[English] 日本語
Yorodumi
- PDB-2yd3: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yd3
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Sigma
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
KeywordsHYDROLASE
Function / homology
Function and homology information


negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier / synaptic membrane adhesion / negative regulation of axon extension / corpus callosum development / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / ECM proteoglycans / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cerebellum development / hippocampus development / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / heparin binding / negative regulation of neuron projection development / presynaptic membrane / growth cone / perikaryon / axon / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif ...: / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / 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
Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsColes, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
CitationJournal: Science / Year: 2011
Title: Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.
Authors: Coles, C.H. / Shen, Y. / Tenney, A.P. / Siebold, C. / Sutton, G.C. / Lu, W. / Gallagher, J.T. / Jones, E.Y. / Flanagan, J.G. / Aricescu, A.R.
History
DepositionMar 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3253
Polymers22,2671
Non-polymers582
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.218, 104.218, 94.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2058-

HOH

-
Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S / PROTEIN TYROSINE PHOSPHATASE SIGMA / R-PTP-S / RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA / R- ...PROTEIN TYROSINE PHOSPHATASE SIGMA / R-PTP-S / RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA / R-PTP-SIGMA / RPTPS


Mass: 22266.994 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 30-228
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: Q13332, protein-tyrosine-phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) DERIVE FROM THE PHLSEC VECTOR. THIS RPTPSIGMA IG1-2 ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) DERIVE FROM THE PHLSEC VECTOR. THIS RPTPSIGMA IG1-2 CRYSTAL WAS OBTAINED AFTER PROTEOLYTIC CLEAVAGE OF RPTPSIGMA IG1-3 PROTEIN (TO RESIDUE 321, PLUS GTKHHHHHH). THIS IS ISOFORM 2 Q13332-6.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.6 / Details: 0.2M SODIUM SULPHATE, 20% W/V PEG 3350, PH 6.6 .

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.06
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 12003 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.6
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.7 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 2.3→32.957 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 569 4.8 %
Rwork0.2007 --
obs0.2024 11897 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.599 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 38.77 Å2
Baniso -1Baniso -2Baniso -3
1--9.002 Å20 Å20 Å2
2---9.002 Å20 Å2
3---16.2234 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 2 82 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051578
X-RAY DIFFRACTIONf_angle_d0.8872136
X-RAY DIFFRACTIONf_dihedral_angle_d13.045605
X-RAY DIFFRACTIONf_chiral_restr0.055235
X-RAY DIFFRACTIONf_plane_restr0.003287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53150.28691420.23612768X-RAY DIFFRACTION100
2.5315-2.89760.28341290.24512808X-RAY DIFFRACTION100
2.8976-3.64990.25761490.21712819X-RAY DIFFRACTION100
3.6499-32.960.19411490.16882933X-RAY DIFFRACTION100
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)
10.26350.0244-0.13630.5995-0.14210.1008-0.09480.1168-0.1924-0.0596-0.02070.01210.08570.0072-0.00110.19340.01870.00160.2194-0.03820.199335.17450.65084.9492
21.0053-0.2464-0.21890.03010.23540.71770.0532-0.1177-0.18260.0131-0.12150.09390.02980.0493-0.00080.1608-0.04490.03020.17660.00640.177220.84777.878820.9315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 29:129)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 130:228)

+
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