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- PDB-8cx3: Crystal structure of full-length mesothelin -

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Basic information

Entry
Database: PDB / ID: 8cx3
TitleCrystal structure of full-length mesothelin
ComponentsIsoform 4 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 / 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
Similarity search - Domain/homology
PHOSPHATE ION / Mesothelin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.609 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: 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
DepositionMay 19, 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 / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens
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

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Assembly

Deposited unit
A: Isoform 4 of Mesothelin
B: Isoform 4 of Mesothelin
C: Isoform 4 of Mesothelin
D: Isoform 4 of Mesothelin
E: Isoform 4 of Mesothelin
F: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,87327
Polymers211,5676
Non-polymers3,30621
Water00
1
A: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6704
Polymers35,2611
Non-polymers4083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7645
Polymers35,2611
Non-polymers5034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6704
Polymers35,2611
Non-polymers4083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,2611
Non-polymers6113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7675
Polymers35,2611
Non-polymers5064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1305
Polymers35,2611
Non-polymers8694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.171, 279.324, 170.046
Angle α, β, γ (deg.)90.000, 125.091, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 35261.242 Da / Num. of mol.: 6
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

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Sugars , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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.: 4
Source method: isolated from a genetically manipulated source
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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Non-polymers , 2 types, 15 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3

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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: 9.05 Å3/Da / Density % sol: 86.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.9-1.1 M sodium/potassium phosphate, pH 8.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.89197 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89197 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.3176
pseudo-merohedral221/2H-1/2K+L, -3/2H-1/2K-L, -L20.3291
pseudo-merohedral331/2H+1/2K+L, 3/2H-1/2K+L, -L30.2979
pseudo-merohedral44H, -K, -H-L40.0554
ReflectionResolution: 3.6→50 Å / Num. obs: 78378 / % possible obs: 91.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 4.87
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 6674 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7UED

7ued


Resolution: 3.609→49.292 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.842 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.237 / SU B: 29.87 / SU ML: 0.234 / Average fsc free: 0.9647 / Average fsc work: 0.9714 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3105 3948 5.062 %
Rwork0.2908 74040 -
all0.292 --
obs-77988 91.046 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 128.434 Å2
Baniso -1Baniso -2Baniso -3
1--6.781 Å2-0 Å213.9 Å2
2--2.742 Å2-0 Å2
3---4.039 Å2
Refinement stepCycle: LAST / Resolution: 3.609→49.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11757 0 203 0 11960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212222
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611377
X-RAY DIFFRACTIONr_angle_refined_deg0.7971.64616609
X-RAY DIFFRACTIONr_angle_other_deg0.2641.55726645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68751479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.9161054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.252102153
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.59510515
X-RAY DIFFRACTIONr_chiral_restr0.0380.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022194
X-RAY DIFFRACTIONr_nbd_refined0.1910.23101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.211172
X-RAY DIFFRACTIONr_nbtor_refined0.170.26164
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.26280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.220
X-RAY DIFFRACTIONr_nbd_other0.1410.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0730.22
X-RAY DIFFRACTIONr_mcbond_it0.4573.9015934
X-RAY DIFFRACTIONr_mcbond_other0.4573.9015934
X-RAY DIFFRACTIONr_mcangle_it0.8435.8487407
X-RAY DIFFRACTIONr_mcangle_other0.8435.8487408
X-RAY DIFFRACTIONr_scbond_it0.2783.9346288
X-RAY DIFFRACTIONr_scbond_other0.2783.9346289
X-RAY DIFFRACTIONr_scangle_it0.5235.8959202
X-RAY DIFFRACTIONr_scangle_other0.5235.8959203
X-RAY DIFFRACTIONr_lrange_it1.9349.11614092
X-RAY DIFFRACTIONr_lrange_other1.9349.11614092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.609-3.70.4722270.46142640.46161460.9740.9873.07190.439
3.7-3.7980.4422210.42646460.42760660.9710.97180.23410.397
3.798-3.9040.3762300.38746970.38757920.9710.97585.06560.352
3.904-4.0190.3463290.36645290.36456640.9770.97685.76980.327
4.019-4.1450.3242320.33547020.33555390.9780.97689.07740.294
4.145-4.2840.3512180.31946600.32153900.9730.97790.50090.275
4.284-4.4380.3332390.31644040.31750970.9740.97991.09280.265
4.438-4.610.3182810.30743210.30850160.9720.97691.74640.261
4.61-4.8030.3052380.28143120.28247990.9750.97994.81140.234
4.803-5.0230.3012370.27241710.27346110.9770.9895.59750.225
5.023-5.2770.2971770.28239750.28343340.9660.97495.80060.237
5.277-5.5720.3621720.26438610.26841780.9530.97596.52940.219
5.572-5.9240.2621750.28436210.28339410.9720.97296.32070.236
5.924-6.3530.2751780.29134210.2936900.9710.96697.53390.24
6.353-6.890.2772020.26531530.26634030.960.96498.58950.219
6.89-7.5920.1991630.20629450.20631590.9750.97298.38560.183
7.592-8.5630.2491460.21826530.2228270.9570.96499.00960.201
8.563-10.0370.193990.20323560.20224620.9720.98199.71570.196
10.037-12.6870.255930.23619390.23720360.9480.95399.80350.232
12.687-20.0020.371910.26214100.26815080.7880.85299.53580.28
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)
12.2444-1.41311.12541.9639-0.56580.9509-0.1074-0.17830.19660.06230.0011-0.2002-0.0032-0.00990.10630.79360.0238-0.24490.4604-0.03891.101536.515160.294187.3873
20.7164-0.1443-0.26843.3563-0.28990.36660.2463-0.15080.06290.2337-0.1335-0.03660.1358-0.2322-0.11280.7565-0.2791-0.32110.5136-0.12081.2139-6.80569.667657.1311
32.750.60950.84620.4676-0.28140.9493-0.22620.0245-0.0586-0.05110.1467-0.0708-0.212-0.23970.07950.90180.1381-0.42040.8465-0.06731.018480.182668.5496117.515
40.639-0.7266-0.08541.5426-0.10150.26370.4188-0.14290.0309-0.5938-0.06980.1958-0.2961-0.2317-0.3491.4460.2529-0.28520.94050.14931.351895.1239103.3966107.3873
52.5659-0.93941.23910.4722-0.46690.7409-0.0924-0.15460.30580.1532-0.19050.0870.05340.21580.28281.0272-0.2277-0.50881.02640.1031.309925.259847.803257.9759
60.84830.97150.82611.46671.24991.3926-0.32960.4845-0.430.27790.4183-0.39630.0316-0.0762-0.08871.5351-0.216-0.13610.9405-0.33332.153919.6768148.64955.2009
Refinement TLS groupSelection: ALL

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