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- PDB-7cym: Crystal structure of LI-Cadherin EC1-4 -

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Basic information

Entry
Database: PDB / ID: 7cym
TitleCrystal structure of LI-Cadherin EC1-4
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 / 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 / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like ...Cadherin / 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. / 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
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 5, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)102,81620
Polymers99,7492
Non-polymers3,06618
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-27 kcal/mol
Surface area46290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.360, 70.840, 134.219
Angle α, β, γ (deg.)90.000, 98.690, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 419
2010B4 - 419

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cadherin-17 / LI-cadherin EC1-4


Mass: 49874.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH17 / Cell line (production host): EXPI293 / Production host: Homo sapiens (human) / References: UniProt: Q12864

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 45 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.79 Å3/Da / Density % sol: 67.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM sodium sulfate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→59.2 Å / Num. obs: 41272 / % possible obs: 99.9 % / Redundancy: 6.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.041 / Net I/σ(I): 1.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5955 / CC1/2: 0.907 / Rpim(I) all: 0.371 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
PDB_EXTRACT3.25data extraction
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZMY

4zmy


Resolution: 2.7→55.25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.891 / SU B: 35.033 / SU ML: 0.311 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 2040 4.9 %RANDOM
Rwork0.222 ---
obs0.2247 39218 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.91 Å2 / Biso mean: 75.276 Å2 / Biso min: 44.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-1.18 Å2
2--3.01 Å20 Å2
3----3.15 Å2
Refinement stepCycle: final / Resolution: 2.7→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 182 33 6872
Biso mean--103.17 62.19 -
Num. residues----835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0147003
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176202
X-RAY DIFFRACTIONr_angle_refined_deg1.8351.7039552
X-RAY DIFFRACTIONr_angle_other_deg0.9191.66114656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7285835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24224.588364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.317151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4711528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2973
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027701
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021182
Refine LS restraints NCS

Ens-ID: 1 / Number: 12410 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 139 -
Rwork0.363 2854 -
all-2993 -
obs--99.97 %
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)
11.12630.01971.33130.4159-0.02191.6978-0.197-0.18430.09920.14970.05340.1172-0.3922-0.23350.14360.37910.0537-0.07470.5266-0.03670.0807-22.1633.76216.897
20.519-0.13430.94550.061-0.24051.93480.0713-0.0152-0.09160.07320.0394-0.01370.0598-0.0328-0.11070.39510.0079-0.17450.4669-0.02670.08910.913-23.99630.454
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 442
2X-RAY DIFFRACTION1A501 - 502
3X-RAY DIFFRACTION1C1 - 4
4X-RAY DIFFRACTION1D1 - 2
5X-RAY DIFFRACTION2B26 - 443
6X-RAY DIFFRACTION2B501
7X-RAY DIFFRACTION2E1 - 4

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