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- PDB-8fn9: Crystal structure of the C-terminal Fg domain of TNR with the sin... -

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Basic information

Entry
Database: PDB / ID: 8fn9
TitleCrystal structure of the C-terminal Fg domain of TNR with the single FN domain of PTPRZ
Components
  • Receptor-type tyrosine-protein phosphatase zeta
  • Tenascin-R
KeywordsSIGNALING PROTEIN / Complex / receptor protein tyrosine phosphatase / extracellular matrix / fibronectin type III / fibrinogen
Function / homology
Function and homology information


axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / regulation of oligodendrocyte progenitor proliferation / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity ...axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / regulation of oligodendrocyte progenitor proliferation / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / neuron cell-cell adhesion / negative regulation of synaptic transmission / Other interleukin signaling / regulation of myelination / negative regulation of cell-cell adhesion / oligodendrocyte differentiation / associative learning / locomotory exploration behavior / regulation of cell differentiation / peptidyl-tyrosine dephosphorylation / neuromuscular process controlling balance / positive regulation of oligodendrocyte differentiation / ECM proteoglycans / hematopoietic progenitor cell differentiation / regulation of cell adhesion / protein dephosphorylation / extracellular matrix organization / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of synaptic transmission, glutamatergic / axonogenesis / axon guidance / regulation of cell migration / central nervous system development / synaptic transmission, glutamatergic / synapse organization / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / neuron projection development / integrin binding / nervous system development / negative regulation of neuron projection development / : / negative regulation of neuron apoptotic process / learning or memory / cell adhesion / membrane raft / synapse / glutamatergic synapse / cell surface / signal transduction / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / : / : / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 ...Tenascin, EGF-like domain / Tenascin EGF domain / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / : / : / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / EGF-like domain, extracellular / EGF-like domain / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Epidermal growth factor-like domain. / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase zeta / Tenascin-R
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBouyain, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM143757 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Protein-protein interactions between tenascin-R and RPTP zeta /phosphacan are critical to maintain the architecture of perineuronal nets.
Authors: Sinha, A. / Kawakami, J. / Cole, K.S. / Ladutska, A. / Nguyen, M.Y. / Zalmai, M.S. / Holder, B.L. / Broerman, V.M. / Matthews, R.T. / Bouyain, S.
History
DepositionDec 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tenascin-R
B: Receptor-type tyrosine-protein phosphatase zeta
C: Tenascin-R
D: Receptor-type tyrosine-protein phosphatase zeta
E: Tenascin-R
F: Receptor-type tyrosine-protein phosphatase zeta
G: Tenascin-R
H: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,72612
Polymers156,5668
Non-polymers1604
Water10,305572
1
A: Tenascin-R
B: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,1412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Tenascin-R
D: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,1412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Tenascin-R
F: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,1412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Tenascin-R
H: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1823
Polymers39,1412
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.325, 75.656, 88.322
Angle α, β, γ (deg.)104.410, 92.401, 91.811
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Tenascin-R / TN-R / Janusin / Restrictin


Mass: 27223.234 Da / Num. of mol.: 4 / Fragment: Fg domain (UNP residues 1129-1358)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNR / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92752
#2: 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: 11918.245 Da / Num. of mol.: 4 / Fragment: UNP residues 310-411
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRZ1, HTPZP2, PTPRZ, PTPRZ2, PTPZ / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: P23471, protein-tyrosine-phosphatase
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG2000 MME, 200 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 102222 / % possible obs: 91.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10193 / CC1/2: 0.486 / Rpim(I) all: 0.517 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2J3F & 1FNA

