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- PDB-7ued: Crystal structure of full length mesothelin bound with MORAb-009 Fab -

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Basic information

Entry
Database: PDB / ID: 7ued
TitleCrystal structure of full length mesothelin bound with MORAb-009 Fab
Components
  • (MORAb-009 Fab ...) x 2
  • Isoform 4 of Mesothelin
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 / cell surface / Golgi apparatus / 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 / cell surface / Golgi apparatus / extracellular region / membrane / plasma membrane
Similarity search - Function
Mesothelin / Stereocilin-related / Mesothelin / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: Isoform 4 of Mesothelin
L: MORAb-009 Fab light chain
H: MORAb-009 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3577
Polymers81,6493
Non-polymers7094
Water59433
1
M: Isoform 4 of Mesothelin
hetero molecules

L: MORAb-009 Fab light chain
H: MORAb-009 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3577
Polymers81,6493
Non-polymers7094
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)133.447, 133.447, 276.087
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody MORAb-009 Fab light chain


Mass: 23140.539 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-009 Fab heavy chain


Mass: 23246.953 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)

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Protein / Sugars , 2 types, 2 molecules M

#1: Protein Isoform 4 of Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor


Mass: 35261.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13421
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 36 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.71 Å3/Da / Density % sol: 66.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris, pH 7, 150 mM sodium citrate, 16.4% 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: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 21609 / % possible obs: 85 % / Redundancy: 3.1 % / Biso Wilson estimate: 66.66 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 6.444
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.499 / Num. unique obs: 1755

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Processing

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

4f3f


Resolution: 3→24.68 Å / SU ML: 0.3659 / Cross valid method: FREE R-VALUE / σ(F): 0.53 / Phase error: 22.7411
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 1109 5.18 %
Rwork0.2007 20310 -
obs0.2026 21419 84.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.9 Å2
Refinement stepCycle: LAST / Resolution: 3→24.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5532 0 44 33 5609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00225700
X-RAY DIFFRACTIONf_angle_d0.55357738
X-RAY DIFFRACTIONf_chiral_restr0.0397869
X-RAY DIFFRACTIONf_plane_restr0.0038986
X-RAY DIFFRACTIONf_dihedral_angle_d12.09052091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.140.29041020.2992032X-RAY DIFFRACTION68.66
3.14-3.30.30051180.29072223X-RAY DIFFRACTION75.22
3.3-3.510.31681270.26122433X-RAY DIFFRACTION81.58
3.51-3.780.27941480.2392591X-RAY DIFFRACTION87.68
3.78-4.160.2221410.19492630X-RAY DIFFRACTION88.22
4.16-4.750.20411500.16072722X-RAY DIFFRACTION90.57
4.75-5.980.20751530.17242776X-RAY DIFFRACTION91.36
5.98-24.680.22131700.17572903X-RAY DIFFRACTION91.65
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)
11.094607539350.7365778307572.298215137411.278491450961.629679904124.35203810170.206934200120.0336715787888-0.1065313562690.100895935288-0.0774964009298-0.02660791732320.464473255907-0.0114198556128-0.1397519243030.5386355251690.0601172947350.1009855702970.546737420841-0.008233439561470.50326180515-2.3264503542129.8165315985-45.1841517068
20.08692198121620.1610376547330.4324753380633.036461550461.132813939131.031336934270.147788131229-0.06508990595470.0339039476030.4018263252-0.35578040970.438374363510.245713080527-0.4578944239280.2461920917450.424215958755-0.0904256114150.1345806463650.67295370687-0.1464467947990.615572654931-31.731334359748.6720924993-22.4988086543
31.174712142911.172330547091.130883110062.551600074791.313837632481.1351821947-0.050463084993-0.001080061903880.0247707778468-0.214735076362-0.05177412065260.104091356117-0.0681498259099-0.2136513725180.09677805988320.4394578211510.0203066561410.05681927079730.572876437057-0.07373302200320.456649559515-22.013244455656.9050256413-35.2893075544
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'M' and resid 299 through 587)MA - C299 - 5871
22(chain 'L' and resid 2 through 504)LD - E2 - 5041
33(chain 'H' and resid 1 through 220)HF1 - 2201 - 220

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