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- PDB-8fna: Crystal structure of the C-terminal Fg domain of human TNR -

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Basic information

Entry
Database: PDB / ID: 8fna
TitleCrystal structure of the C-terminal Fg domain of human TNR
ComponentsTenascin-R
KeywordsSIGNALING PROTEIN / Extracellular matrix / Fibrinogen
Function / homology
Function and homology information


axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / neuron cell-cell adhesion / negative regulation of synaptic transmission / negative regulation of cell-cell adhesion ...axon extension involved in regeneration / negative regulation of axon extension involved in regeneration / perineuronal net / tenascin complex / positive regulation of transmission of nerve impulse / neuroblast migration / telencephalon cell migration / neuron cell-cell adhesion / negative regulation of synaptic transmission / negative regulation of cell-cell adhesion / regulation of cell differentiation / locomotory exploration behavior / associative learning / neuromuscular process controlling balance / ECM proteoglycans / regulation of cell adhesion / regulation of cell migration / extracellular matrix organization / positive regulation of synaptic transmission, glutamatergic / synaptic transmission, glutamatergic / long-term synaptic potentiation / axon guidance / synapse organization / Schaffer collateral - CA1 synapse / negative regulation of neuron projection development / collagen-containing extracellular matrix / cell adhesion / membrane raft / glutamatergic synapse / cell surface / extracellular space / extracellular region
Similarity search - Function
Tenascin, EGF-like domain / Tenascin EGF domain / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / 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 ...Tenascin, EGF-like domain / Tenascin EGF domain / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / 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 signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tenascin-R
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3513
Polymers27,2191
Non-polymers1322
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-12 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.423, 47.423, 203.403
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1670-

HOH

21A-1710-

HOH

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Components

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


Mass: 27219.246 Da / Num. of mol.: 1 / Fragment: Fg domain (UNP residues 1129-1358)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNR / Production host: Escherichia coli (E. coli) / References: UniProt: Q92752
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG3350, 0.2 M L-proline, 100 mM HEPES sodium, pH 7.5, 5 mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 27862 / % possible obs: 99.2 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.06 / Net I/σ(I): 10.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2576 / CC1/2: 0.845 / Rpim(I) all: 0.24 / % possible all: 94.9

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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: 1.75→38.08 Å / SU ML: 0.1424 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.4322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1852 2001 7.2 %
Rwork0.1601 25792 -
obs0.1619 27793 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.33 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 7 240 2019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311882
X-RAY DIFFRACTIONf_angle_d1.13152554
X-RAY DIFFRACTIONf_chiral_restr0.0669243
X-RAY DIFFRACTIONf_plane_restr0.0126340
X-RAY DIFFRACTIONf_dihedral_angle_d14.5406696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.25581320.19381687X-RAY DIFFRACTION93.96
1.79-1.840.20881460.17491799X-RAY DIFFRACTION99.64
1.84-1.890.20121470.17051849X-RAY DIFFRACTION100
1.89-1.960.20971360.16751801X-RAY DIFFRACTION100
1.96-2.030.18321380.14611801X-RAY DIFFRACTION100
2.03-2.110.20591420.14861840X-RAY DIFFRACTION99.95
2.11-2.20.14671430.13681832X-RAY DIFFRACTION100
2.2-2.320.19091460.14441834X-RAY DIFFRACTION100
2.32-2.460.15491400.15681866X-RAY DIFFRACTION100
2.46-2.650.19481390.15621849X-RAY DIFFRACTION99.85
2.65-2.920.17881430.15241858X-RAY DIFFRACTION99.55
2.92-3.340.16641480.15921861X-RAY DIFFRACTION99.36
3.34-4.210.16421430.14831884X-RAY DIFFRACTION98.64
4.21-38.080.21681580.18512031X-RAY DIFFRACTION99.09
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)
13.48227605640.0515478945676-0.09390814517593.14572724917-0.4742707552455.78941361243-0.04076706336150.3264516594240.172265490326-0.5806441083530.104615059072-0.05169448828-0.5776798643120.320075732287-0.07320987412060.43080406271-0.09844788315020.08966501966340.2517853759510.01099007375960.2342660208125.901166749512.353883903374.2871844032
22.67264478606-0.37849444545-0.9249890530031.765531517790.4843227557013.476344347680.0814047053650.2316794173130.161104117483-0.269841488804-0.00628357767971-0.0378230710898-0.258886439384-0.0241464562256-0.07654488267740.1926152416440.001537057433980.02210374076830.1147026561040.01977324389540.1376089374416.69147382447.8676518980386.2364973852
33.337065308990.0941317749312.619309626791.615883367840.5518958053775.659488781740.1220847644350.0958910364341-0.0938850479591-0.07941025133190.00299295478691-0.1501454954370.1450658197060.293991781432-0.1181076795610.1880320225240.007967620793060.0298797022910.198404645152-0.02668801934670.23230484950326.7727140904-2.2493596800390.6908705897
48.10063584794-4.45723486367-0.1274600405614.66236249456-0.6778530942672.407080294240.1696845250610.805844768897-0.41818324763-0.242982993554-0.1487435951430.2431539043070.157481505266-0.213209375041-0.1122720011190.280451161624-0.0379962090917-0.009371536810.253778725732-0.06175408810840.1698378078813.2870039693-4.989972185179.8401701998
52.11059417660.126163174143-0.3806624635131.838736025660.2435653157292.905052860080.01041158532460.107721351988-0.124175645945-0.08077017465970.00701943751740.03629832546510.100975946659-0.0869680612093-0.009123753813280.1498669975970.000344368569941-0.008590370855460.112933117181-0.0134261212690.17256025859213.335052656-3.3947537876693.8990290768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1131 through 1169 )1131 - 11691 - 39
22chain 'A' and (resid 1170 through 1223 )1170 - 122340 - 93
33chain 'A' and (resid 1224 through 1241 )1224 - 124194 - 111
44chain 'A' and (resid 1242 through 1262 )1242 - 1262112 - 132
55chain 'A' and (resid 1263 through 1345 )1263 - 1345133 - 215

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