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- PDB-8vm1: Structural Elucidation of the Mesothelin Mucin16 CA125 Interaction -

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Basic information

Entry
Database: PDB / ID: 8vm1
TitleStructural Elucidation of the Mesothelin Mucin16 CA125 Interaction
ComponentsMesothelin, cleaved form,Mucin-16
KeywordsCELL ADHESION / linked complex
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 / Post-translational modification: synthesis of GPI-anchored proteins / Dectin-2 family / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / Post-translational modification: synthesis of GPI-anchored proteins / Dectin-2 family / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / vesicle / cell adhesion / endoplasmic reticulum lumen / external side of plasma membrane / cell surface / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Mucin-16 / Mesothelin / Stereocilin-related / Mesothelin / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain
Similarity search - Domain/homology
Mesothelin / Mucin-16
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRupert, P.B. / Strong, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01A|176563 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA015704 United States
CitationJournal: Structure / Year: 2024
Title: Structural elucidation of the mesothelin-mucin-16/CA125 interaction.
Authors: Rupert, P.B. / Buerger, M. / Friend, D.J. / Strong, R.K.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
A: Mesothelin, cleaved form,Mucin-16
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9093
Polymers21,8981
Non-polymers1,0112
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.203, 73.237, 75.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 21898.006 Da / Num. of mol.: 1
Fragment: residues 296-359 of mesothelin (Uniprot numbering),SEA 10 domain of mucin-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF, MUC16, CA125 / Production host: Homo sapiens (human) / References: UniProt: Q13421, UniProt: Q8WXI7
#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 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.65 Å3/Da / Density % sol: 66.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Bis-Tris, NH4CL, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 9868 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.034 / Rrim(I) all: 0.074 / Χ2: 2.697 / Net I/σ(I): 20.9 / Num. measured all: 52276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.65-2.75.80.6284800.8220.950.2830.6911.229100
2.7-2.746.40.6794770.9060.9750.2870.7380.866100
2.74-2.86.40.4975010.9110.9770.2130.5420.97399.8
2.8-2.856.40.4344770.9190.9790.1860.4731.126100
2.85-2.926.30.374880.9380.9840.1610.4041.208100
2.92-2.986.10.3224880.9460.9860.1420.3531.664100
2.98-3.0660.2614890.9750.9940.1170.2871.939100
3.06-3.145.80.214860.9830.9960.0950.2322.31599.2
3.14-3.235.10.1584860.9870.9970.0770.1762.65398.6
3.23-3.345.50.1634800.9880.9970.0760.1812.90999.8
3.34-3.465.80.125000.9920.9980.0550.1323.26599.8
3.46-3.65.30.14910.9940.9980.0480.1113.697100
3.6-3.764.20.0714840.990.9980.0410.0834.30497.8
3.76-3.964.30.0744930.9940.9990.040.0844.2397.4
3.96-4.214.30.0624870.9950.9990.0320.074.38299.2
4.21-4.534.60.0544960.9960.9990.0280.0624.33498.6
4.53-4.994.80.055000.9960.9990.0250.0574.29598.6
4.99-5.714.60.0515030.9960.9990.0260.0574.23898.6
5.71-7.194.20.0515150.9950.9990.0270.0584.30798.3
7.19-504.20.0485470.9970.9990.0260.0554.46795.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→33.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.921 / SU B: 24.55 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29849 480 5 %RANDOM
Rwork0.24781 ---
obs0.25049 9117 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.658 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å2-0 Å2
2--1.17 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 2.65→33.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 67 8 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0131576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171474
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.722149
X-RAY DIFFRACTIONr_angle_other_deg1.1481.6323413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0575184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.77921.97476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.76215258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7191510
X-RAY DIFFRACTIONr_chiral_restr0.0590.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1166.668739
X-RAY DIFFRACTIONr_mcbond_other3.1026.665738
X-RAY DIFFRACTIONr_mcangle_it4.55310.003922
X-RAY DIFFRACTIONr_mcangle_other4.55210.005923
X-RAY DIFFRACTIONr_scbond_it4.1547.496837
X-RAY DIFFRACTIONr_scbond_other4.1537.497837
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.29711.111228
X-RAY DIFFRACTIONr_long_range_B_refined7.32380.2661646
X-RAY DIFFRACTIONr_long_range_B_other7.32480.2421646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 46 -
Rwork0.287 656 -
obs--100 %
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)
14.09231.38311.19175.0308-0.15122.6244-0.0119-0.16260.15540.64540.0511-0.2135-0.56530.1466-0.03920.2015-0.0463-0.01360.1083-0.01940.0277-49.4092-7.7553-5.5096
23.7173-1.0715-0.12894.91930.66323.66020.03060.00370.0854-0.35210.0369-0.2341-0.20820.2859-0.06750.0751-0.06080.03330.0713-0.02090.0182-23.581-3.53577.8181
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A299 - 361
2X-RAY DIFFRACTION2A362 - 483

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