[English] 日本語
Yorodumi
- PDB-4wvr: Crystal structure of Dscam1 Ig7 domain, isoform 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wvr
TitleCrystal structure of Dscam1 Ig7 domain, isoform 5
ComponentsDown syndrome cell adhesion molecule, isoform AK
KeywordsCELL ADHESION / Ig fold
Function / homology
Function and homology information


DSCAM interactions / mushroom body development / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity ...DSCAM interactions / mushroom body development / detection of molecule of bacterial origin / central nervous system morphogenesis / ventral cord development / detection of mechanical stimulus involved in sensory perception of touch / axon extension involved in axon guidance / axon guidance receptor activity / dendrite self-avoidance / cell-cell adhesion mediator activity / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / phagocytosis / neuron development / antigen binding / axon guidance / central nervous system development / perikaryon / neuron projection / axon / neuronal cell body / dendrite / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Down syndrome cell adhesion molecule, C-terminal / Down syndrome cell adhesion molecule C terminal / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell adhesion molecule Dscam1 / Down syndrome cell adhesion molecule 1, isoform AK
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å
AuthorsChen, Q. / Yu, Y. / Li, S. / Cheng, L.
CitationJournal: Sci Adv / Year: 2016
Title: Structural basis of Dscam1 homodimerization: Insights into context constraint for protein recognition
Authors: Li, S.A. / Cheng, L. / Yu, Y. / Chen, Q.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 8, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Down syndrome cell adhesion molecule, isoform AK
B: Down syndrome cell adhesion molecule, isoform AK
C: Down syndrome cell adhesion molecule, isoform AK
D: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)42,8324
Polymers42,8324
Non-polymers00
Water5,332296
1
A: Down syndrome cell adhesion molecule, isoform AK
D: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)21,4162
Polymers21,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area9850 Å2
MethodPISA
2
B: Down syndrome cell adhesion molecule, isoform AK
C: Down syndrome cell adhesion molecule, isoform AK


Theoretical massNumber of molelcules
Total (without water)21,4162
Polymers21,4162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-6 kcal/mol
Surface area9950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.964, 73.964, 67.207
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Down syndrome cell adhesion molecule, isoform AK / Dscam1 Ig7 domain / isoform 5


Mass: 10708.091 Da / Num. of mol.: 4 / Fragment: UNP residues 617-713
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dscam1, Dscam, CG17800, Dmel_CG17800 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0E9K5, UniProt: Q0E9H6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM Calcium chloride dihydrate, 30%(w/v) polyethylene glycol monomethyl ether 550, 0.1M Bis-Tris PH6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2014
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 30014 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 17.7

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DMK

3dmk


Resolution: 1.948→28.912 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1488 4.96 %
Rwork0.1822 --
obs0.1842 29981 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→28.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 0 296 3216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042995
X-RAY DIFFRACTIONf_angle_d0.8694067
X-RAY DIFFRACTIONf_dihedral_angle_d12.7381103
X-RAY DIFFRACTIONf_chiral_restr0.029483
X-RAY DIFFRACTIONf_plane_restr0.004531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9484-2.01130.25931420.23142525X-RAY DIFFRACTION98
2.0113-2.08320.2591420.22322615X-RAY DIFFRACTION100
2.0832-2.16660.29141260.20412621X-RAY DIFFRACTION100
2.1666-2.26510.26031450.20382562X-RAY DIFFRACTION100
2.2651-2.38450.24961280.19412621X-RAY DIFFRACTION100
2.3845-2.53380.2471460.20252553X-RAY DIFFRACTION100
2.5338-2.72930.25771330.20922624X-RAY DIFFRACTION100
2.7293-3.00370.27751310.20212587X-RAY DIFFRACTION100
3.0037-3.43780.17561380.18282581X-RAY DIFFRACTION100
3.4378-4.32890.18231350.15292608X-RAY DIFFRACTION100
4.3289-28.91540.20571220.15622596X-RAY DIFFRACTION100

+
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