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- PDB-7u9j: Crystal structure of Mesothelin-207 fragment -

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Basic information

Entry
Database: PDB / ID: 7u9j
TitleCrystal structure of Mesothelin-207 fragment
ComponentsIsoform 3 of Mesothelin
KeywordsCELL ADHESION / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsZhan, J. / Esser, L. / Lin, D. / Tang, W.K. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cancer Res Commun / Year: 2023
Title: Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies.
Authors: Zhan, J. / Lin, D. / Watson, N. / Esser, L. / Tang, W.K. / Zhang, A. / Liu, X. / Hassan, R. / Gleinich, A. / Shajahan, A. / Azadi, P. / Pastan, I. / Xia, D.
History
DepositionMar 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_oper
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 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
A: Isoform 3 of Mesothelin
B: Isoform 3 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5369
Polymers48,8762
Non-polymers6617
Water8,251458
1
A: Isoform 3 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8145
Polymers24,4381
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 3 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7224
Polymers24,4381
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.762, 78.611, 74.332
Angle α, β, γ (deg.)90.000, 108.150, 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
Components on special symmetry positions
IDModelComponents
11A-808-

HOH

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Components

#1: Protein Isoform 3 of Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor


Mass: 24437.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q13421
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 100 mM potassium chloride, 12.5% PEG3350, 100 mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 27430 / % possible obs: 87.9 % / Redundancy: 2.4 % / Biso Wilson estimate: 17.74 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.103 / Net I/σ(I): 5.571
Reflection shellResolution: 2.091→2.18 Å / Rmerge(I) obs: 0.291 / Num. unique obs: 2180 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4F3F

4f3f


Resolution: 2.09→33.99 Å / SU ML: 0.2307 / Cross valid method: FREE R-VALUE / σ(F): 0.99 / Phase error: 19.7645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2163 1391 5.12 %
Rwork0.1705 25768 -
obs0.1728 27159 86.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.66 Å2
Refinement stepCycle: LAST / Resolution: 2.09→33.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3370 0 38 459 3867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293489
X-RAY DIFFRACTIONf_angle_d0.60444731
X-RAY DIFFRACTIONf_chiral_restr0.0403514
X-RAY DIFFRACTIONf_plane_restr0.0046602
X-RAY DIFFRACTIONf_dihedral_angle_d12.45441298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.170.2902990.23761911X-RAY DIFFRACTION64.42
2.17-2.250.28771250.2132307X-RAY DIFFRACTION77.55
2.25-2.350.25261410.20652427X-RAY DIFFRACTION82.71
2.35-2.480.24671430.19312562X-RAY DIFFRACTION86.59
2.48-2.630.25091340.18842635X-RAY DIFFRACTION88.41
2.63-2.840.23351480.1732722X-RAY DIFFRACTION91.34
2.84-3.120.22151590.16622750X-RAY DIFFRACTION92.79
3.12-3.570.20771530.15282737X-RAY DIFFRACTION92.69
3.57-4.50.15691540.1322824X-RAY DIFFRACTION94.27
4.5-33.990.1961350.16972893X-RAY DIFFRACTION94.24
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)
12.692989501971.918309378470.9622817110712.840508726671.478473950421.25047236148-0.03928186249580.0872820081328-0.0137323121411-0.0978758212980.116165649906-0.279145794283-0.1052735765390.127326068582-0.04076783769060.1515974062640.01410050542130.05254210174860.143037158530.01090160090690.27569533502842.8061662557-14.740659193418.6993177964
22.661681314-0.665522502417-0.8090855939610.3538843307660.1194758414130.4297024317270.08554097467760.09797903604720.384936076048-0.0940165147669-0.0254351008789-0.212142856956-0.008067140988710.0956291822799-0.02580809183920.116796026144-0.001496349787970.02505116618410.1551616354320.01251026522640.1947232594638.07721741353-23.300118006522.2897917969
38.981343932626.161701463494.63993170179.29951328621.885398033317.14643936264-0.2516151953910.0244062049777-0.265169382101-0.7632155340110.3225867569930.7647569116640.00888583862566-0.277886592129-0.1266298906820.2109381950990.0176603818857-0.02264155159220.242872867980.03086337997760.403687152395-25.358058908-2.6745036317112.3467451111
43.310418930510.420530309196-0.8781614968541.81163147515-0.6898257863431.25793503066-0.0347579985420.0543140577083-0.123800674065-0.00524862206930.0162755556285-0.0645544283175-0.01481944790270.009438633322220.002751349080650.1156130901180.01726001620230.01043261461240.0986805559532-0.006578282031430.14089366-6.57782344218-1.6623356078314.5774364339
52.165617131020.5365855537590.4762670035340.7120179529760.3095996473320.2970022448080.006962116867750.07943910822610.0359032723759-0.1170185966760.02540951481070.07654643547890.029188005918-0.0400046730354-0.03545269643090.133545177478-0.0109212766444-0.009628503086710.139794404351-0.003048876533310.13279519616224.9348335328.3911102679920.7095121588
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 299 through 391 )BB299 - 3911 - 93
22chain 'B' and (resid 392 through 507 )BB392 - 50794 - 209
33chain 'A' and (resid 299 through 312 )AA299 - 3121 - 14
44chain 'A' and (resid 313 through 408 )AA313 - 40815 - 110
55chain 'A' and (resid 409 through 507 )AA409 - 507111 - 209

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