[English] 日本語
Yorodumi
- PDB-3s97: PTPRZ CNTN1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3s97
TitlePTPRZ CNTN1 complex
Components
  • Contactin-1
  • Receptor-type tyrosine-protein phosphatase zeta
KeywordsCELL ADHESION / Carbonic anhdyrase like Immunoglobulin / CELL ADHESION complex
Function / homology
Function and homology information


perineuronal net / regulation of oligodendrocyte progenitor proliferation / L1CAM interactions / MDK and PTN in ALK signaling / cell-cell adhesion mediator activity / transmembrane receptor protein tyrosine phosphatase activity / Neurofascin interactions / central nervous system myelin formation / positive regulation of sodium ion transport / Other interleukin signaling ...perineuronal net / regulation of oligodendrocyte progenitor proliferation / L1CAM interactions / MDK and PTN in ALK signaling / cell-cell adhesion mediator activity / transmembrane receptor protein tyrosine phosphatase activity / Neurofascin interactions / central nervous system myelin formation / positive regulation of sodium ion transport / Other interleukin signaling / regulation of myelination / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / positive regulation of oligodendrocyte differentiation / hematopoietic progenitor cell differentiation / side of membrane / protein dephosphorylation / Notch signaling pathway / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / NOTCH2 Activation and Transmission of Signal to the Nucleus / cerebellum development / axonogenesis / axon guidance / Activated NOTCH1 Transmits Signal to the Nucleus / central nervous system development / locomotory behavior / cell-cell adhesion / positive regulation of neuron projection development / neuron projection development / integrin binding / presynaptic membrane / carbohydrate binding / gene expression / negative regulation of neuron apoptotic process / postsynaptic membrane / learning or memory / cell adhesion / axon / synapse / positive regulation of gene expression / glutamatergic synapse / signal transduction / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Contactin-1 / : / : / : / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Protein tyrosine phosphatase, catalytic domain ...Contactin-1 / : / : / : / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / Immunoglobulin / Immunoglobulin domain / 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 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase zeta / Contactin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2971 Å
AuthorsBouyain, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: A complex between contactin-1 and the protein tyrosine phosphatase PTPRZ controls the development of oligodendrocyte precursor cells.
Authors: Lamprianou, S. / Chatzopoulou, E. / Thomas, J.L. / Bouyain, S. / Harroch, S.
History
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Jul 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Sep 13, 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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase zeta
B: Receptor-type tyrosine-protein phosphatase zeta
C: Contactin-1
D: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,1548
Polymers107,2694
Non-polymers8854
Water3,009167
1
A: Receptor-type tyrosine-protein phosphatase zeta
C: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0774
Polymers53,6352
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-3 kcal/mol
Surface area21680 Å2
MethodPISA
2
B: Receptor-type tyrosine-protein phosphatase zeta
D: Contactin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0774
Polymers53,6352
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-3 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)334.108, 45.957, 78.947
Angle α, β, γ (deg.)90.00, 101.37, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Receptor-type tyrosine-protein phosphatase zeta / R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine ...R-PTP-zeta / Protein-tyrosine phosphatase receptor type Z polypeptide 1 / Protein-tyrosine phosphatase receptor type Z polypeptide 2 / R-PTP-zeta-2


Mass: 30886.701 Da / Num. of mol.: 2
Fragment: Carbonic anhydrase like domain (UNP Residues 34-302)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HTPZP2, PTPRZ, PTPRZ1, PTPRZ2, PTPZ / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: P23471, protein-tyrosine-phosphatase
#2: Protein Contactin-1 / Glycoprotein gp135 / Neural cell surface protein F3


Mass: 22747.986 Da / Num. of mol.: 2
Fragment: Immunoglobulin domains 2 and 3 (UNP Residues 133-329)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CNTN1 / Plasmid: pSGHP1 / Production host: Homo Sapiens (human) / References: UniProt: Q12860
#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.: 167 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% (w/v) PEG 1,500, 50 mM Na-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: Mar 23, 2010
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.297→50 Å / Num. obs: 51002 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.297-2.385.20.493181.3
2.38-2.485.80.432188.9
2.48-2.596.40.39195.5
2.59-2.736.90.336198.6
2.73-2.97.20.267199.6
2.9-3.127.30.219199.9
3.12-3.447.30.1781100
3.44-3.937.40.1511100
3.93-4.957.50.1371100
4.95-507.30.088199.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.91
Highest resolutionLowest resolution
Rotation2.5 Å33.56 Å
Translation2.5 Å33.56 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3JXF and 1CS6

