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- PDB-4f3f: Crystal Structure of Msln7-64 MORAb-009 FAB complex -

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Basic information

Entry
Database: PDB / ID: 4f3f
TitleCrystal Structure of Msln7-64 MORAb-009 FAB complex
Components
  • MORAb-009 Fab heavy chain
  • MORAb-009 Fab light chain
  • Mesothelin
KeywordsIMMUNE SYSTEM / Antibody Fab / Recognize mesothelin / 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
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 - #40 / Mesothelin / Stereocilin-related / Mesothelin / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsXia, D. / Pastan, I. / Ma, J. / Tang, W.K. / Esser, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Recognition of mesothelin by the therapeutic antibody MORAb-009: structural and mechanistic insights.
Authors: Ma, J. / Tang, W.K. / Esser, L. / Pastan, I. / Xia, D.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Source and taxonomy
Revision 1.2Mar 26, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MORAb-009 Fab light chain
B: MORAb-009 Fab heavy chain
C: Mesothelin


Theoretical massNumber of molelcules
Total (without water)55,7193
Polymers55,7193
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-31 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.163, 146.163, 80.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Antibody MORAb-009 Fab light chain


Mass: 23243.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody MORAb-009 Fab heavy chain


Mass: 24422.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor / Megakaryocyte-potentiating factor / MPF ...CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor / Megakaryocyte-potentiating factor / MPF / Mesothelin / cleaved form


Mass: 8053.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Escherichia coli (E. coli) / References: UniProt: Q13421
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
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: 4.48 Å3/Da / Density % sol: 72.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Trisodium citrate pH 5.6, 17% Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2011 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 29927 / Num. obs: 29264 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.76 / Num. unique all: 2373 / Rsym value: 0.101 / % possible all: 80

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: dev_965)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F33, Difference Fourier revealed MSLN7-64

4f33


Resolution: 2.65→34.076 Å / SU ML: 0.38 / σ(F): 0.66 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1448 5.1 %Random
Rwork0.1771 ---
all0.1794 28414 --
obs0.1794 28414 98.89 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.96 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-25.2257 Å20 Å2-0 Å2
2--25.2257 Å20 Å2
3----1.1986 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 122 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173820
X-RAY DIFFRACTIONf_angle_d1.5845178
X-RAY DIFFRACTIONf_dihedral_angle_d17.6231383
X-RAY DIFFRACTIONf_chiral_restr0.076578
X-RAY DIFFRACTIONf_plane_restr0.007657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.74470.33131190.30132449X-RAY DIFFRACTION90
2.7447-2.85450.33261360.25882681X-RAY DIFFRACTION99
2.8545-2.98440.27551440.23612739X-RAY DIFFRACTION100
2.9844-3.14160.26731490.21072672X-RAY DIFFRACTION100
3.1416-3.33830.25841510.20422731X-RAY DIFFRACTION100
3.3383-3.59580.22191390.18712694X-RAY DIFFRACTION100
3.5958-3.95720.22711640.16942728X-RAY DIFFRACTION100
3.9572-4.52860.1961510.14052721X-RAY DIFFRACTION100
4.5286-5.70130.18461450.14132745X-RAY DIFFRACTION100
5.7013-34.07860.18741500.16282806X-RAY DIFFRACTION100
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)
12.3904-1.29710.92434.4417-0.55554.43780.0243-0.1407-0.3123-0.09560.2017-0.08610.47020.1431-0.1690.1992-0.0247-0.03780.2364-0.02890.250773.77220.9665.196
21.63040.2965-0.04532.3481-0.79821.6159-0.2290.1051-0.287-0.39580.57350.9580.0333-0.72310.04170.3752-0.1544-0.08220.4580.14690.74751.3466-7.0561.8226
31.3974-0.3554-0.69651.89-0.30185.27110.2207-0.0416-0.2063-0.20840.17360.53540.5302-1.37-0.30260.2832-0.0896-0.08040.56380.24520.420551.018527.5978-9.3711
42.4686-0.54490.60445.00020.73112.80420.0848-0.0674-0.2186-0.3650.19740.2465-0.0596-0.1389-0.25270.1831-0.0597-0.0080.28220.04910.213862.375633.2353-8.5619
51.98591.07511.07652.5314-0.0272.70770.07220.108-0.1004-0.36120.37710.16960.1842-0.1954-0.39610.2499-0.0537-0.03420.3060.08120.257260.438429.5347-6.7116
61.30811.6419-0.072.207-0.02420.0552-0.1158-0.1569-0.4195-0.50220.52910.73640.3044-0.50130.03450.4063-0.1915-0.2360.70980.29030.808445.627113.2375-9.9665
73.52310.33760.44533.47390.79276.9407-0.3138-0.4736-0.02260.24370.63441.2892-0.4016-1.1555-0.29440.51620.1097-0.01120.6740.28720.936742.24635.47853.5503
85.2187-2.41295.64287.2116-5.61768.38550.30971.1915-0.3771-1.1065-0.1593-0.45780.7392.0508-0.01490.44490.00680.06310.5442-0.05690.338486.240640.8932-6.5999
94.9443-1.0787-0.05074.8376-0.98217.1455-0.2190.2672-0.3294-0.7270.31480.11530.90710.2142-0.19040.3067-0.10910.02660.2509-0.00960.194576.05938.5316-6.9756
103.6808-0.04941.48060.32420.97323.75740.02110.01610.948-0.1621-0.14540.1429-0.58780.48420.22920.3201-0.1526-0.04130.35290.02310.319578.216747.476-7.3569
116.73751.8941-1.79786.4256-1.16194.49320.3142-0.96011.09021.132-0.1685-0.0089-0.87370.14-0.07580.55640.0236-0.02930.2461-0.06170.338874.996151.7166-1.0931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 212 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 25 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 130 )
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 220 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 17 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 24 )
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 50 )
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 64 )

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