2j3f

1fna


Resolution: 1.8→42.96 Å / SU ML: 0.2088 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.0225
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2102 2178 2.13 %
Rwork0.174 99925 -
obs0.1747 102103 91.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10361 0 4 572 10937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010710753
X-RAY DIFFRACTIONf_angle_d0.876714598
X-RAY DIFFRACTIONf_chiral_restr0.06271480
X-RAY DIFFRACTIONf_plane_restr0.00761927
X-RAY DIFFRACTIONf_dihedral_angle_d13.69193948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.3351340.28375802X-RAY DIFFRACTION85.48
1.84-1.880.30571090.24776304X-RAY DIFFRACTION91.65
1.88-1.930.25261470.2276314X-RAY DIFFRACTION92.04
1.93-1.980.25391450.22296265X-RAY DIFFRACTION92.01
1.98-2.040.2251340.2046226X-RAY DIFFRACTION91.27
2.04-2.110.2261490.19236215X-RAY DIFFRACTION89.94
2.11-2.180.21941280.18675789X-RAY DIFFRACTION85.36
2.18-2.270.22891320.1746021X-RAY DIFFRACTION87.89
2.27-2.370.22291350.18256512X-RAY DIFFRACTION95.08
2.37-2.50.22231350.18416470X-RAY DIFFRACTION94.75
2.5-2.650.25721410.19016458X-RAY DIFFRACTION93.98
2.65-2.860.2451380.18526344X-RAY DIFFRACTION92.67
2.86-3.150.22431370.18655895X-RAY DIFFRACTION86.1
3.15-3.60.20731380.15896452X-RAY DIFFRACTION94.28
3.6-4.540.15481370.13836560X-RAY DIFFRACTION95.86
4.54-42.960.17461390.1556298X-RAY DIFFRACTION91.8
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)
12.375499612860.4010197873910.5822819812951.847792186720.5893650965281.76200285212-0.1174637802890.05749269376810.135809971159-0.2522083273740.1226641840880.0449624486764-0.131498900466-0.017451461953-0.007961165633320.1653394778070.0198121685019-0.0009742215747090.1461872304590.005025477428610.139418756312-13.7336579338-29.69634795770.4562770696
20.7041562150860.2432162935940.5220341460460.756257792665-0.6119417181891.42048713906-0.33601340544-0.1037929194530.4791069242220.438164322120.194046603808-0.4744844673690.04770864360570.336828554109-0.001318401057890.4286747765260.112763816219-0.2002452418610.47616221263-0.1727030760860.61285882456612.8492765767-21.733630778193.6350383066
32.94776038858-0.05691111234180.8165835824961.773586696080.5435414244861.473773307380.0388421930014-0.005436453001340.200859869959-0.122668029544-0.06083386174630.06020684906790.0201160560209-0.0841281165471-0.0002031873049220.268745923916-0.05071006885150.002370563057890.2169739711350.03288441102020.138202973536-57.4251907643-17.555716699627.0007984596
41.094899848480.178438952551-0.06445148646010.782097298339-0.6012454558821.18057783446-0.03989323392920.09096522417040.01524255003510.01173900245950.325757958281-0.520511818724-0.153050011330.41388940803-2.63033991158E-80.374276712524-0.060409038276-0.00929625373280.558335609789-0.1314771083870.432849679534-31.3282432136-8.9257913472650.3982192928
51.817254848040.138570695532-0.4175316636992.24161192443-0.5672885766851.28633024716-0.1013349218820.00556230115796-0.191069008371-0.1114226365630.10817447060.1223385194180.0440517343364-0.0378788161875-0.0001659723621560.1388453529590.03601180520810.02564243798990.169303139187-0.007374492366720.239115378879-36.310673623812.878875119180.2801626318
60.829376321791-0.7847805121930.1190875012650.9910444701320.5121310343761.461731564030.002158679572920.198585724167-0.1298715251140.325676020662-0.3482183218920.4380023727660.322802272447-0.111716085367-0.0004862044205040.3884147040970.002994108469010.1243429758020.312258646799-0.01340246834430.506802078085-62.8584775539-4.9237178674697.0135317745
71.873028844270.273345000758-0.7873409521812.00728324027-0.4038123580061.44776196732-0.137700251652-0.049809846592-0.129293706768-0.08825851700240.110896623439-0.03384262322780.1250893068510.022010651111-0.0001574541636760.274493325496-0.0241094053312-0.03787299731350.2013297020950.02553538467590.123015104215-32.853355554424.803766752936.9253055454
81.542040012350.1587504422180.01818895785480.559966335391-0.009493455675461.460286930410.02373149455350.1761504339480.0860458166194-0.227801682768-0.1191359751850.279870489420.197467138435-0.107229173483-1.10704927952E-70.387854324392-0.02364123951310.01437191886310.3626139592440.03890256296710.351333482033-58.77949120366.8779249283754.5294465238
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AA - B1130 - 13781
22chain 'B'BC309 - 4091 - 99
33chain 'C'CD - E1130 - 13781
44chain 'D'DF310 - 4091 - 100
55chain 'E'EG - H1129 - 13781
66chain 'F'FI308 - 4101 - 103
77chain 'G'GJ - K1129 - 13781
88chain 'H'HL310 - 4101 - 100

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