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- PDB-8fnb: Crystal structure of the C-terminal Fg domain of human TNC with t... -

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Basic information

Entry
Database: PDB / ID: 8fnb
TitleCrystal structure of the C-terminal Fg domain of human TNC with the mutations Y2140H and S2164H
ComponentsTenascin
KeywordsSIGNALING PROTEIN / Extracellular matrix / fibrinogen
Function / homology
Function and homology information


perisynaptic extracellular matrix / 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 / syndecan binding / response to fibroblast growth factor / cellular response to prostaglandin D stimulus ...perisynaptic extracellular matrix / 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 / 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 / Syndecan interactions / neuromuscular junction development / odontogenesis of dentin-containing tooth / basement membrane / ECM proteoglycans / Integrin cell surface interactions / response to mechanical stimulus / regulation of cell adhesion / cellular response to retinoic acid / regulation of cell migration / 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) / osteoblast differentiation / : / regulation of inflammatory response / response to ethanol / cell adhesion / endoplasmic reticulum lumen / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / glutamatergic synapse / extracellular space / extracellular region / membrane
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF 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 ...Tenascin, EGF-like domain / Tenascin EGF 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 / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / EGF-like domain signature 1. / 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
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 1.3Oct 23, 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: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0996
Polymers52,8272
Non-polymers2724
Water7,800433
1
A: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5493
Polymers26,4131
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tenascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5493
Polymers26,4131
Non-polymers1362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.045, 101.561, 56.667
Angle α, β, γ (deg.)90.000, 122.353, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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: 26413.355 Da / Num. of mol.: 2 / Fragment: Fg domain (UNP residues 1975-2201) / Mutation: Y2140H, S2164H
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: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 200 mM lithium sulfate, 25% PEG1500, 50 mM Tris, 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: RAYONIX MX300-HS / Detector: CCD / Date: Aug 2, 2014
RadiationMonochromator: 1 / Protocol: 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: 46455 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.27 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 4286 / CC1/2: 0.987 / Rpim(I) all: 0.104

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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 entry 2J3F

