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- PDB-2b1o: Solution Structure of Ca2+-bound DdCAD-1 -

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Basic information

Entry
Database: PDB / ID: 2b1o
TitleSolution Structure of Ca2+-bound DdCAD-1
ComponentsCalcium-dependent cell adhesion molecule-1
KeywordsCELL ADHESION / DdCAD-1 / Calcium / Cell adherison
Function / homology
Function and homology information


sorocarp morphogenesis / contractile vacuole / sorocarp development / response to curcumin / aggregation involved in sorocarp development / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / biological process involved in interaction with symbiont / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / endocytic vesicle / ruffle ...sorocarp morphogenesis / contractile vacuole / sorocarp development / response to curcumin / aggregation involved in sorocarp development / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / biological process involved in interaction with symbiont / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / endocytic vesicle / ruffle / phagocytic vesicle / lipid droplet / extracellular matrix / filopodium / cell-cell junction / lamellipodium / cell cortex / regulation of gene expression / defense response to Gram-negative bacterium / calmodulin binding / external side of plasma membrane / calcium ion binding / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Calcium-dependent cell adhesion molecule-1 / Calcium-dependent cell adhesion molecule 1, membrane-binding domain / Calcium-dependent cell adhesion molecule, C-terminal domain superfamily / Membrane binding / Calcium-dependent cell adhesion molecule, N-terminal / Beta/Gamma crystallin / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Immunoglobulin-like ...Calcium-dependent cell adhesion molecule-1 / Calcium-dependent cell adhesion molecule 1, membrane-binding domain / Calcium-dependent cell adhesion molecule, C-terminal domain superfamily / Membrane binding / Calcium-dependent cell adhesion molecule, N-terminal / Beta/Gamma crystallin / Crystallins / Gamma-B Crystallin; domain 1 / Gamma-crystallin-like / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Calcium-dependent cell adhesion molecule 1
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLin, Z. / Sriskanthadevan, S. / Huang, H.B. / Siu, C.H. / Yang, D.W.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Solution structures of the adhesion molecule DdCAD-1 reveal new insights into Ca(2+)-dependent cell-cell adhesion
Authors: Lin, Z. / Sriskanthadevan, S. / Huang, H.B. / Siu, C.H. / Yang, D.W.
#1: Journal: J.Biomol.Nmr / Year: 2004
Title: (1)H, (13)C and (15)N resonance assignments of Ca(2+)-free DdCAD-1: a Ca(2+)-dependent cell-cell adhesion molecule
Authors: Lin, Z. / Huang, H.B. / Siu, C.H. / Yang, D.W.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _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.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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Calcium-dependent cell adhesion molecule-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9394
Polymers23,8191
Non-polymers1203
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Calcium-dependent cell adhesion molecule-1 / Ca2+-bound DdCAD-1 / DdCAD-1 / GP24


Mass: 23818.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: cadA / Plasmid: pET-M / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P54657
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1114D 13C/15N-separated NOESY
1213D 15N-separated NOESY
1313D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.5mM DdCAD-1 U-15N, 13C; 5mM CaCl2, 10mM PIPES buffer, 2mM DTT, 0.05mM SODIUM AZIDE, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 5mM CaCl2, 0.05mM SODIUM / pH: 6.2 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker DRXBrukerDRX5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2004.126.16.02Delaglioprocessing
NMRView5.2.2.01Johnsondata analysis
CYANA1.0.5Peterstructure solution
Amber7Davidrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: Energy minimization in Amber force field
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 10

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