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- PDB-6ztb: Crystal Structure of human P-Cadherin EC1_EC2 -

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Basic information

Entry
Database: PDB / ID: 6ztb
TitleCrystal Structure of human P-Cadherin EC1_EC2
ComponentsCadherin-3
KeywordsCELL ADHESION / Calcium / Cell Membrane / Glycoprotein
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 / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsRondeau, J.M. / Lehmann, S.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: PCA062, a P-cadherin Targeting Antibody-Drug Conjugate, Displays Potent Antitumor Activity Against P-cadherin-expressing Malignancies.
Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / ...Authors: Sheng, Q. / D'Alessio, J.A. / Menezes, D.L. / Karim, C. / Tang, Y. / Tam, A. / Clark, S. / Ying, C. / Connor, A. / Mansfield, K.G. / Rondeau, J.M. / Ghoddusi, M. / Geyer, F.C. / Gu, J. / McLaughlin, M.E. / Newcombe, R. / Elliot, G. / Tschantz, W.R. / Lehmann, S. / Fanton, C.P. / Miller, K. / Huber, T. / Rendahl, K.G. / Jeffry, U. / Pryer, N.K. / Lees, E. / Kwon, P. / Abraham, J.A. / Damiano, J.S. / Abrams, T.J.
History
DepositionJul 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0728
Polymers23,8591
Non-polymers2127
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-44 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.889, 76.522, 46.208
Angle α, β, γ (deg.)90.000, 107.790, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23859.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: P22223
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.655M NaCl, 85mM HEPES, 15.0% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.4→57.55 Å / Num. obs: 78188 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.328 % / Biso Wilson estimate: 23.62 Å2 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.026 / Χ2: 1.012 / Net I/σ(I): 23.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.4-1.443.4090.8580.5232.0619631578357580.6299.6
1.44-1.483.3870.6980.4042.6319058564556260.4899.7
1.48-1.523.3510.4740.2993.5518479553955140.35699.5
1.52-1.573.2690.3620.234.5717306531952940.27699.5
1.57-1.623.1120.2790.1745.9616051519551580.2199.3
1.62-1.673.4550.1780.1228.7917210499749810.14599.7
1.67-1.743.4280.1290.09111.3716600486348420.10899.6
1.74-1.813.4210.090.06515.8415861467046360.07799.3
1.81-1.893.3560.0580.04821.1314852445744250.05799.3
1.89-1.983.1290.0460.03726.2913259429542380.04498.7
1.98-2.093.2770.0330.02933.1513175407040200.03598.8
2.09-2.213.4530.0250.02539.8413216385438270.02999.3
2.21-2.373.410.0210.02344.0812203360835790.02799.2
2.37-2.563.3380.0180.02148.0211313343333890.02598.7
2.56-2.83.0160.0180.0249.359066306630060.02498
2.8-3.133.2440.0140.01757.769073284027970.0298.5
3.13-3.613.4480.0110.01664.028503249624660.01898.8
3.61-4.433.3920.010.01565.657048210020780.01899
4.43-6.263.120.0110.01563.235113165416390.01899.1
6.26-57.553.5020.0110.01867.5932049309150.02198.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å57.55 Å
Translation2.5 Å57.55 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.3.0phasing
BUSTERrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L3W

1l3w


Resolution: 1.4→57.55 Å / Cor.coef. Fo:Fc: 0.9445 / Cor.coef. Fo:Fc free: 0.9426 / SU R Cruickshank DPI: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.05 / SU Rfree Blow DPI: 0.05 / SU Rfree Cruickshank DPI: 0.048
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 3910 5 %RANDOM
Rwork0.1982 ---
obs0.1989 78177 99.3 %-
Displacement parametersBiso max: 138.78 Å2 / Biso mean: 30.79 Å2 / Biso min: 16.23 Å2
Baniso -1Baniso -2Baniso -3
1-4.953 Å20 Å2-0.686 Å2
2---4.6818 Å20 Å2
3----0.2712 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: final / Resolution: 1.4→57.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 7 340 2009
Biso mean--26.81 39.51 -
Num. residues----217
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d579SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes246HARMONIC5
X-RAY DIFFRACTIONt_it1708HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion236SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2123SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1708HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2333HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion4.52
X-RAY DIFFRACTIONt_other_torsion13.55
LS refinement shellResolution: 1.4→1.44 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2535 288 5.01 %
Rwork0.2378 5456 -
all0.2386 5744 -
obs--99.3 %
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)
11.8921.6016-0.37221.77-0.22430.6259-0.1304-0.0359-0.003-0.12830.0947-0.1272-0.06210.1060.0357-0.0328-0.03280.0093-0.0119-0.0135-0.024716.553517.29876.5369
22.40380.493-0.46320.74540.14810.571-0.0933-0.117-0.0794-0.0131-0.0530.11060.0644-0.07280.1464-0.0355-0.03080.0114-0.0027-0.0106-0.0242-27.4410.049813.091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ I|106 - I|208 }I106 - 208
2X-RAY DIFFRACTION2{ I|209 - I|322 }I209 - 322

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