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- PDB-3s97: PTPRZ CNTN1 complex -

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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 / central nervous system myelin formation / transmembrane receptor protein tyrosine phosphatase activity / Neurofascin interactions / positive regulation of sodium ion transport / regulation of myelination ...perineuronal net / regulation of oligodendrocyte progenitor proliferation / L1CAM interactions / MDK and PTN in ALK signaling / cell-cell adhesion mediator activity / central nervous system myelin formation / transmembrane receptor protein tyrosine phosphatase activity / Neurofascin interactions / positive regulation of sodium ion transport / regulation of myelination / Other interleukin signaling / oligodendrocyte differentiation / peptidyl-tyrosine dephosphorylation / positive regulation of oligodendrocyte differentiation / NOTCH2 Activation and Transmission of Signal to the Nucleus / hematopoietic progenitor cell differentiation / protein dephosphorylation / side of membrane / Activated NOTCH1 Transmits Signal to the Nucleus / Notch signaling pathway / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine phosphatase activity / axon guidance / cerebellum development / central nervous system development / locomotory behavior / cell-cell adhesion / positive regulation of neuron projection development / neuron projection development / integrin binding / presynaptic membrane / carbohydrate binding / negative regulation of neuron apoptotic process / gene expression / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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Experiment

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

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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

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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

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Phasing

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

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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'

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