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- PDB-8fn8: Crystal structure of the C-terminal Fg domain of TNC with the sin... -

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Basic information

Entry
Database: PDB / ID: 8fn8
TitleCrystal structure of the C-terminal Fg domain of TNC with the single FN domain of PTPRZ
Components
  • Receptor-type tyrosine-protein phosphatase zeta
  • Tenascin
KeywordsSIGNALING PROTEIN / Complex / receptor protein tyrosine phosphatase / extracellular matrix / fibronectin type III / fibrinogen
Function / homology
Function and homology information


perineuronal net / perisynaptic extracellular matrix / regulation of oligodendrocyte progenitor proliferation / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / MDK and PTN in ALK signaling ...perineuronal net / perisynaptic extracellular matrix / regulation of oligodendrocyte progenitor proliferation / tenascin complex / interstitial matrix / extracellular matrix of synaptic cleft / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / MDK and PTN in ALK signaling / transmembrane receptor protein tyrosine phosphatase activity / syndecan binding / response to fibroblast growth factor / cellular response to prostaglandin D stimulus / prostate gland epithelium morphogenesis / cellular response to vitamin D / negative regulation of cell adhesion / extracellular matrix structural constituent / regulation of myelination / Other interleukin signaling / Syndecan interactions / neuromuscular junction development / odontogenesis of dentin-containing tooth / peptidyl-tyrosine dephosphorylation / oligodendrocyte differentiation / positive regulation of oligodendrocyte differentiation / basement membrane / ECM proteoglycans / Integrin cell surface interactions / response to mechanical stimulus / hematopoietic progenitor cell differentiation / regulation of cell adhesion / protein dephosphorylation / cellular response to retinoic acid / protein-tyrosine-phosphatase / axonogenesis / protein tyrosine phosphatase activity / regulation of cell migration / central nervous system development / morphogenesis of an epithelium / Post-translational protein phosphorylation / regulation of cell growth / response to wounding / integrin binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / neuron projection development / osteoblast differentiation / : / regulation of inflammatory response / response to ethanol / negative regulation of neuron apoptotic process / learning or memory / cell adhesion / endoplasmic reticulum lumen / focal adhesion / positive regulation of cell population proliferation / synapse / positive regulation of gene expression / glutamatergic synapse / signal transduction / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Teneurin EGF domain / Teneurin-like EGF domain / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / : / : / Fibrinogen-related domains (FReDs) ...Tenascin, EGF-like domain / Tenascin EGF domain / Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / Teneurin EGF domain / Teneurin-like EGF 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / EGF-like domain signature 2. / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 1.3Oct 16, 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
B: Receptor-type tyrosine-protein phosphatase zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3383
Polymers38,2982
Non-polymers401
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-14 kcal/mol
Surface area14420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.707, 61.520, 92.428
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Tenascin / TN / Cytotactin / GMEM / GP 150-225 / Glioma-associated-extracellular matrix antigen / Hexabrachion ...TN / Cytotactin / GMEM / GP 150-225 / Glioma-associated-extracellular matrix antigen / Hexabrachion / JI / Myotendinous antigen / Neuronectin / Tenascin-C / TN-C


Mass: 26383.326 Da / Num. of mol.: 1 / Fragment: Fg domain (UNP residues 1975-2201)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNC, HXB / Plasmid: pET32 / Production host: Escherichia coli (E. coli) / References: UniProt: P24821
#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: 11914.256 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% w/v PEG3350, 100 mM Tris-HCl, pH 8.0

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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: 1.89→50 Å / Num. obs: 25470 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 20.95 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.054 / Rrim(I) all: 0.126 / Net I/σ(I): 16.2
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2506 / CC1/2: 0.949 / Rpim(I) all: 0.172 / Rrim(I) all: 0.384 / % possible all: 99.2

