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- PDB-6ulm: Crystal structure of human cadherin 17 EC1-2 -

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Basic information

Entry
Database: PDB / ID: 6ulm
TitleCrystal structure of human cadherin 17 EC1-2
ComponentsCadherin-17
KeywordsCELL ADHESION / cdh17 / intestinal epithelia / cancer / calcium-binding
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 / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly ...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 / calcium-dependent cell-cell adhesion / cell-cell adhesion mediated by cadherin / adherens junction organization / catenin complex / cell-cell junction assembly / Adherens junctions interactions / homophilic cell-cell adhesion / spleen development / integrin-mediated signaling pathway / adherens junction / beta-catenin binding / integrin binding / cell morphogenesis / cell junction / cell migration / 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 / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGray, M.E. / Sotomayor, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of the nonclassical cadherin-17 N-terminus and implications for its adhesive binding mechanism.
Authors: Gray, M.E. / Sotomayor, M.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
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
B: Cadherin-17
A: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6228
Polymers51,3812
Non-polymers2406
Water3,657203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, assay for oligomerization, bead aggregation assay
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8114
Polymers25,6911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cadherin-17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8114
Polymers25,6911
Non-polymers1203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.394, 81.609, 106.813
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B10 - 212
2111A10 - 212

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.968254, 0.186706, 0.166207), (-0.197243, -0.97912, -0.049178), (0.153555, -0.0804, 0.984864)1.53952, -2.01017, 14.21636

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Components

#1: Protein Cadherin-17 / Intestinal peptide-associated transporter HPT-1 / Liver-intestine cadherin / LI-cadherin


Mass: 25690.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH17 / Variant: VAR_055567 / Plasmid: pET21a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: Q12864
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7, 0.1 M KCl, 15% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 28521 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.46
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1406 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q2V

3q2v


Resolution: 2.15→47.53 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 10.68 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.228 / ESU R Free: 0.2
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 1412 5 %RANDOM
Rwork0.2062 ---
obs0.2087 26913 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 104.63 Å2 / Biso mean: 30.462 Å2 / Biso min: 13.07 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å20 Å20 Å2
2---0.38 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 2.15→47.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3179 0 6 203 3388
Biso mean--24.38 30.89 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133256
X-RAY DIFFRACTIONr_bond_other_d00.0172936
X-RAY DIFFRACTIONr_angle_refined_deg1.2691.6544430
X-RAY DIFFRACTIONr_angle_other_deg1.1971.5676863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3215403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26124.246179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0631516
X-RAY DIFFRACTIONr_chiral_restr0.0560.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.023657
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02627
Refine LS restraints NCSNumber: 1534 / Type: TIGHT THERMAL / Rms dev position: 4.84 Å / Weight position: 0.5
LS refinement shellResolution: 2.15→2.205 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 105 -
Rwork0.265 1939 -
all-2044 -
obs--98.84 %
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)
10.89150.68271.1150.58160.67342.06320.1434-0.25950.00240.0978-0.2245-0.01030.1727-0.30070.08110.0512-0.0154-0.01630.1056-0.01410.018812.866-7.19323.556
20.3709-0.04560.34940.2888-0.02340.8642-0.0108-0.0204-0.0185-0.04320.01090.0109-0.0157-0.0055-0.00010.0162-0.0012-0.02470.0027-0.00030.07523.621-9.385-21.952
30.58250.5990.06371.0290.97136.06690.1288-0.08910.1303-0.01650.0020.0928-0.12370.1138-0.13080.081-0.04970.03930.0347-0.02570.0358-9.3296.2158.959
40.2097-0.0639-0.12160.692-0.51541.28150.03280.0376-0.0364-0.0189-0.00390.04480.0407-0.0271-0.02880.0184-0.0017-0.01030.01370.00250.0497-6.04510.736-35.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B4 - 97
2X-RAY DIFFRACTION1B301 - 302
3X-RAY DIFFRACTION2B98 - 212
4X-RAY DIFFRACTION2B303
5X-RAY DIFFRACTION3A10 - 97
6X-RAY DIFFRACTION3A301 - 302
7X-RAY DIFFRACTION4A98 - 214
8X-RAY DIFFRACTION4A303

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