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- PDB-4zmv: Crystal structure of human P-cadherin (ss-X-dimer pocket I) -

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Basic information

Entry
Database: PDB / ID: 4zmv
TitleCrystal structure of human P-cadherin (ss-X-dimer pocket I)
ComponentsCadherin-3
KeywordsCELL ADHESION / dimerization / conformational change
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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cadherin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCaaveiro, J.M.M. / Kudo, S. / Tsumoto, K.
CitationJournal: Structure / Year: 2016
Title: Adhesive Dimerization of Human P-Cadherin Catalyzed by a Chaperone-like Mechanism
Authors: Kudo, S. / Caaveiro, J.M. / Tsumoto, K.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.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_conn.ptnr2_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: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,79915
Polymers46,8942
Non-polymers90513
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-115 kcal/mol
Surface area20890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.440, 98.910, 109.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 23447.102 Da / Num. of mol.: 2 / Fragment: UNP residues 108-320 / Mutation: V4I, A5P, N22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH3, CDHP / Plasmid: Champion pET SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22223

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Non-polymers , 5 types, 92 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.55 Å3/Da / Density % sol: 72.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2 M Lithium sulfate 10 mM nickel sulfate 100 mM TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.1 Å / Num. obs: 33412 / % possible obs: 98.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.6 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMN

4zmn


Resolution: 2.4→45.1 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 14.673 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 1697 5.1 %RANDOM
Rwork0.20609 ---
obs0.20769 31692 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.076 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å20 Å2
2---0.82 Å20 Å2
3----1.06 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 39 79 3416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193396
X-RAY DIFFRACTIONr_bond_other_d0.0010.023148
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9654620
X-RAY DIFFRACTIONr_angle_other_deg0.837310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2565426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59325.676148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95215554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2471512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213774
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02682
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_it1.9573.0181710
X-RAY DIFFRACTIONr_mcbond_other1.9583.0171709
X-RAY DIFFRACTIONr_mcangle_it3.0584.5212134
X-RAY DIFFRACTIONr_mcangle_other3.0574.5222135
X-RAY DIFFRACTIONr_scbond_it3.1663.3571686
X-RAY DIFFRACTIONr_scbond_other3.1633.3571686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1434.8892487
X-RAY DIFFRACTIONr_long_range_B_refined5.88123.893509
X-RAY DIFFRACTIONr_long_range_B_other5.88623.8223489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 129 -
Rwork0.33 2308 -
obs--97.17 %
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)
11.5902-1.01531.71381.9343-1.60122.8948-0.0849-0.13050.04240.206-0.0272-0.0987-0.032-0.08740.11210.1876-0.03080.0270.0314-0.00350.014-4.7052-20.320917.8844
20.7141-0.298-0.26771.80571.52642.77820.01640.046-0.0016-0.0170.0525-0.21350.16070.3525-0.06890.14850.0037-0.00170.08430.02260.04161.7348-5.209716.566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 213
2X-RAY DIFFRACTION2B0 - 213

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