[English] 日本語
Yorodumi
- PDB-2a4e: Crystal structure of mouse cadherin-11 EC1-2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a4e
TitleCrystal structure of mouse cadherin-11 EC1-2
ComponentsCadherin-11
KeywordsCELL ADHESION / cadherin / dimer / calcium binding
Function / homology
Function and homology information


Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / focal adhesion assembly / cell-substrate adhesion / homophilic cell-cell adhesion / negative regulation of cell migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / calcium ion binding ...Regulation of CDH11 function / corticospinal tract morphogenesis / Adherens junctions interactions / focal adhesion assembly / cell-substrate adhesion / homophilic cell-cell adhesion / negative regulation of cell migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / calcium ion binding / synapse / glutamatergic synapse / plasma membrane / cytoplasm
Similarity search - Function
Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like ...Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsPatel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Arkus, N. / Rajebhosale, M. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2006
Title: Type II cadherin ectodomain structures: implications for classical cadherin specificity.
Authors: Patel, S.D. / Ciatto, C. / Chen, C.P. / Bahna, F. / Rajebhosale, M. / Arkus, N. / Schieren, I. / Jessell, T.M. / Honig, B. / Price, S.R. / Shapiro, L.
History
DepositionJun 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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 / _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_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-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9074
Polymers23,7871
Non-polymers1203
Water27015
1
A: Cadherin-11
hetero molecules

A: Cadherin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8158
Polymers47,5742
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_767-x+2,-x+y+1,-z+7/31
Unit cell
Length a, b, c (Å)203.249, 203.249, 42.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

-
Components

#1: Protein Cadherin-11 / Osteoblast-cadherin / OB-cadherin / OSF-4


Mass: 23787.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh11, Cad-11 / Plasmid: pSMT3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P55288
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.37 Å3/Da / Density % sol: 77.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, hepes, sucrose, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 8610 / % possible obs: 99.9 %
Reflection shellResolution: 3.2→3.31 Å / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
DENZOdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZVN and 1ZXK for the EC1 domain, and the EC2 domains of PDB entries 1NCJ, 1EDH, and 1L3W, for the EC2 domain.

1zvn

1zxk

1ncj

1edh

1l3w


Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.907 / SU B: 31.513 / SU ML: 0.267 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.621 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 433 4.8 %RANDOM
Rwork0.211 ---
all0.213 ---
obs-8536 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 74.397 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 3 15 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221647
X-RAY DIFFRACTIONr_angle_refined_deg1.7641.9512243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98425.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.8315265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.619158
X-RAY DIFFRACTIONr_chiral_restr0.1140.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021278
X-RAY DIFFRACTIONr_nbd_refined0.2570.2777
X-RAY DIFFRACTIONr_nbtor_refined0.3280.21127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.265
X-RAY DIFFRACTIONr_metal_ion_refined0.2010.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.26
X-RAY DIFFRACTIONr_mcbond_it0.6261.51041
X-RAY DIFFRACTIONr_mcangle_it1.13121678
X-RAY DIFFRACTIONr_scbond_it1.5423659
X-RAY DIFFRACTIONr_scangle_it2.6834.5565
LS refinement shellResolution: 3.2→3.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.486 38 -
Rwork0.298 582 -
all-620 -
obs--94.66 %
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)
15.1873-0.9071-1.22974.6112-1.4482.9963-0.31990.70540.1109-0.1625-0.0504-0.6908-0.17470.01720.3702-0.2544-0.1732-0.0612-0.0722-0.1005-0.0339150.856106.31244.761
213.59272.06745.68123.54140.25557.5510.36520.00340.1056-0.1306-0.15210.0430.38010.0273-0.2131-0.22950.0299-0.11290.1123-0.0995-0.4663106.119107.05333.527
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 972 - 98
22100 - 207101 - 208

+
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://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