3jxf

1cs6


Resolution: 2.2971→33.561 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.82 / σ(F): 1.36 / Phase error: 27.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 2537 4.98 %
Rwork0.2006 --
obs0.2033 50971 95.76 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.989 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9131 Å20 Å2-2.8472 Å2
2--7.4625 Å20 Å2
3----2.5494 Å2
Refinement stepCycle: LAST / Resolution: 2.2971→33.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7410 0 56 167 7633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077656
X-RAY DIFFRACTIONf_angle_d1.05610363
X-RAY DIFFRACTIONf_dihedral_angle_d15.852851
X-RAY DIFFRACTIONf_chiral_restr0.0681130
X-RAY DIFFRACTIONf_plane_restr0.0051335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2971-2.34130.34781020.27511956X-RAY DIFFRACTION70
2.3413-2.38910.35981170.27942336X-RAY DIFFRACTION84
2.3891-2.4410.371360.2752403X-RAY DIFFRACTION87
2.441-2.49780.30871270.26222536X-RAY DIFFRACTION92
2.4978-2.56020.32161460.24252687X-RAY DIFFRACTION95
2.5602-2.62940.30211520.2412717X-RAY DIFFRACTION99
2.6294-2.70680.30481320.22932758X-RAY DIFFRACTION98
2.7068-2.79410.29021480.24032733X-RAY DIFFRACTION100
2.7941-2.89390.34341470.23662806X-RAY DIFFRACTION99
2.8939-3.00970.31731450.24242796X-RAY DIFFRACTION100
3.0097-3.14660.28951420.24162791X-RAY DIFFRACTION100
3.1466-3.31240.31131480.23922824X-RAY DIFFRACTION100
3.3124-3.51970.28741460.23092813X-RAY DIFFRACTION100
3.5197-3.79110.24291470.19682819X-RAY DIFFRACTION100
3.7911-4.1720.19221510.16452842X-RAY DIFFRACTION100
4.172-4.77420.22011480.12962803X-RAY DIFFRACTION100
4.7742-6.00930.1661480.1542861X-RAY DIFFRACTION100
6.0093-33.56480.20331550.17062953X-RAY DIFFRACTION99
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)
11.0176-0.1405-0.26230.9334-0.4792.4623-0.02220.05160.0601-0.06410.0647-0.1332-0.04090.1499-0.05650.1852-0.04010.00170.2659-0.08820.240257.739412.79832.4369
21.00580.0694-0.09951.56230.66851.72780.082-0.1198-0.05950.0315-0.10020.0364-0.0386-0.18460.00990.1373-0.0254-0.01520.2807-0.01060.191916.9435-1.816413.7682
31.883-0.22850.16731.7481.00062.59560.0282-0.09380.08220.16250.0071-0.0023-0.1542-0.3234-0.01490.2319-0.01780.04010.2646-0.0260.20743.790814.628538.8288
41.9119-0.61280.5680.7546-0.26870.84020.121-0.1092-0.10930.1915-0.0968-0.07720.1608-0.0697-0.03130.3122-0.0279-0.05050.1604-0.00390.251964.87154.897638.3423
51.1694-0.2734-0.42811.78170.42381.73220.27180.4487-0.6128-0.268-0.23670.46360.4074-0.2933-0.05020.3479-0.0053-0.11270.485-0.19930.507117.8443-17.0288-19.8431
61.90140.21480.36991.75590.67132.49140.0060.21460.1219-0.3256-0.12650.1263-0.48640.21040.14040.3453-0.02190.01990.4619-0.03820.221228.08933.6455-23.2651
70.06310.10370.12520.2116-0.0497-0.0799-0.0028-0.007-0.10830.004-0.0045-0.0376-0.0074-0.0373-00.17840.00010.01140.1672-0.0480.170338.93152.622912.3907
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain 'A'
2X-RAY DIFFRACTION2Chain 'B'
3X-RAY DIFFRACTION3Chain 'C' and ((resseq 133:236))
4X-RAY DIFFRACTION4Chain 'C' and ((resseq 237:329))
5X-RAY DIFFRACTION5Chain 'D' and ((resseq 237:329))
6X-RAY DIFFRACTION6Chain 'D' and ((resseq 133:236))
7X-RAY DIFFRACTION7Chain 'F'

+
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