[English] 日本語
Yorodumi
- PDB-8cxc: Novel Anti-Mesothelin Antibodies Enable Crystallography of the In... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cxc
TitleNovel Anti-Mesothelin Antibodies Enable Crystallography of the Intact Mesothelin Ectodo- main and Engineering of Potent, T cell-engaging Bispecific Therapeutics
Components
  • 3F2 Antibody heavy chain
  • 3F2 Antibody light chain
  • Mesothelin, cleaved form
  • scFv Amatuximab
KeywordsANTITUMOR PROTEIN / Antibody / complex / tumor associated antigen
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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 Å
AuthorsBandaranayake, A.D. / Rupert, P.B. / Lin, I. / Pilat, K. / Ruff, R.O. / Friend, D.J. / Chan, M.K. / Clarke, M. / Carter, J. / Meshinchi, S. ...Bandaranayake, A.D. / Rupert, P.B. / Lin, I. / Pilat, K. / Ruff, R.O. / Friend, D.J. / Chan, M.K. / Clarke, M. / Carter, J. / Meshinchi, S. / Mehlin, C. / Olson, J.M. / Strong, R.K. / Correnti, C.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Front. Drug Discov. / Year: 2023
Title: Novel mesothelin antibodies enable crystallography of the intact mesothelin ectodomain and engineering of potent, T cell-engaging bispecific therapeutics
Authors: Lin, I. / Rupert, P.B. / Pilat, K. / Ruff, R.O. / Friend, D.J. / Chan, M.K. / Clarke, M. / Hoffstrom, B.G. / Carter, J. / Meshinchi, S. / Bandaranayake, A.D. / Mehlin, C. / Olson, J.M. / ...Authors: Lin, I. / Rupert, P.B. / Pilat, K. / Ruff, R.O. / Friend, D.J. / Chan, M.K. / Clarke, M. / Hoffstrom, B.G. / Carter, J. / Meshinchi, S. / Bandaranayake, A.D. / Mehlin, C. / Olson, J.M. / Strong, R.K. / Correnti, C.E.
History
DepositionMay 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.0May 1, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: 3F2 Antibody light chain
H: 3F2 Antibody heavy chain
M: Mesothelin, cleaved form
A: scFv Amatuximab


Theoretical massNumber of molelcules
Total (without water)108,4664
Polymers108,4664
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.303, 204.175, 123.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222

-
Components

#1: Antibody 3F2 Antibody light chain


Mass: 23391.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody 3F2 Antibody heavy chain


Mass: 23018.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Protein Mesothelin, cleaved form


Mass: 36963.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Homo sapiens (human) / References: UniProt: Q13421
#4: Antibody scFv Amatuximab


Mass: 25092.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: tris 8.0, zinc chloride, ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.25→50 Å / Num. obs: 13542 / % possible obs: 84.7 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.088 / Rrim(I) all: 0.151 / Χ2: 5.041 / Net I/σ(I): 12.6 / Num. measured all: 34767
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.25-4.322.50.7846690.2630.5760.9793.4885.5
4.32-4.42.40.6546610.4410.4840.8192.95185.4
4.4-4.492.40.6776540.5770.4910.8433.49383.8
4.49-4.582.50.5416620.7580.3910.6723.73283.1
4.58-4.682.60.4026900.7550.2890.4993.58586.6
4.68-4.792.50.3576750.840.2540.4412.985.2
4.79-4.912.60.3166720.8990.220.3882.67386.9
4.91-5.042.70.2637180.9340.180.3212.67688.4
5.04-5.192.70.2166950.9220.1470.2623.26289.6
5.19-5.352.70.2227000.930.150.273.33488.5
5.35-5.542.70.1866950.9740.1270.2262.74788.8
5.54-5.772.70.2226930.9430.1540.2723.14586.8
5.77-6.032.70.1937010.9260.1350.2373.32386.9
6.03-6.352.60.1676880.9530.1140.2034.61186.4
6.35-6.742.50.1276810.9710.0890.1564.68584.1
6.74-7.262.60.116710.970.0790.1366.10283.9
7.26-7.992.80.086920.9840.0540.0976.38885.6
7.99-9.142.70.0696950.9880.0470.08410.46385.1
9.14-11.492.30.0546570.9930.0420.06912.46779.5
11.49-501.90.0685730.9820.0570.08928.48565.6

