[English] 日本語
Yorodumi
- PDB-5xnp: Crystal structures of human SALM5 in complex with human PTPdelta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xnp
TitleCrystal structures of human SALM5 in complex with human PTPdelta
Components
  • Leucine-rich repeat and fibronectin type-III domain-containing protein 5
  • Receptor-type tyrosine-protein phosphatase delta
KeywordsMEMBRANE PROTEIN/HYDROLASE / Regulating some neural developments / MEMBRANE PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / negative regulation of macrophage activation / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / synaptic membrane adhesion / positive regulation of dendritic spine morphogenesis / regulation of postsynaptic density assembly ...trans-synaptic signaling by trans-synaptic complex / cell surface receptor protein tyrosine phosphatase signaling pathway / negative regulation of macrophage activation / Receptor-type tyrosine-protein phosphatases / presynaptic membrane assembly / transmembrane receptor protein tyrosine phosphatase activity / presynapse assembly / synaptic membrane adhesion / 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 / regulation of presynapse assembly / regulation of immune response / cell adhesion molecule binding / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampal mossy fiber to CA3 synapse / postsynaptic density membrane / modulation of chemical synaptic transmission / GABA-ergic synapse / negative regulation of inflammatory response / Schaffer collateral - CA1 synapse / neuron differentiation / presynaptic membrane / signaling receptor binding / glutamatergic synapse / cell surface / signal transduction / extracellular exosome / plasma membrane
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / : / 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 ...: / Receptor-type tyrosine-protein phosphatase delta, PTPase domain, repeat 1 / BspA type Leucine rich repeat region (6 copies) / : / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / 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 / Leucine-rich repeat profile. / Fibronectin type III domain / Fibronectin type 3 domain / Leucine-rich repeat / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Leucine-rich repeat domain 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 delta / Leucine-rich repeat and fibronectin type-III domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.729 Å
AuthorsLiu, H. / Lin, Z. / Xu, F.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of SALM5-induced PTP delta dimerization for synaptic differentiation
Authors: Lin, Z. / Liu, J. / Ding, H. / Xu, F. / Liu, H.
History
DepositionMay 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 22, 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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
B: Leucine-rich repeat and fibronectin type-III domain-containing protein 5
D: Receptor-type tyrosine-protein phosphatase delta
E: Receptor-type tyrosine-protein phosphatase delta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,13642
Polymers145,0294
Non-polymers3,10638
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11920 Å2
ΔGint-182 kcal/mol
Surface area64920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.384, 249.384, 249.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

-
Components

-
Protein , 2 types, 4 molecules ABDE

#1: Protein Leucine-rich repeat and fibronectin type-III domain-containing protein 5


Mass: 40468.383 Da / Num. of mol.: 2 / Fragment: UNP residues 18-374
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRFN5, C14orf146, SALM5 / Production host: Homo sapiens (human) / References: UniProt: Q96NI6
#2: Protein Receptor-type tyrosine-protein phosphatase delta / R-PTP-delta


Mass: 32046.260 Da / Num. of mol.: 2 / Fragment: UNP residues 21-320 / Mutation: 181-189 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRD / Production host: Homo sapiens (human) / References: UniProt: P23468, protein-tyrosine-phosphatase

-
Sugars , 1 types, 8 molecules

#3: 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

-
Non-polymers , 5 types, 124 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: Tartrate Na/K, MES pH 6.0, lithium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.729→50 Å / Num. obs: 26924 / % possible obs: 99.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.109 / Χ2: 1.563 / Net I/σ(I): 18.75
Reflection shellResolution: 3.729→3.79 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1340 / CC1/2: 0.727 / Χ2: 1.656 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNQ, 4YH7

5xnq

4yh7


Resolution: 3.729→48.908 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.44
RfactorNum. reflection% reflection
Rfree0.2638 1316 4.92 %
Rwork0.2316 --
obs0.2332 26749 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.729→48.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10166 0 158 94 10418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310526
X-RAY DIFFRACTIONf_angle_d0.73914352
X-RAY DIFFRACTIONf_dihedral_angle_d12.3856476
X-RAY DIFFRACTIONf_chiral_restr0.0471680
X-RAY DIFFRACTIONf_plane_restr0.0041868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7292-3.87850.30971230.29742835X-RAY DIFFRACTION100
3.8785-4.05490.35971480.29062796X-RAY DIFFRACTION99
4.0549-4.26860.26771440.26422813X-RAY DIFFRACTION99
4.2686-4.53580.25561530.23032821X-RAY DIFFRACTION100
4.5358-4.88580.22631440.21392841X-RAY DIFFRACTION100
4.8858-5.37690.27511500.22022808X-RAY DIFFRACTION100
5.3769-6.15360.27691540.24052821X-RAY DIFFRACTION99
6.1536-7.74790.29621590.22892845X-RAY DIFFRACTION100
7.7479-48.91240.21761410.20752853X-RAY DIFFRACTION96

+
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