[English] 日本語
Yorodumi
- PDB-2v5r: Structural basis for Dscam isoform specificity -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v5r
TitleStructural basis for Dscam isoform specificity
ComponentsDSCAM
KeywordsCELL ADHESION / DOWN SYNDROME CELL ADHESION MOLECULE DSCAM NEUROBIOLOGY SPL IMMUNOGLOBULIN DOMAIN / MEMBRANE / DEVELOPMENTAL PROTEIN
Function / homology
Function and homology information


DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / 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 / peripheral nervous system development ...DSCAM interactions / detection of molecule of bacterial origin / mushroom body development / 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 / peripheral nervous system development / axonal fasciculation / regulation of axonogenesis / regulation of dendrite morphogenesis / phagocytosis / neuron development / antigen binding / axon guidance / perikaryon / cell adhesion / neuron projection / axon / neuronal cell body / dendrite / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
: / DSCAM/DSCAML C-terminal Fn3-like domain / 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 ...: / DSCAM/DSCAML C-terminal Fn3-like domain / 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 / 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 / Cell adhesion molecule Dscam1
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMeijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Schmucker, D. / Wang, J.-H.
CitationJournal: Nature / Year: 2007
Title: Structural Basis of Dscam Isoform Specificity
Authors: Meijers, R. / Puettmann-Holgado, R. / Skiniotis, G. / Liu, J.-H. / Walz, T. / Wang, J.-H. / Schmucker, D.
History
DepositionJul 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_ref_seq_dif.details
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DSCAM
B: DSCAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,90612
Polymers86,9522
Non-polymers1,95410
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-7.6 kcal/mol
Surface area49080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)277.781, 70.548, 72.771
Angle α, β, γ (deg.)90.00, 105.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.863, -0.001, 0.506), (-1, -0.001), (0.506, -0.863)
Vector: -19.04812, -46.12549, 70.22813)
DetailsTHE DIMERIC STATE DESCRIBED IN REMARK 350 BELOW HASHAS BEEN EXPERIMENTALLY VALIDATED USIING BEAD AGGREGATIONASSAYS.

-
Components

#1: Protein DSCAM / DOWN SYNDROME CELL ADHESION MOLECULE DSCAM


Mass: 43476.008 Da / Num. of mol.: 2
Fragment: N-TERMINAL FOUR DOMAINS (D1, D2, D3 AND D4), RESIDUES 36-423
Source method: isolated from a genetically manipulated source
Details: ISOFORM 4.9/6.9 / Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Organ: BRAIN / Variant: SPLICING VARIANT 4.9/6.9 / Plasmid: BACNBLUE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NBA1, UniProt: Q0E9K4*PLUS
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Has protein modificationY
Sequence detailsTHE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE ...THE CONFLICTS GIVEN IN THE SEQADV RECORDS BELOW ARE AS A RESULT OF A SPLICE VARIANT FORM OF THE PROTEIN WHERE EXON 4 COVERING RESIDUES 102 TO 156 CONSISTS OF ISOFORM 9 AND EXON 6 COVERING RESIDUES 205 TO 245 CONSISTS OF ISOFORM 9.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 69 % / Description: NONE
Crystal growDetails: 10 % PEG 8000, 1MM SPERMIDINE, 0.1 M TRISHCL PH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 9, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 53580 / % possible obs: 86 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.9
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 1.9 / % possible all: 55.5

-
Processing

Software
NameClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V5M

2v5m


Resolution: 3→20 Å
Details: B GROUP REFINEMENT NCS REFINEMENT DOMAIN D4 (RESIDUES 309-391) IS LESS WELL DEFINED
RfactorNum. reflection% reflection
Rfree0.303 -5 %
Rwork0.271 --
obs-22250 86 %
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 124 0 6232

+
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