[English] 日本語
Yorodumi
- PDB-2yd6: Crystal structure of the N-terminal Ig1-2 module of Human Recepto... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yd6
TitleCrystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta
ComponentsPTPRD PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / synaptic membrane adhesion / presynapse assembly / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of receptor signaling pathway via JAK-STAT / phosphate-containing compound metabolic process / positive regulation of synapse assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of immune response / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / neuron differentiation / nervous system development / presynaptic membrane / cellular response to hypoxia / signaling receptor binding / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / 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 ...Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / : / 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 / Tyrosine specific protein phosphatases domain profile. / 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
CITRATE ANION / Receptor-type tyrosine-protein phosphatase delta / Receptor-type tyrosine-protein phosphatase delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 23, 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: PTPRD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7053
Polymers23,4801
Non-polymers2252
Water4,576254
1
A: PTPRD PROTEIN
hetero molecules

A: PTPRD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4106
Polymers46,9602
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2330 Å2
ΔGint-25.5 kcal/mol
Surface area19750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.710, 48.710, 145.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein PTPRD PROTEIN / RPTPD / RECEPTOR PROTEIN TYROSINE PHOSPHATASE DELTA


Mass: 23480.199 Da / Num. of mol.: 1 / Fragment: IG1-2, RESIDUES 21-220
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: Q3KPJ2, UniProt: P23468*PLUS, protein-tyrosine-phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES ...THE N-TERMINAL THREE AMINO ACID RESIDUES (ETG) AND THE C- TERMINAL NINE AMINO ACID RESIDUES (GTKHHHHHH) DERIVE FROM THE PHLSEC VECTOR.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5.6
Details: 0.085M TRI-SODIUM CITRATE DIHYDRATE, 25% PEG 4000, 15% GLYCEROL, PH 5.6 .

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→49 Å / Num. obs: 45165 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.4
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.6.0077refinement
xia2data reduction
XDSdata reduction
xia2data scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YD4

2yd4


Resolution: 1.35→48.64 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.467 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2250 5 %RANDOM
Rwork0.141 ---
obs0.142 42829 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 14 254 1775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221721
X-RAY DIFFRACTIONr_bond_other_d0.0010.021221
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9752370
X-RAY DIFFRACTIONr_angle_other_deg0.8553.0012999
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62523.87580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.88415310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2461518
X-RAY DIFFRACTIONr_chiral_restr0.2670.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.99139773
X-RAY DIFFRACTIONr_sphericity_free12.5435255
X-RAY DIFFRACTIONr_sphericity_bonded7.97752888
LS refinement shellResolution: 1.35→1.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.197 157 -
Rwork0.185 3070 -
obs--98.47 %

+
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