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- PDB-6i07: Crystal structure of EpCAM in complex with scFv -

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Basic information

Entry
Database: PDB / ID: 6i07
TitleCrystal structure of EpCAM in complex with scFv
Components
  • Epithelial cell adhesion molecule
  • Single chain FvSingle-chain variable fragment
KeywordsIMMUNE SYSTEM / single chain Fv / scFv / EpCAM
Function / homology
Function and homology information


cadherin binding involved in cell-cell adhesion / signal transduction involved in regulation of gene expression / negative regulation of cell-cell adhesion mediated by cadherin / ureteric bud development / positive regulation of stem cell proliferation / bicellular tight junction / lateral plasma membrane / stem cell differentiation / Cell surface interactions at the vascular wall / basolateral plasma membrane ...cadherin binding involved in cell-cell adhesion / signal transduction involved in regulation of gene expression / negative regulation of cell-cell adhesion mediated by cadherin / ureteric bud development / positive regulation of stem cell proliferation / bicellular tight junction / lateral plasma membrane / stem cell differentiation / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / positive regulation of cell population proliferation / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Epithelial cell adhesion molecule N-terminal domain / Transmembrane glycoprotein EPCAM/Trop-2 / : / Epithelial cell adhesion molecule, N-terminal domain / EPCAM/Trop-2, C-terminal / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats.
Similarity search - Domain/homology
Epithelial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsCasaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. ...Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: MM-131, a bispecific anti-Met/EpCAM mAb, inhibits HGF-dependent and HGF-independent Met signaling through concurrent binding to EpCAM.
Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. ...Authors: Casaletto, J.B. / Geddie, M.L. / Abu-Yousif, A.O. / Masson, K. / Fulgham, A. / Boudot, A. / Maiwald, T. / Kearns, J.D. / Kohli, N. / Su, S. / Razlog, M. / Raue, A. / Kalra, A. / Hakansson, M. / Logan, D.T. / Welin, M. / Chattopadhyay, S. / Harms, B.D. / Nielsen, U.B. / Schoeberl, B. / Lugovskoy, A.A. / MacBeath, G.
History
DepositionOct 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0Mar 11, 2020Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Single chain Fv
B: Single chain Fv
C: Epithelial cell adhesion molecule
D: Epithelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0535
Polymers112,9604
Non-polymers921
Water2,108117
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.886, 91.071, 181.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUMETMETCC26 - 733 - 50
21GLUGLUMETMETDD26 - 733 - 50
12TYRTYRPHEPHECC95 - 25972 - 236
22TYRTYRPHEPHEDD95 - 25972 - 236

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.920778, 0.388974, -0.029443), (0.389299, 0.921092, -0.00602), (0.024778, -0.017005, -0.999548)-24.18966, 4.63553, -74.47176

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Components

#1: Antibody Single chain Fv / Single-chain variable fragment


Mass: 27857.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human)
#2: Protein Epithelial cell adhesion molecule / Ep-CAM / Adenocarcinoma-associated antigen / Cell surface glycoprotein Trop-1 / Epithelial cell ...Ep-CAM / Adenocarcinoma-associated antigen / Cell surface glycoprotein Trop-1 / Epithelial cell surface antigen / Epithelial glycoprotein / EGP / Epithelial glycoprotein 314 / hEGP314 / KS 1/4 antigen / KSA / Major gastrointestinal tumor-associated protein GA733-2 / Tumor-associated calcium signal transducer 1


Mass: 28622.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PCA is pyroglutamic acid post translational modification
Source: (gene. exp.) Homo sapiens (human) / Gene: EPCAM, GA733-2, M1S2, M4S1, MIC18, TACSTD1, TROP1 / Cell line (production host): EXPI293F cells / Production host: Homo sapiens (human) / References: UniProt: P16422
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 6.4 / Details: 0.1 M PCTP pH 6.4, 21 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→28.7 Å / Num. obs: 56398 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 53.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.7
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 4.6 % / Rmerge(I) obs: 1.175 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4410 / CC1/2: 0.514 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVZ, 4MZV

1svz

4mzv


Resolution: 2.35→28.7 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.137 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.246 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27876 2851 5.1 %RANDOM
Rwork0.23016 ---
obs0.23267 53487 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 87.131 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20 Å2
2--0.37 Å20 Å2
3---1.79 Å2
Refinement stepCycle: 1 / Resolution: 2.35→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 6 117 7241
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0137271
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176581
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.6479838
X-RAY DIFFRACTIONr_angle_other_deg1.1831.57715354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9755894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07723.333366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06151275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6991536
X-RAY DIFFRACTIONr_chiral_restr0.0510.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028050
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021474
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_it5.9289.2443612
X-RAY DIFFRACTIONr_mcbond_other5.9279.2433611
X-RAY DIFFRACTIONr_mcangle_it9.13513.8394494
X-RAY DIFFRACTIONr_mcangle_other9.13413.844495
X-RAY DIFFRACTIONr_scbond_it5.289.6263659
X-RAY DIFFRACTIONr_scbond_other5.289.6253660
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.27914.255345
X-RAY DIFFRACTIONr_long_range_B_refined12.1457656
X-RAY DIFFRACTIONr_long_range_B_other12.1447657
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: C / Ens-ID: 1 / Number: 3180 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.320.5
medium thermal11.712
LS refinement shellResolution: 2.348→2.409 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 194 -
Rwork0.365 3790 -
obs--96.77 %

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