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- PDB-8fsl: Human Mesothelin bound to a neutralizing VH domain antibody -

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Basic information

Entry
Database: PDB / ID: 8fsl
TitleHuman Mesothelin bound to a neutralizing VH domain antibody
Components
  • Mesothelin
  • VH domain
KeywordsANTITUMOR PROTEIN / Mesothelin VH
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
Biological speciesEscherichia coli (E. coli)
Insect expression vector pBlueBacmsGCA1His (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsCalero, G.
Funding support1items
OrganizationGrant numberCountry
Other privateNA
CitationJournal: Mol Ther Oncolytics / Year: 2023
Title: Preclinical assessment of a novel human antibody VH domain targeting mesothelin as an antibody-drug conjugate.
Authors: Sun, Z. / Chu, X. / Adams, C. / Ilina, T.V. / Guerrero, M. / Lin, G. / Chen, C. / Jelev, D. / Ishima, R. / Li, W. / Mellors, J.W. / Calero, G. / Dimitrov, D.S.
History
DepositionJan 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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: VH domain
C: VH domain
D: VH domain
E: Mesothelin
F: Mesothelin
B: VH domain


Theoretical massNumber of molelcules
Total (without water)115,5636
Polymers115,5636
Non-polymers00
Water00
1
A: VH domain
C: VH domain
E: Mesothelin


Theoretical massNumber of molelcules
Total (without water)57,7823
Polymers57,7823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: VH domain
F: Mesothelin
B: VH domain


Theoretical massNumber of molelcules
Total (without water)57,7823
Polymers57,7823
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.116, 114.116, 340.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4

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Components

#1: Antibody
VH domain


Mass: 12806.857 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor


Mass: 32167.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Insect expression vector pBlueBacmsGCA1His (others)
Gene: MSLN, MPF
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q13421
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: 1.96 Å3/Da / Density % sol: 75 % / Description: 40%
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / Details: PEG3350 20% 0.15 M ammonium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.98008 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98008 Å / Relative weight: 1
ReflectionResolution: 2.9→114 Å / Num. obs: 51008 / % possible obs: 99 % / Redundancy: 109 % / Biso Wilson estimate: 101.44 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.055 / Rrim(I) all: 0.384 / Net I/σ(I): 15.6
Reflection shellResolution: 2.9→2.99 Å / Redundancy: 110 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 111 / Num. unique obs: 4354 / CC1/2: 0.21 / Rpim(I) all: 0.47 / Rrim(I) all: 0.36 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158_4158refinement
PHENIX1.19.2-4158_4158refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→39.9 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2539 1999 3.93 %
Rwork0.2385 --
obs0.2391 50922 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7817 0 0 0 7817
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118021
X-RAY DIFFRACTIONf_angle_d1.33910891
X-RAY DIFFRACTIONf_dihedral_angle_d19.322897
X-RAY DIFFRACTIONf_chiral_restr0.0661205
X-RAY DIFFRACTIONf_plane_restr0.011395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.41971390.40443414X-RAY DIFFRACTION100
2.97-3.050.4271410.41243425X-RAY DIFFRACTION100
3.05-3.140.39581390.40943432X-RAY DIFFRACTION100
3.14-3.240.39291420.36663459X-RAY DIFFRACTION100
3.24-3.360.34951410.32323456X-RAY DIFFRACTION100
3.36-3.490.35281400.3133418X-RAY DIFFRACTION100
3.49-3.650.28371410.29183453X-RAY DIFFRACTION100
3.65-3.850.30011410.27323481X-RAY DIFFRACTION100
3.85-4.090.29471430.22353467X-RAY DIFFRACTION100
4.09-4.40.2091420.21233499X-RAY DIFFRACTION100
4.4-4.840.221430.19683490X-RAY DIFFRACTION100
4.84-5.540.21751450.20643560X-RAY DIFFRACTION100
5.54-6.980.25751470.23753578X-RAY DIFFRACTION100
6.98-39.90.19741550.19393791X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -51.4914 Å / Origin y: -26.0968 Å / Origin z: 26.3841 Å
111213212223313233
T0.9353 Å20.0706 Å2-0.0823 Å2-0.4784 Å2-0.0947 Å2--0.5395 Å2
L0.1668 °2-0.0049 °2-0.0421 °2-1.2633 °2-0.8161 °2--0.0921 °2
S0.0109 Å °-0.0491 Å °-0.0136 Å °0.0809 Å °-0.0102 Å °0.0993 Å °-0.0907 Å °0.1167 Å °0.009 Å °
Refinement TLS groupSelection details: all

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