[English] 日本語
Yorodumi
- PDB-3kld: PTPRG CNTN4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3kld
TitlePTPRG CNTN4 complex
Components
  • Contactin 4
  • Receptor-type tyrosine-protein phosphatase gamma
KeywordsCELL ADHESION / PROTEIN COMPLEX / RECEPTOR PROTEIN TYROSINE PHOSPHATASE / NEURAL RECOGNITION MOLECULE / Glycoprotein / Membrane / Phosphoprotein / Protein phosphatase / Transmembrane
Function / homology
Function and homology information


negative regulation of neuron differentiation / side of membrane / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / brain development / neuron projection development / negative regulation of neuron projection development / nervous system development / cell adhesion ...negative regulation of neuron differentiation / side of membrane / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / brain development / neuron projection development / negative regulation of neuron projection development / nervous system development / cell adhesion / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Carbonic Anhydrase II ...: / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain / Immunoglobulin I-set / Immunoglobulin I-set domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase gamma / Contactin-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsBouyain, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The protein tyrosine phosphatases PTPRZ and PTPRG bind to distinct members of the contactin family of neural recognition molecules.
Authors: Bouyain, S. / Watkins, D.J.
History
DepositionNov 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 31, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Contactin 4
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1666
Polymers73,2812
Non-polymers8854
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.432, 138.957, 50.565
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Contactin 4 / AxCAM / BIG-2


Mass: 42919.570 Da / Num. of mol.: 1 / Fragment: Ig domains 1-4 (UNP residues 25-404)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CNTN4 / Plasmid: pSGHP1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q14BL8
#2: Protein Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 30361.684 Da / Num. of mol.: 1
Fragment: carbonic anhydrase-like domain (UNP residues 55-320)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ptprg / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: Q05909, protein-tyrosine-phosphatase
#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.: 4
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 1500 - 50 mM Sodium cacodylate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 12, 2009
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 46797 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.156 / Χ2: 1.027 / Net I/σ(I): 5.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 3.6 / Num. unique all: 3857 / Χ2: 0.931 / % possible all: 80.3

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.64
Highest resolutionLowest resolution
Rotation2.5 Å37.87 Å
Translation2.5 Å37.87 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.999→37.867 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2254 5.02 %RANDOM
Rwork0.179 ---
obs0.182 44869 91.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.871 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 181.5 Å2 / Biso mean: 36.5 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1-13.783 Å2-0 Å2-0 Å2
2---7.85 Å20 Å2
3----5.933 Å2
Refinement stepCycle: LAST / Resolution: 1.999→37.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5067 0 56 415 5538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115263
X-RAY DIFFRACTIONf_angle_d1.3547141
X-RAY DIFFRACTIONf_chiral_restr0.093771
X-RAY DIFFRACTIONf_plane_restr0.006930
X-RAY DIFFRACTIONf_dihedral_angle_d17.1521918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.999-2.0420.3121150.221984209970
2.042-2.090.3231130.2022179229276
2.09-2.1420.241200.1932335245581
2.142-2.20.2861270.1822396252384
2.2-2.2650.231280.1922461258987
2.265-2.3380.2721390.1882614275391
2.338-2.4210.2781420.1852724286694
2.421-2.5180.2361480.1852762291096
2.518-2.6330.2671440.1822747289196
2.633-2.7720.2671480.1942796294497
2.772-2.9450.2611500.1922833298398
2.945-3.1720.2541520.1952886303899
3.172-3.4910.2231520.18628903042100
3.491-3.9960.2081550.16629323087100
3.996-5.0330.1781560.13929663122100
5.033-37.8730.1921650.16531103275100
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)
1-0.10030.7175-0.30490.5138-0.40650.87050.1114-0.00650.13050.1020.01360.5074-0.2853-0.0311-0.08860.30880.0457-0.02070.11350.02230.242411.959751.081121.5854
20.6367-0.052-0.4242.4752-0.57110.17030.0466-0.01490.0466-0.35020.13820.76520.06640.0071-0.17790.1877-0.0147-0.0410.16640.05750.391912.077275.2566-11.4419
30.5460.0416-0.28231.70640.01560.31450.0729-0.03010.0538-0.4668-0.0994-0.0076-0.04560.04290.00690.24540.03790.03030.1180.01380.128129.25260.7374-12.769
40.5271-0.04430.00780.6621-0.1092-0.0985-0.02190.01470.00890.10440.0384-0.06150.091-0.0495-0.0120.1909-0.02220.00020.1671-00.116732.928835.959222.269
50.74080.00550.04970.97150.12671.1705-0.037-0.0625-0.01280.15260.0156-0.0672-0.04790.25010.01620.1559-0.0030.00450.19320.00980.123340.848996.5695-3.6802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 25:121A25 - 121
2X-RAY DIFFRACTION2chain A and resid 122:224A122 - 224
3X-RAY DIFFRACTION3chain A and resid 225:314A225 - 314
4X-RAY DIFFRACTION4chain A and resid 315:402A315 - 402
5X-RAY DIFFRACTION5chain BB56 - 320

+
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://pdbjlvh1.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