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- PDB-7ev1: Crystal structure of LI-Cadherin EC1-2 -

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Basic information

Entry
Database: PDB / ID: 7ev1
TitleCrystal structure of LI-Cadherin EC1-2
ComponentsCadherin-17
KeywordsCELL ADHESION / LI-cadherin / dimerization / MD simulations / SAXS / cell-adhesion / analytical ultracentrifugation / protein chemistry
Function / homology
Function and homology information


oligopeptide transmembrane transport / positive regulation of integrin activation by cell surface receptor linked signal transduction / proton-dependent oligopeptide secondary active transmembrane transporter activity / marginal zone B cell differentiation / germinal center B cell differentiation / oligopeptide transport / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions ...oligopeptide transmembrane transport / positive regulation of integrin activation by cell surface receptor linked signal transduction / proton-dependent oligopeptide secondary active transmembrane transporter activity / marginal zone B cell differentiation / germinal center B cell differentiation / oligopeptide transport / cell-cell adhesion mediated by cadherin / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / catenin complex / Adherens junctions interactions / cell-cell junction assembly / adherens junction organization / homophilic cell adhesion via plasma membrane adhesion molecules / spleen development / integrin-mediated signaling pathway / adherens junction / cell morphogenesis / integrin binding / cell junction / basolateral plasma membrane / cell adhesion / cadherin binding / calcium ion binding / cell surface / nucleoplasm / plasma membrane
Similarity search - Function
Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Cadherin-17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsCaaveiro, J.M.M. / Yui, A. / Tsumoto, K.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Mechanism of dimerization and structural features of human LI-cadherin.
Authors: Yui, A. / Caaveiro, J.M.M. / Kuroda, D. / Nakakido, M. / Nagatoishi, S. / Goda, S. / Maruno, T. / Uchiyama, S. / Tsumoto, K.
History
DepositionMay 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-17
B: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,71610
Polymers46,3942
Non-polymers3238
Water11,385632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, size exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-27 kcal/mol
Surface area22200 Å2
Unit cell
Length a, b, c (Å)48.900, 79.680, 62.490
Angle α, β, γ (deg.)90.000, 99.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cadherin-17 / LI-cadherin


Mass: 23196.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH17 / Plasmid: pET28-SUMO / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: Q12864
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.54 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M Ammonium acetate, 30% 2-propanol, TRIS pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→41.31 Å / Num. obs: 93370 / % possible obs: 96.3 % / Redundancy: 5.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.2
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 12915 / CC1/2: 0.687 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMY

4zmy


Resolution: 1.38→32.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.767 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1812 2334 2.5 %RANDOM
Rwork0.1431 ---
obs0.144 91034 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.38 Å2 / Biso mean: 16.079 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.93 Å2
2---0.21 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.38→32.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 11 645 3924
Biso mean--24.62 26.79 -
Num. residues----416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133398
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173082
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6564642
X-RAY DIFFRACTIONr_angle_other_deg1.4111.5677221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3655434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.07224.239184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16715573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1911517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_rigid_bond_restr1.70236480
LS refinement shellResolution: 1.38→1.416 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 149 -
Rwork0.277 6131 -
all-6280 -
obs--88.04 %

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