[English] 日本語
Yorodumi
- PDB-2wv3: Neuroplastin-55 binds to and signals through the fibroblast growt... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wv3
TitleNeuroplastin-55 binds to and signals through the fibroblast growth factor receptor
ComponentsNEUROPLASTINNPTN
KeywordsCELL ADHESION / IGCAM / MEMBRANE / GLYCOPROTEIN / CELL MEMBRANE / TRANSMEMBRANE / DISULFIDE BOND / ALTERNATIVE SPLICING / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


regulation of receptor localization to synapse / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse ...regulation of receptor localization to synapse / trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission / : / type 1 fibroblast growth factor receptor binding / excitatory synapse assembly / dendrite self-avoidance / cell-cell adhesion mediator activity / positive regulation of fibroblast growth factor receptor signaling pathway / positive regulation of long-term neuronal synaptic plasticity / inhibitory synapse / negative regulation of cytokine production / positive regulation of protein localization / homophilic cell adhesion via plasma membrane adhesion molecules / immunological synapse / regulation of cell adhesion / cell adhesion molecule binding / synaptic membrane / long-term synaptic potentiation / positive regulation of long-term synaptic potentiation / axon guidance / synapse organization / visual learning / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / positive regulation of neuron projection development / presynaptic membrane / positive regulation of cytosolic calcium ion concentration / postsynaptic membrane / transmembrane transporter binding / postsynaptic density / positive regulation of ERK1 and ERK2 cascade / membrane => GO:0016020 / positive regulation of protein phosphorylation / axon / dendrite / cell surface / plasma membrane
Similarity search - Function
Neuroplastin / Basigin-like / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Neuroplastin / Basigin-like / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSoroka, V. / Owczarek, S. / Kastrup, J.S. / Berezin, V. / Bock, E. / Gajhede, M.
CitationJournal: Faseb J. / Year: 2010
Title: Neuroplastin-55 Binds to and Signals Through the Fibroblast Growth Factor Receptor
Authors: Owczarek, S. / Kiryushko, D. / Larsen, M.H. / Kastrup, J.S. / Gajhede, M. / Sandi, C. / Berezin, V. / Bock, E. / Soroka, V.
History
DepositionOct 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: diffrn_source / software / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NEUROPLASTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0283
Polymers21,5851
Non-polymers4422
Water2,036113
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.390, 81.080, 137.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2020-

HOH

-
Components

#1: Protein NEUROPLASTIN / NPTN / STROMAL CELL-DERIVED RECEPTOR 1 / GLYCOPROTEIN 55/65 / SDR-1 / GP55/65 / NEUROPLASTIN-55


Mass: 21585.117 Da / Num. of mol.: 1 / Fragment: IG2 AND IG3 OF NEUROPLASTIN-65, RESIDUES 29-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PPIC9K / Cell line (production host): HIS 4 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): GS115 / References: UniProt: P97546
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.95 Å3/Da / Density % sol: 57.98 % / Description: NONE
Crystal growpH: 7.4
Details: NEUROPLASTIN-55 AT A CONCENTRATION OF 4 MG/ML IN 5 MM SODIUM PHOSPHATE AND 150 MM NACL, PH 7.4, WAS MIXED WITH THE RESERVOIR SOLUTION CONTAINING 13-15% W/V PEG 4000, 0.2 M AMMONIUM SULFATE, ...Details: NEUROPLASTIN-55 AT A CONCENTRATION OF 4 MG/ML IN 5 MM SODIUM PHOSPHATE AND 150 MM NACL, PH 7.4, WAS MIXED WITH THE RESERVOIR SOLUTION CONTAINING 13-15% W/V PEG 4000, 0.2 M AMMONIUM SULFATE, AND 0.1 M SODIUM ACETATE, PH 4.6.

-
Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.95→33.6 Å / Num. obs: 20597 / % possible obs: 99.2 % / Observed criterion σ(I): 1.45 / Redundancy: 7.1 % / Biso Wilson estimate: 28.88 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.95→33.601 Å / SU ML: 0.29 / σ(F): 1.45 / Phase error: 28.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2486 1044 5.1 %
Rwork0.2076 --
obs0.2097 20427 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.633 Å2 / ksol: 0.395 e/Å3
Displacement parametersBiso mean: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1-13.6388 Å20 Å2-0 Å2
2--2.0433 Å2-0 Å2
3----15.6822 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 28 113 1636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061596
X-RAY DIFFRACTIONf_angle_d1.0572166
X-RAY DIFFRACTIONf_dihedral_angle_d16.64621
X-RAY DIFFRACTIONf_chiral_restr0.071234
X-RAY DIFFRACTIONf_plane_restr0.004277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9501-2.05290.32521420.26222729X-RAY DIFFRACTION99
2.0529-2.18150.26521470.23522721X-RAY DIFFRACTION99
2.1815-2.34990.27751420.2282743X-RAY DIFFRACTION100
2.3499-2.58630.31961580.23172751X-RAY DIFFRACTION100
2.5863-2.96030.28041500.22622772X-RAY DIFFRACTION100
2.9603-3.72890.25071480.18712803X-RAY DIFFRACTION100
3.7289-33.60640.19991570.18612864X-RAY DIFFRACTION98

+
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