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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: 1.89→40.88 Å / SU ML: 0.1506 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.9442
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 1979 7.89 %
Rwork0.164 23105 -
obs0.1672 25084 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.24 Å2
Refinement stepCycle: LAST / Resolution: 1.89→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 1 229 2788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322679
X-RAY DIFFRACTIONf_angle_d0.66683637
X-RAY DIFFRACTIONf_chiral_restr0.0459373
X-RAY DIFFRACTIONf_plane_restr0.0043478
X-RAY DIFFRACTIONf_dihedral_angle_d13.413981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.23771280.19531515X-RAY DIFFRACTION91.53
1.94-1.990.2191390.17631584X-RAY DIFFRACTION95.04
1.99-2.050.24241380.17081601X-RAY DIFFRACTION96.77
2.05-2.120.21361370.16761603X-RAY DIFFRACTION97.32
2.12-2.190.21831410.1661646X-RAY DIFFRACTION98.51
2.19-2.280.21881400.15851637X-RAY DIFFRACTION98.29
2.28-2.380.23961400.17591636X-RAY DIFFRACTION98.72
2.38-2.510.22451410.1771656X-RAY DIFFRACTION99.17
2.51-2.670.22851420.18631657X-RAY DIFFRACTION99.34
2.67-2.870.21531440.18551677X-RAY DIFFRACTION99.29
2.87-3.160.25041430.18131675X-RAY DIFFRACTION99.51
3.16-3.620.19821450.16061697X-RAY DIFFRACTION99.3
3.62-4.560.16751460.13311713X-RAY DIFFRACTION99.36
4.56-40.880.16621550.15431808X-RAY DIFFRACTION99.49
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)
12.648990862710.136030120961-0.07688072350022.021521696830.1621959684132.191410241420.03914170754650.02057500009990.0560682475099-0.04094461051770.0386289757307-0.353940169813-0.1404318535470.388877452839-0.07246513376260.185081770293-0.05109157839440.03166183740620.264728209233-0.02771108581990.22459211342738.119386216457.973838790359.2595526826
22.436320019340.46131238378-0.07139661630692.3838705281-0.1991398857751.55721931921-0.06217965860560.182918915358-0.0176298717642-0.3407148116470.02213310194680.0481145708304-0.09220020002810.0479128516680.05753799543190.11147876779-0.0180045665440.001755216721980.1776439368860.02322518525440.08146325342823.974343145847.790578962753.0532881792
31.92388085233-0.595312286049-0.02750182805693.328391247690.04626825546940.9101964091880.03002862799810.2286585965960.363281903123-0.640611248996-0.00922296440267-0.0716998345103-0.183953619954-0.0784223280858-0.02760498915640.217528077778-0.03295570554430.01408590492470.2275784091110.004035780244970.14550967844326.543178028250.495086448849.2124660109
42.9323531413-0.0789281182695-0.5195697073423.00305825990.3961338803811.5937727303-0.0102594942696-0.210296985480.06717713570860.06413666050570.0805858946495-0.1716967837440.0001620903288040.120701581181-0.05790374262270.136006074933-0.0168815114414-0.004233631037810.153158564072-0.0009489629133870.11286426291928.382949703347.658883430462.5189145657
51.841225156120.397523717486-0.3296343962182.675574229830.4358048271982.03675890659-0.0587383833916-0.191629870563-0.03712850941050.06354153833940.0790231552638-0.01223651573540.02707965757710.121361251185-0.04903419827580.0877964835872-0.0183182411745-0.009939750924530.128260671740.001679218947340.061997994742523.174900245745.147609639765.0977511376
63.07887800054-0.658443424686-1.283601220522.156890284440.5932335255821.51373224375-0.0532710796069-0.135461115558-0.2453812056640.195662202017-0.0056564154065-0.08938707859230.2299591014870.07296347681550.05994269053610.176858801798-0.00411945569916-0.00821824172550.1996800372990.01463162724850.12035896091522.702078494940.265244598766.9964213929
71.488907677740.6081929399090.9949787476062.083948086490.1784369702691.45919349241-0.1086840112920.191212923588-0.41331033297-0.09649132088830.137251573752-0.249569623910.1891682785030.153623082685-0.03129481221130.167904599634-0.01981613969450.009000324136790.202060845492-0.0126837401740.19968407610522.683787476431.364862666758.6192710008
82.349388829341.49319992219-0.4929416459114.21606829988-0.1095877788251.8385613947-0.152547303760.214759497024-0.306780251012-0.292442558540.1694921222110.36498584180.407121613877-0.0707632868543-0.03840853023960.176177128357-0.0121781070808-0.01430524512570.177165194456-0.02768115713640.2057735325417.183927314231.804955672655.9219919158
92.73017837421-0.0278003449720.2355644807272.70825345380.01065568621611.48055950241-0.1821149484820.162802196268-0.107647089661-0.3779716107180.07806952564450.4507870217040.129713659735-0.1305153357450.05141017006550.129565524473-0.0233412264593-0.03346835874280.1281524860360.0063255035360.13489071858210.766270454341.294360437256.9888661543
