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- PDB-5jym: Human P-cadherin EC12 with scFv TSP11 bound -

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Basic information

Entry
Database: PDB / ID: 5jym
TitleHuman P-cadherin EC12 with scFv TSP11 bound
Components
  • Antibody scFv TSP11
  • Cadherin-3
KeywordsCELL ADHESION/IMMUNE SYSTEM / Cadherin / Cell adhesion / Antibody / Protein-protein interaction / OXIDOREDUCTASE / CELL ADHESION-IMMUNE SYSTEM complex
Function / homology
Function and homology information


negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / retina homeostasis ...negative regulation of timing of catagen / positive regulation of melanosome transport / hair cycle process / positive regulation of tyrosinase activity / positive regulation of keratinocyte proliferation / positive regulation of melanin biosynthetic process / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / retina homeostasis / Adherens junctions interactions / cell-cell junction assembly / adherens junction organization / positive regulation of insulin-like growth factor receptor signaling pathway / keratinization / homophilic cell adhesion via plasma membrane adhesion molecules / visual perception / adherens junction / negative regulation of transforming growth factor beta receptor signaling pathway / cell morphogenesis / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / cell migration / cell junction / cell adhesion / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of gene expression / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsCaaveiro, J.M.M. / Kudo, S. / Tsumoto, K.
CitationJournal: Sci Rep / Year: 2017
Title: Disruption of cell adhesion by an antibody targeting the cell-adhesive intermediate (X-dimer) of human P-cadherin
Authors: Kudo, S. / Caaveiro, J.M.M. / Nagatoishi, S. / Miyafusa, T. / Matsuura, T. / Sudou, Y. / Tsumoto, K.
History
DepositionMay 14, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
Revision 1.4Oct 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: Cadherin-3
B: Antibody scFv TSP11
C: Cadherin-3
D: Antibody scFv TSP11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,92112
Polymers101,6004
Non-polymers3218
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-58 kcal/mol
Surface area40420 Å2
Unit cell
Length a, b, c (Å)58.700, 83.430, 199.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASPASPAA1 - 2131 - 213
21ASPASPASPASPCC1 - 2131 - 213
12GLNGLNGLUGLUBB1 - 2471 - 247
22GLNGLNGLUGLUDD1 - 2471 - 247

NCS ensembles :
ID
1
2

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Components

#1: Protein Cadherin-3 / Placental cadherin / P-cadherin


Mass: 23290.814 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / Variant (production host): Rosetta2 / References: UniProt: P22223
#2: Antibody Antibody scFv TSP11


Mass: 27509.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAbout scFv TSP11 (chain B, D), residues 123-141(SAGGGGSGGGGSGGGGSDI) belong to the linker joining ...About scFv TSP11 (chain B, D), residues 123-141(SAGGGGSGGGGSGGGGSDI) belong to the linker joining the heavy to the light chain of the antibody, and Residues 250-257(SAHHHHHH) belong to the purification tag.

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 150 mM CaCl2, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→99.91 Å / Num. obs: 36872 / % possible obs: 99.6 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Net I/σ(I): 14.5
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.8 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.0.9data reduction
SCALA3.3.21data scaling
PHASER2.5.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOK

1qok


Resolution: 2.45→99.91 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 22.685 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.534 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27037 1832 5 %RANDOM
Rwork0.22336 ---
obs0.22569 34984 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---2.88 Å20 Å2
3---2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.45→99.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 8 119 6873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.026917
X-RAY DIFFRACTIONr_bond_other_d0.0040.026285
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.949412
X-RAY DIFFRACTIONr_angle_other_deg0.966314549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9865865
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97424.983295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.162151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8661522
X-RAY DIFFRACTIONr_chiral_restr0.0810.21042
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217805
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021533
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_it1.7363.023487
X-RAY DIFFRACTIONr_mcbond_other1.7353.023486
X-RAY DIFFRACTIONr_mcangle_it2.8144.5254343
X-RAY DIFFRACTIONr_mcangle_other2.8134.5254344
X-RAY DIFFRACTIONr_scbond_it2.0463.2033430
X-RAY DIFFRACTIONr_scbond_other2.0463.2033428
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3354.7115069
X-RAY DIFFRACTIONr_long_range_B_refined5.0223.87307
X-RAY DIFFRACTIONr_long_range_B_other4.99323.7647278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A115490.12
12C115490.12
21B118430.1
22D118430.1
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 124 -
Rwork0.322 2428 -
obs--96.05 %
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)
11.8803-1.67560.36812.3465-0.58060.43810.06110.0534-0.1886-0.0254-0.03610.06880.07230.0075-0.0250.0918-0.0201-0.02170.1166-0.00340.0324-1.275137.5287-10.0325
23.3426-1.37990.53323.8121-0.43691.7379-0.09510.37160.6399-0.0568-0.1629-0.3307-0.59180.31680.25790.2268-0.0862-0.07730.14850.08590.1416-1.730375.9888-16.553
30.42670.00270.01092.1452-0.94861.16710.05710.04010.12340.1941-0.2009-0.2068-0.1960.090.14390.0418-0.012-0.01260.15050.02490.085-19.767462.22-43.9681
43.09310.3623-0.56543.74811.09962.0841-0.06420.3043-0.85510.3150.0687-0.13780.494-0.0122-0.00450.1374-0.0068-0.01140.1331-0.09860.2803-18.090322.1942-41.0637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 213
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION2B1 - 247
4X-RAY DIFFRACTION3C1 - 213
5X-RAY DIFFRACTION3C301 - 303
6X-RAY DIFFRACTION4D1 - 247

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