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f33

4f33


Resolution: 4.31→45.78 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.88 / SU B: 142.637 / SU ML: 0.788 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 667 4.9 %RANDOM
Rwork0.2435 ---
obs0.2463 12857 83.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 741.35 Å2 / Biso mean: 263.302 Å2 / Biso min: 100.06 Å2
Baniso -1Baniso -2Baniso -3
1--5.08 Å2-0 Å20 Å2
2---7.25 Å20 Å2
3---12.34 Å2
Refinement stepCycle: final / Resolution: 4.31→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6984 0 0 0 6984
Num. residues----938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0137172
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176458
X-RAY DIFFRACTIONr_angle_refined_deg1.9081.6419781
X-RAY DIFFRACTIONr_angle_other_deg1.1661.57514916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8635933
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94223.241290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.432151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.471524
X-RAY DIFFRACTIONr_chiral_restr0.060.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021573
LS refinement shellResolution: 4.314→4.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 45 -
Rwork0.442 874 -
all-919 -
obs--79.16 %
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)
15.67343.49130.71917.06161.6277.44410.56580.05480.1191-0.8301-1.0865-0.28170.608-0.6530.52060.63990.3430.0780.7475-0.03730.11787.31274.00428.833
27.282-4.8945-0.309114.422710.52549.8294-0.03570.36120.7001-0.5618-0.0616-0.1164-0.20080.12020.09730.48460.0366-0.24470.73520.24690.2633-20.76196.31130.051
34.7269-1.7834-2.434612.35534.22158.81290.6982-0.67960.3370.075-0.2167-0.4030.9961-0.4208-0.48150.4177-0.1059-0.01490.4285-0.0390.0419.4978.37850.623
46.52562.66444.21293.84663.623812.54130.60520.0209-0.59270.7077-0.4619-0.01391.6019-0.7525-0.14330.2932-0.1803-0.08610.46560.14550.2133-24.16887.57344.025
511.2533-9.3701-0.60418.10061.43787.05280.34941.2314-1.6286-0.0485-0.5810.99821.69351.1320.23160.5920.3341-0.06850.7161-0.71511.068719.63342.151-27.783
66.2148.10660.592622.36079.09265.93490.9466-0.6043-0.5651-0.1045-0.7305-0.9557-0.79070.0532-0.21610.95950.6782-0.29861.11480.0140.504729.40845.426-11.853
720.58286.6502-10.36694.9044-8.111213.4709-0.0347-0.98151.1975-0.80350.05770.07041.4787-0.0011-0.0230.76610.57010.011.1727-0.12440.320926.81741.0770.876
83.5336-0.2074-0.79354.5421-0.819619.15180.41820.23030.00440.10030.1814-0.7251-0.0288-0.3466-0.59950.42490.5488-0.00130.7675-0.10080.742735.69755.24812.511
93.3601-1.67760.01251.7124-0.345920.8010.4483-0.0232-0.0988-0.12490.171-0.1130.66110.4406-0.61930.50040.5173-0.11350.6342-0.04640.456730.20958.67936.964
109.2746-0.2164.6680.4111-0.84083.88552.07832.2188-3.6048-0.431-0.06580.09652.20820.4568-2.01242.557-0.7641-0.95992.1028-1.16392.1996-9.51333.978-34.168
1113.6787-5.4356-1.326212.6346-0.51149.68970.3275-0.9866-1.0402-0.8373-0.49390.90062.0467-1.4310.16650.5446-0.3163-0.05780.48770.01130.1132-3.77747.994-16.712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L2 - 107
2X-RAY DIFFRACTION2L108 - 212
3X-RAY DIFFRACTION3H1 - 119
4X-RAY DIFFRACTION4H120 - 220
5X-RAY DIFFRACTION5M302 - 361
6X-RAY DIFFRACTION6M362 - 404
7X-RAY DIFFRACTION7M405 - 431
8X-RAY DIFFRACTION8M432 - 506
9X-RAY DIFFRACTION9M507 - 589
10X-RAY DIFFRACTION10A2 - 108
11X-RAY DIFFRACTION11B2 - 118

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more