04621571869770.08571127144660.0397907940222-0.5884741139080.2242778004680.07473941865980.210166261507-0.0384830782142-0.0538028418730.5885045047660.06735926340590.36529287685811.3413495293-0.81283907767137.4232006991
41.828783686190.9708537719570.7351744217197.58300754993-0.2388242921053.499541052260.03932952104710.79550379998-0.100415347035-1.676939555350.203401804075-1.19334466509-0.1481693145271.05892630399-0.2421316363040.814287563533-0.116853692299-0.0133144938990.9784413758730.1091410250720.59611622750715.4768364287-11.2929414217-6.22473367896
51.45362578142-0.4772706076530.2324157750352.282068135750.9049956975154.49106295739-0.1594641601790.246397881049-0.209080312846-0.4579729635260.0455110111360.202038129269-0.1316844440210.09351536612570.03401044108370.499362653033-0.165838518452-0.1363642838470.6669076058390.2217968268010.4190626922337.27311805654-8.472299653163.09300762759
61.78391899743-0.4111281875160.07355530376980.7335402071620.0784007241740.54149467679-0.0242626142413-0.1879638777910.1173046281010.06316392378080.0422561137153-0.3859112725630.04962857022330.252760897726-0.1162761988810.142517263467-0.0156574899874-4.45411489417E-50.8429095837680.08903726215840.42758999042529.1195867737-20.271529451833.3180617899
71.3011466257-0.1143478744470.3326820761160.9835255052310.2941288577061.11940372163-0.199499777396-0.383341768579-0.08243045877420.1231470460750.149664633694-0.07708799378990.2270886839890.208606654674-0.1343833864860.1134323719910.0177166248656-0.01892100195240.8184814321290.1208361631030.38776055259420.5466598176-19.250756087637.8987554388
80.762460520618-0.3579358858620.6820745589980.4627334097720.5720435303883.29399981067-0.06047243567690.1582398573860.0773331154402-0.1524497969440.03403188009880.0239180273549-0.04545533858320.317573132732-0.01847809532730.219575635854-0.05117100652010.03296770158150.6694567297570.0993210140350.38297244594420.1788294256-26.93717796318.5132129646
91.21152320495-0.5993344137740.1701137086034.86341487523-0.9961956550181.1795150586-0.01319640437790.5039835237060.273621857729-0.720620752918-0.129972099961-0.0985500503414-0.4433760111950.5150573717290.1732615007110.547194718959-0.199572763409-0.07523729876920.9030426132570.2760806785430.41855042694918.9076306184-7.086115038870.52694806392
101.31827793352-0.196232810541-0.230761165112.447663955960.01801127833570.571871243272-0.09724851099450.3852146896190.209666035365-0.293577930339-0.000708272220104-0.306446546379-0.416645154530.4421470016190.05504173274470.445079660988-0.241552259411-0.05299617867310.8892891904770.2453085578190.4619800660323.8758979583-9.968754183738.14591072245
110.390016008401-0.3585506697450.07903286112221.251002709490.4969208301620.7252682972570.1128067944260.2613338387230.222517855182-0.890700793023-0.0682736106865-0.280897959381-0.2053073183160.3560756073930.09569929016960.582628738079-0.123877426950.0722204077481.082818732260.2007643899010.48605137144929.2945328791-13.98893502860.856009443735
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'BA2' and (resid 584 through 590 )BA2A584 - 5901 - 7
22chain 'BA2' and (resid 591 through 598 )BA2A591 - 5988 - 15
33chain 'H' and (resid 1 through 120 )HB1 - 1201 - 120
44chain 'H' and (resid 121 through 135 )HB121 - 135121 - 135
55chain 'H' and (resid 136 through 214 )HB136 - 214136 - 214
66chain 'L' and (resid 1 through 30 )LC1 - 301 - 30
77chain 'L' and (resid 31 through 103 )LC31 - 10331 - 103
88chain 'L' and (resid 104 through 116 )LC104 - 116104 - 116
99chain 'L' and (resid 117 through 142 )LC117 - 142117 - 142
1010chain 'L' and (resid 143 through 190 )LC143 - 190143 - 190
1111chain 'L' and (resid 191 through 213 )LC191 - 213191 - 213

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