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- PDB-5jyl: Human P-cadherin MEC1 with scFv TSP7 bound -

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Basic information

Entry
Database: PDB / ID: 5jyl
TitleHuman P-cadherin MEC1 with scFv TSP7 bound
Components
  • Cadherin-3
  • scFv TSP7
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 / Adherens junctions interactions / catenin complex ...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 / Adherens junctions interactions / catenin complex / retina homeostasis / 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 / positive regulation of canonical Wnt signaling pathway / cell junction / cell adhesion / response to xenobiotic stimulus / cadherin binding / 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 / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cadherin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / 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: Cadherin-3
B: scFv TSP7
C: Cadherin-3
D: scFv TSP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2278
Polymers76,9694
Non-polymers2584
Water1,51384
1
A: Cadherin-3
B: scFv TSP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7075
Polymers38,4852
Non-polymers2233
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Cadherin-3
D: scFv TSP7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5203
Polymers38,4852
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.570, 49.410, 111.660
Angle α, β, γ (deg.)90.00, 101.89, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHRAA5 - 996 - 100
21ALAALATHRTHRCC5 - 996 - 100
12GLNGLNLEULEUBB1 - 2421 - 242
22GLNGLNLEULEUDD1 - 2421 - 242

NCS ensembles :
ID
1
2

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

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


Mass: 11138.497 Da / Num. of mol.: 2 / Fragment: UNP residues 108-207
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 scFv TSP7


Mass: 27346.043 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)

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Non-polymers , 4 types, 88 molecules

#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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsMET 0 in chain A, C is N-terminal extension to inhibit strand-swap dimerization. About scFv TSP7 ...MET 0 in chain A, C is N-terminal extension to inhibit strand-swap dimerization. About scFv TSP7 (chain B, D), residues 120-138(SAGGGGSGGGGSGGGGSDI) belong to the linker joining the heavy to the light chain of the antibody, and Residues 246-253(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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM potassium phosphate monobasic, 20% 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: Jun 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→109.26 Å / Num. obs: 23310 / % possible obs: 99.1 % / Redundancy: 5.4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.125 / Net I/σ(I): 10.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.4 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOK

1qok


Resolution: 2.55→109.26 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / SU B: 27.018 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R: 0.973 / ESU R Free: 0.339 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 1222 5.2 %RANDOM
Rwork0.2141 ---
obs0.21693 22077 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.579 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å21.69 Å2
2---1.1 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.55→109.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4998 0 13 84 5095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.025128
X-RAY DIFFRACTIONr_bond_other_d0.0030.024684
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.956943
X-RAY DIFFRACTIONr_angle_other_deg0.955310844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6375640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1324.732224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94115848
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2411520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025799
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021157
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_it0.9922.5462575
X-RAY DIFFRACTIONr_mcbond_other0.9922.5462574
X-RAY DIFFRACTIONr_mcangle_it1.7293.8123207
X-RAY DIFFRACTIONr_mcangle_other1.7293.8133208
X-RAY DIFFRACTIONr_scbond_it1.0462.6562553
X-RAY DIFFRACTIONr_scbond_other1.0282.6462549
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7763.9183730
X-RAY DIFFRACTIONr_long_range_B_refined3.50719.5795356
X-RAY DIFFRACTIONr_long_range_B_other3.39319.5645348
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)
11A49720.13
12C49720.13
21B112230.16
22D112230.16
LS refinement shellResolution: 2.55→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 91 -
Rwork0.325 1548 -
obs--93.23 %
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)
14.84310.7136-0.25882.59370.24762.3321-0.1926-0.1293-0.14970.12880.07460.09360.2784-0.00510.1180.07510.010.06270.00730.00920.0642-20.3766-4.3216-40.4772
21.815-0.0074-0.09132.22470.82282.2233-0.0074-0.05970.14190.13790.02910.0251-0.25290.0511-0.02170.09020.01360.03990.02430.01290.04869.289612.5556-39.6528
32.05030.2033-0.45472.9285-0.94244.8996-0.00470.03450.133-0.03570.0840.0599-0.2852-0.0209-0.07940.09510.02270.05330.0303-0.02040.131-25.233915.8939-34.1594
40.9493-0.08950.04321.78350.48833.44370.0162-0.0338-0.15890.1039-0.0425-0.24710.49670.4420.02630.26540.07540.12620.20840.06180.1601-20.0518-3.6954-6.659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 100
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C5 - 100
4X-RAY DIFFRACTION4D1 - 242

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