102.50938518220.1454735842660.09465414669492.87226535734-0.8284561244391.89080677402-0.1322433332820.2218379150010.2586605536780.08487761207780.0434610282520.174726642787-0.1789338080120.2051018806440.08684737346160.1647924651240.003163093029770.006059158288750.110090460796-0.01249455971380.085152339813319.543741381349.676600472562.1160543247
116.28840059766-1.41190989777-3.81154682932.916703648581.287042993156.282290736330.1828726413090.160225625740.530868270106-0.1287536256910.3280403603830.250134882310.436110422716-0.0710042268398-0.537622714490.2299066719910.00987756833564-0.04890121171860.2124360044610.04665751973240.294220787561-3.0339171053224.399447172754.7657233963
124.0651779705-3.339330001130.9045102609059.17630401956-1.708267477942.563438255720.5324461695560.624712022308-0.122792162425-0.943320950142-0.551903244758-1.095505828530.3669000040410.447656705331-0.01555446104130.3757668979020.03272775998240.02658946216550.301701223696-0.009009426457090.37461334476313.133977087211.626663039652.3241436937
135.68417799204-0.6529436046970.05934954273893.61978356715-0.4463071457714.486690939430.212504584923-0.222614370220.8009504701860.027759906413-0.05072639528960.125117687973-0.484257035178-0.171325869728-0.187911094490.215238481572-0.0306969127901-0.01018686692340.195079701842-0.01088892362980.308758891999-2.135964103130.032930845757.5573726005
141.52144735488-0.569617478152-0.1220404645892.608833629862.461301913892.429489265690.111775474644-0.259383403288-0.05469595445920.998787844941-0.0680882701120.04122901916880.212344724820.134849665488-0.0266216671190.21963833717-0.01596789757690.0003291195473280.2106414242360.02548302720550.2042359472222.7148527449516.934864405761.8599736481
153.016485526010.1844004694541.394912256213.9769886671-1.857247615323.230251916950.103047917285-0.256032315877-1.17745614590.396887558251-0.0006798898877830.806581345180.182072106496-0.274626893089-0.0979971112490.578309411390.0210141414195-0.03073435954760.349906624411-0.01392917818950.6714136049080.4765023258830.8851646898659.9938486632
161.331886891120.647862486657-0.06236263516053.96434174401-0.03492135226711.837116375320.166873600931-0.241962616148-0.04325774371660.220837815584-0.0332824322777-0.3234329619990.203499496170.242571937196-0.1208896162280.2498538449730.00712370488013-0.04988568083530.226378391138-0.01830139895730.2521018889497.5409579827821.882274960562.7560258333
171.23986893995-0.2912133542540.02857314370152.616026086810.4448333062591.002141858280.07855119978150.127977509006-0.1795942211140.212184710516-0.125362856564-0.116904965990.3155066908130.01100174530320.03809301155980.242205688687-0.00374481882584-0.03689513712210.1813652349740.002006907018620.2291888906016.2243804311110.719084378557.6029275925
182.57542739627-0.4095484255260.07809694717823.187814688950.4891003388711.796035019130.1636169207650.174175665002-0.195786572253-0.305604926529-0.1877755631490.4646509293750.0969161158092-0.195623083519-0.02180931066010.233223872801-0.0121662031467-0.03483775831130.2115523384020.04006451874150.211419388481-0.069567656451715.231764944756.806459593
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1975 through 2015 )AA1975 - 20151 - 41
22chain 'A' and (resid 2016 through 2045 )AA2016 - 204542 - 71
33chain 'A' and (resid 2046 through 2057 )AA2046 - 205772 - 83
44chain 'A' and (resid 2058 through 2078 )AA2058 - 207884 - 104
55chain 'A' and (resid 2079 through 2097 )AA2079 - 2097105 - 123
66chain 'A' and (resid 2098 through 2114 )AA2098 - 2114124 - 140
77chain 'A' and (resid 2115 through 2132 )AA2115 - 2132141 - 158
88chain 'A' and (resid 2133 through 2149 )AA2133 - 2149159 - 175
99chain 'A' and (resid 2150 through 2173 )AA2150 - 2173176 - 199
1010chain 'A' and (resid 2174 through 2191 )AA2174 - 2191200 - 217
1111chain 'B' and (resid 310 through 318 )BC310 - 3181 - 9
1212chain 'B' and (resid 319 through 331 )BC319 - 33110 - 22
1313chain 'B' and (resid 332 through 342 )BC332 - 34223 - 33
1414chain 'B' and (resid 343 through 352 )BC343 - 35234 - 43
1515chain 'B' and (resid 353 through 360 )BC353 - 36044 - 51
1616chain 'B' and (resid 361 through 371 )BC361 - 37152 - 62
1717chain 'B' and (resid 372 through 392 )BC372 - 39263 - 83
1818chain 'B' and (resid 393 through 410 )BC393 - 41084 - 101

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  • 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

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