[English] 日本語
Yorodumi
- PDB-4num: Crystal structure of mouse N-cadherin EC1-2 A78SI92M -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4num
TitleCrystal structure of mouse N-cadherin EC1-2 A78SI92M
ComponentsCadherin-2
KeywordsCELL ADHESION / cell adhesion molecule
Function / homology
Function and homology information


mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome ...mesenchymal cell migration / regulation of oligodendrocyte progenitor proliferation / regulation of postsynaptic density protein 95 clustering / radial glial cell differentiation / neuroligin clustering involved in postsynaptic membrane assembly / positive regulation of synaptic vesicle clustering / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / Adherens junctions interactions / desmosome / synaptic vesicle clustering / gamma-catenin binding / neural crest cell development / telencephalon development / glial cell differentiation / neuroepithelial cell differentiation / type B pancreatic cell development / cell-cell adhesion mediated by cadherin / neuronal stem cell population maintenance / alpha-catenin binding / fascia adherens / apicolateral plasma membrane / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Myogenesis / regulation of Rho protein signal transduction / catenin complex / brain morphogenesis / postsynaptic specialization membrane / cell-cell junction assembly / adherens junction organization / blood vessel morphogenesis / regulation of myelination / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / cortical actin cytoskeleton / regulation of axonogenesis / nitric-oxide synthase binding / homophilic cell adhesion via plasma membrane adhesion molecules / plasma membrane raft / intercalated disc / homeostasis of number of cells / presynaptic active zone membrane / regulation of synaptic transmission, glutamatergic / synapse assembly / striated muscle cell differentiation / T-tubule / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / modulation of chemical synaptic transmission / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / brain development / cerebral cortex development / sarcolemma / beta-catenin binding / cell-cell adhesion / regulation of protein localization / cell-cell junction / cell migration / lamellipodium / apical part of cell / basolateral plasma membrane / protein phosphatase binding / positive regulation of MAPK cascade / postsynaptic density / cell adhesion / cadherin binding / neuron projection / apical plasma membrane / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / protein kinase binding / enzyme binding / cell surface / protein-containing complex / RNA binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsJin, X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural and energetic determinants of adhesive binding specificity in type I cadherins.
Authors: Vendome, J. / Felsovalyi, K. / Song, H. / Yang, Z. / Jin, X. / Brasch, J. / Harrison, O.J. / Ahlsen, G. / Bahna, F. / Kaczynska, A. / Katsamba, P.S. / Edmond, D. / Hubbell, W.L. / Shapiro, L. / Honig, B.
History
DepositionDec 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cadherin-2
B: Cadherin-2
C: Cadherin-2
D: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,08716
Polymers94,6064
Non-polymers48112
Water00
1
A: Cadherin-2
B: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5448
Polymers47,3032
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-33 kcal/mol
Surface area22500 Å2
MethodPISA
2
C: Cadherin-2
D: Cadherin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5448
Polymers47,3032
Non-polymers2406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-34 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.751, 221.152, 72.239
Angle α, β, γ (deg.)90.00, 103.85, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.357777, -0.35282, -0.864589), (-0.498966, -0.710386, 0.496371), (-0.789321, 0.608991, 0.078115)54.63142, 55.99346, 15.10757
3given(0.545494, 0.381725, 0.746139), (-0.715767, 0.675328, 0.177792), (-0.43602, -0.631046, 0.641613)-13.47838, -15.16053, 70.66274
4given(0.441286, 0.022909, -0.897074), (0.059476, -0.998223, 0.003765), (-0.895393, -0.055015, -0.441864)15.37048, 107.61206, 28.73595

-
Components

#1: Protein
Cadherin-2 / Neural cadherin / N-cadherin


Mass: 23651.531 Da / Num. of mol.: 4 / Fragment: unp residues 160-374 / Mutation: A78S, I92M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh2 / Production host: Escherichia coli (E. coli) / References: UniProt: P15116
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG3350, 0.2M sodium chloride, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 11, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.2→20 Å / Num. all: 27180 / Num. obs: 25725 / % possible obs: 94.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→19.97 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.864 / SU B: 21.577 / SU ML: 0.331 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.453 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25284 1295 5 %RANDOM
Rwork0.21926 ---
all0.292 25551 --
obs0.22098 24430 94.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.826 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å2-0 Å21.7 Å2
2---3.65 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 3.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6648 0 12 0 6660
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196812
X-RAY DIFFRACTIONr_bond_other_d0.0010.026452
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.9669328
X-RAY DIFFRACTIONr_angle_other_deg0.719314854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7965860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45525.031318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.936151086
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.11548
X-RAY DIFFRACTIONr_chiral_restr0.0620.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021476
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 75 -
Rwork0.349 1255 -
obs--66.73 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more