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- PDB-4zmt: Crystal structure of human P-cadherin (ss-X-dimer-long) -

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Basic information

Entry
Database: PDB / ID: 4zmt
TitleCrystal structure of human P-cadherin (ss-X-dimer-long)
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 / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / cell-cell adhesion mediated by cadherin / catenin complex / adherens junction organization ...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 / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / cell-cell adhesion mediated by cadherin / catenin complex / adherens junction organization / cell-cell junction assembly / Adherens junctions interactions / retina homeostasis / 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 junction / cell migration / 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 / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / 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_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_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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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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
C: Cadherin-3
D: Cadherin-3
E: Cadherin-3
F: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,42324
Polymers152,7016
Non-polymers72118
Water34219
1
A: Cadherin-3
B: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1418
Polymers50,9002
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-48 kcal/mol
Surface area22070 Å2
MethodPISA
2
C: Cadherin-3
D: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1418
Polymers50,9002
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-48 kcal/mol
Surface area22080 Å2
MethodPISA
3
E: Cadherin-3
F: Cadherin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1418
Polymers50,9002
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-48 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.210, 105.830, 90.210
Angle α, β, γ (deg.)90.00, 96.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUAA0 - 2121 - 213
21LEULEUBB0 - 2121 - 213
12ASPASPAA0 - 2131 - 214
22ASPASPCC0 - 2131 - 214
13ASPASPAA0 - 2131 - 214
23ASPASPDD0 - 2131 - 214
14LEULEUAA0 - 2121 - 213
24LEULEUEE0 - 2121 - 213
15VALVALAA0 - 2091 - 210
25VALVALFF0 - 2091 - 210
16LEULEUBB0 - 2121 - 213
26LEULEUCC0 - 2121 - 213
17ALAALABB0 - 2141 - 215
27ALAALADD0 - 2141 - 215
18ASNASNBB0 - 2151 - 216
28ASNASNEE0 - 2151 - 216
19VALVALBB0 - 2091 - 210
29VALVALFF0 - 2091 - 210
110ASPASPCC0 - 2131 - 214
210ASPASPDD0 - 2131 - 214
111LEULEUCC0 - 2121 - 213
211LEULEUEE0 - 2121 - 213
112VALVALCC0 - 2091 - 210
212VALVALFF0 - 2091 - 210
113ALAALADD0 - 2141 - 215
213ALAALAEE0 - 2141 - 215
114VALVALDD0 - 2091 - 210
214VALVALFF0 - 2091 - 210
115VALVALEE0 - 2091 - 210
215VALVALFF0 - 2091 - 210

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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


Mass: 25450.221 Da / Num. of mol.: 6 / Fragment: UNP residues 108-338
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
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3,550 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→43.31 Å / Num. obs: 43436 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2 / % possible all: 97.1

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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: 2.7→42.31 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / SU B: 36.593 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 1.171 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24941 2190 5 %RANDOM
Rwork0.22823 ---
obs0.22933 41234 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.351 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å2-1.68 Å2
2---2.33 Å20 Å2
3----1.62 Å2
Refinement stepCycle: 1 / Resolution: 2.7→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9578 0 18 19 9615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199778
X-RAY DIFFRACTIONr_bond_other_d0.0060.029077
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9513294
X-RAY DIFFRACTIONr_angle_other_deg1.234321044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96651235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26425.757436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.227151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3311533
X-RAY DIFFRACTIONr_chiral_restr0.0720.21533
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110972
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022011
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_it1.1952.9364973
X-RAY DIFFRACTIONr_mcbond_other1.1962.9364972
X-RAY DIFFRACTIONr_mcangle_it2.0374.4026197
X-RAY DIFFRACTIONr_mcangle_other2.0374.4026198
X-RAY DIFFRACTIONr_scbond_it1.2953.0874805
X-RAY DIFFRACTIONr_scbond_other1.2953.0874806
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1884.5657098
X-RAY DIFFRACTIONr_long_range_B_refined3.50322.7179623
X-RAY DIFFRACTIONr_long_range_B_other3.50322.7179624
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)
11A118580.09
12B118580.09
21A119650.08
22C119650.08
31A117270.09
32D117270.09
41A117150.1
42E117150.1
51A90410.11
52F90410.11
61B118700.09
62C118700.09
71B116420.1
72D116420.1
81B117790.1
82E117790.1
91B90140.11
92F90140.11
101C117350.09
102D117350.09
111C116590.11
112E116590.11
121C89990.11
122F89990.11
131D116650.1
132E116650.1
141D89310.11
142F89310.11
151E89050.12
152F89050.12
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 156 -
Rwork0.384 2998 -
obs--96.72 %
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)
11.01560.44990.17283.13270.64081.14030.0316-0.01630.02930.0342-0.03670.1258-0.0064-0.00570.00510.0115-0.00540.02750.10.0220.082514.4268-3.667740.6387
21.7773-1.17811.082.9021-1.57722.41380.03060.0855-0.02-0.0886-0.05990.06690.0185-0.03340.02920.046-0.03360.0430.0872-0.07720.077419.0667-4.052822.1372
32.90040.2816-1.94760.5712-0.30222.0352-0.09430.18160.0345-0.064-0.00260.0244-0.11390.00010.09690.31060.0099-0.05730.1414-0.0280.18133.709331.756910.8609
41.60790.59240.80771.39290.75831.0494-0.11360.14250.2397-0.05310.11990.0542-0.150.179-0.00630.35260.0117-0.0240.32280.08170.21928.002935.1892-7.0298
50.2149-0.33790.30233.2811-2.02351.7729-0.0147-0.0045-0.0142-0.0293-0.0071-0.0213-0.0076-0.07910.02180.1351-0.0244-0.05150.20210.02580.2114-18.743623.086832.5145
61.8591-0.3150.02383.26710.66561.40090.0929-0.1727-0.4127-0.2054-0.02710.20990.0038-0.1453-0.06580.3021-0.0735-0.13640.3210.14370.3982-31.807622.542621.2938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 213
2X-RAY DIFFRACTION2B0 - 215
3X-RAY DIFFRACTION3C0 - 213
4X-RAY DIFFRACTION4D0 - 214
5X-RAY DIFFRACTION5E0 - 215
6X-RAY DIFFRACTION6F0 - 209

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