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- PDB-1q5b: lambda-shaped TRANS and CIS interactions of cadherins model based... -

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Basic information

Entry
Database: PDB / ID: 1q5b
Titlelambda-shaped TRANS and CIS interactions of cadherins model based on fitting C-cadherin (1L3W) to 3D map of desmosomes obtained by electron tomography
ComponentsEP-cadherin
KeywordsSTRUCTURAL PROTEIN / CADHERIN / TRANS INTERACTION / DESMOSOME / JUNCTION / ADHESION
Function / homology2-acetamido-2-deoxy-alpha-D-glucopyranose
Function and homology information
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / electron tomography / Resolution: 30 Å
AuthorsHe, W. / Cowin, P. / Stokes, D.L.
CitationJournal: Science / Year: 2003
Title: Untangling desmosomal knots with electron tomography.
Authors: Wanzhong He / Pamela Cowin / David L Stokes /
Abstract: Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion ...Cell adhesion by adherens junctions and desmosomes relies on interactions between cadherin molecules. However, the molecular interfaces that define molecular specificity and that mediate adhesion remain controversial. We used electron tomography of plastic sections from neonatal mouse skin to visualize the organization of desmosomes in situ. The resulting three-dimensional maps reveal individual cadherin molecules forming discrete groups and interacting through their tips. Fitting of an x-ray crystal structure for C-cadherin to these maps is consistent with a flexible intermolecular interface mediated by an exchange of amino-terminal tryptophans. This flexibility suggests a novel mechanism for generating both cis and trans interactions and for propagating these adhesive interactions along the junction.
History
DepositionAug 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _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 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_asym.entity_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure viewerMolecule:
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Assembly

Deposited unit
A: EP-cadherin
B: EP-cadherin
C: EP-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)304,65784
Polymers293,2603
Non-polymers11,39781
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein EP-cadherin / C-cadherin


Mass: 97753.352 Da / Num. of mol.: 3 / Fragment: residues 1-546 of PDB entry 1L3W / Source method: isolated from a natural source / Details: Desmosome preparation from newborn mouse skin / Source: (natural) Mus musculus (house mouse) / Tissue: skin
#2: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 39
Source method: isolated from a genetically manipulated source
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
#3: Sugar
ChemComp-NDG / 2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-glucopyranosamineCOMMON NAMEGMML 1.0
a-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Ca
Compound detailsCOMPOUND COMBINED TRANS AND CIS INTERACTION WITH THREE CADHERIN MOLECULES,THE INTERACTION INVOLVED ...COMPOUND COMBINED TRANS AND CIS INTERACTION WITH THREE CADHERIN MOLECULES,THE INTERACTION INVOLVED DEFINED BY N-TERMINAL TRYPTOPHAN SIDE CHAIN INSERTED INTO ANOTHER CADHERIN'S HYDROPHOBIC POCKET
Sequence detailsSEQUENCE SEQUENCE IS TAKEN FROM XENOPUS LAEVIS, AFRICAN CLAWED FROG, SWISSPROT ENTRY P33148, CADF_ ...SEQUENCE SEQUENCE IS TAKEN FROM XENOPUS LAEVIS, AFRICAN CLAWED FROG, SWISSPROT ENTRY P33148, CADF_XENLA BUT THE SOURCE ORGANISM IS MUS MUSCULUS.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: electron tomography

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1SKINTISSUEultra thin section of high pressure frozen/freeze-substitution prepared new-born mice skin sample. freezing substitution with 1% OsO4 and 0.1% Ur-Ac in acetone0
2desmosomecadherin interactions in intact desmosome complex from newborn mouse skin. This shows the lambda-shaped TRANS and CIS interaction1
Buffer solutionName: PBS with 1mM CaCl2 / pH: 7.4 / Details: PBS with 1mM CaCl2
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Specimen supportDetails: 200 mesh copper grid coated with formvar before picking 50nm thin section, then both side coated 5-10 nm thin carbon, imaging at room temperature
VitrificationCryogen name: NITROGEN
Details: high pressure frozen and freezing substituted with 1% OsO4/0.1% Ur-Ac. in acetone, LX-112 resin embeded sample. 50nm thin section
Crystal grow
*PLUS
Method: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Nov 23, 2002 / Details: Dose is for whole dataset, not individual images
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 68276 X / Nominal defocus max: 500 nm / Nominal defocus min: 300 nm / Cs: 2 mm
Specimen holderTemperature: 295 K / Tilt angle max: 79 ° / Tilt angle min: -78 °
Image recordingElectron dose: 1200 e/Å2 / Film or detector model: GENERIC GATAN / Details: 1024x1024 pixels CCD

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Processing

EM software
IDNameVersionCategoryDetails
1IMOD3D reconstruction
2Amira3model fittingAmiraMOL
CTF correctionDetails: no CTF correction. Imaging at underfocus 0.4 micron with CM200FEG microscope at 50,000 magnification
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: +/- 75 degree dual-axis electron tomography with IMOD
Resolution: 30 Å / Actual pixel size: 7.266 Å
Magnification calibration: CCD pixel size calibrated with gold crystal and silicon crystal
Details: sectioned sample thickness 47.2 nm; +/- 75 degree dual-axis tilt-series with increment 1 degree, dual-axis electron tomography with IMOD. 1.169nm alignment error
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: best visual fit using the program AmiraMOL 3.0
Details: METHOD--tracking 3D density REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1L3W

1l3w

Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms12573 0 666 0 13239

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