2j3f


Resolution: 1.8→34.83 Å / SU ML: 0.156 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.0513
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1738 1915 4.3 %
Rwork0.1519 42647 -
obs0.1528 44562 94.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 12 433 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853660
X-RAY DIFFRACTIONf_angle_d0.87184934
X-RAY DIFFRACTIONf_chiral_restr0.0528476
X-RAY DIFFRACTIONf_plane_restr0.0083648
X-RAY DIFFRACTIONf_dihedral_angle_d14.09841298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.26781050.2032404X-RAY DIFFRACTION74.38
1.84-1.890.23781210.18462664X-RAY DIFFRACTION83.48
1.89-1.950.21881300.1792881X-RAY DIFFRACTION89.88
1.95-2.010.18111310.15593020X-RAY DIFFRACTION93.67
2.01-2.080.19451400.15863070X-RAY DIFFRACTION95.62
2.08-2.170.19591390.15663108X-RAY DIFFRACTION96.69
2.17-2.260.17511470.1563118X-RAY DIFFRACTION97.52
2.26-2.380.21341420.14673139X-RAY DIFFRACTION98.03
2.38-2.530.18781440.14863189X-RAY DIFFRACTION98.46
2.53-2.730.17131430.15213181X-RAY DIFFRACTION99.16
2.73-30.22161430.1683193X-RAY DIFFRACTION99.52
3-3.440.18561450.15013211X-RAY DIFFRACTION99.82
3.44-4.330.1351430.13083234X-RAY DIFFRACTION99.41
4.33-34.830.13741420.15293235X-RAY DIFFRACTION98.57
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)
11.29552707635-0.257661601110.01143282214091.39791907721-0.3520312194261.024631234430.007374825923060.04505574452350.161286872271-0.108700300986-0.01102168421050.116072654859-0.0597302308371-0.06286582655061.01610495925E-70.301679281410.0109883381379-0.02740855940870.2374718826160.007718839397680.242596316192-6.5621663332842.359787509848.5234646654
20.548589140647-0.224401543018-0.1161108023520.400665929142-0.2820797565040.3754921788110.06085772607750.02497385845440.0954156114111-0.167671024045-0.02254943552960.04805583587230.00980737763509-0.0368451993401-4.22268136861E-70.2630101734210.01896033515810.00145356628790.26913550075-0.003213305912680.274178071016-6.8673233531938.487799033756.7230157383
32.562049464430.3577985632930.1821367640381.64575906844-0.2383252433280.9008191330250.0317228540528-0.07951345473570.05595614410320.0276486575366-0.0353653620547-0.08633022877250.03514833568310.104049239722-1.10561159056E-70.2280239850030.02248309405940.01213532712560.245750766107-0.008231386475390.1764810380532.341889580330.904661862161.2133817088
40.7564900773250.400236656796-0.1359602244681.03494287691-0.3299812082661.42332301221-0.01010955558760.0684001859377-0.0825661345321-0.20131703069-0.07711219957940.07085910609490.06506381578920.0494105117484-4.26681421632E-80.270185958883-0.000425239178201-0.008165281066890.234808825929-0.01615870190190.195239173225-3.2236015698525.806752022353.7770040614
50.515053276828-0.504329369133-0.2103401547270.6038887280830.1419223720220.755878514133-0.0516733199445-0.150777051608-0.124905516090.21274122211-0.0277362940438-0.08957601319790.2486882067280.0514756834218-3.91231113143E-70.3176676634240.0273520736532-0.02706592562740.285670538150.03302975462530.37549362841313.81340405439.503908957633.1196386263
61.38468308488-0.293183993097-0.4347427536471.06393840461-0.02998822962231.026632080490.1014376087790.1198889861810.0325750177966-0.05243078124790.00128990889664-0.1834018880450.01518491209070.12758088476-1.54667426169E-70.2251905994020.009559420028770.01970380342780.2205299279150.01744508666150.27707611024310.343798592752.352754936921.3408173438
70.785760968166-0.8449435673110.3107280008351.05684224687-0.07068258278021.744267535890.0210759552511-0.04137368566460.000211297909630.137609709526-0.0126014648497-0.0006061315192190.1371493339550.00248555335097-3.51562759631E-70.2353424472120.0019918340460.005674686197130.2556722577010.02072593945890.2372598858243.4877135027553.041435243530.6152372278
81.3775570918-0.4430822394570.5530891167091.17403380346-0.1204949207670.9167702088370.05383536649640.07449993731440.0293296186248-0.169653015997-0.02299033274070.1367177253740.0142865905148-0.1875196210774.88074665572E-80.223927490577-0.002583160732490.01355952238520.264397391370.02650208183420.213709493864-5.225771718958.533612064421.8184647408
91.402805105750.0754588130754-0.3309743603531.08530798840.5550267225420.8328297207070.03858558934850.08647652714450.020025081952-0.0447451265972-0.0689938630478-0.215814235227-0.09603374712890.0291673949027-1.50204600894E-80.198835068792-0.007140693128880.03194972749890.2411794223230.006606603315210.2558260321825.751213064463.038521586525.9231490927
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1976 through 2057 )AA1976 - 20571 - 82
22chain 'A' and (resid 2058 through 2078 )AA2058 - 207883 - 103
33chain 'A' and (resid 2079 through 2150 )AA2079 - 2150104 - 175
44chain 'A' and (resid 2151 through 2194 )AA2151 - 2194176 - 219
55chain 'B' and (resid 1976 through 2014 )BC1976 - 20141 - 39
66chain 'B' and (resid 2015 through 2057 )BC2015 - 205740 - 82
77chain 'B' and (resid 2058 through 2097 )BC2058 - 209783 - 122
88chain 'B' and (resid 2098 through 2150 )BC2098 - 2150123 - 175
99chain 'B' and (resid 2151 through 2194 )BC2151 - 2194176 - 219

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