[English] 日本語
Yorodumi
- PDB-8fnb: Crystal structure of the C-terminal Fg domain of human TNC with t... -

+
Open data


ID or keywords:

Loading...

-
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 / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D ...perisynaptic extracellular matrix / tenascin complex / interstitial matrix / mesenchymal-epithelial cell signaling involved in prostate gland development / peripheral nervous system axon regeneration / bud outgrowth involved in lung branching / cellular response to prostaglandin D stimulus / syndecan binding / response to fibroblast growth factor / cellular response to vitamin D / prostate gland epithelium morphogenesis / 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 / regulation of cell growth / morphogenesis of an epithelium / Post-translational protein phosphorylation / osteoblast differentiation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / integrin binding / regulation of inflammatory response / collagen-containing extracellular matrix / response to ethanol / cell adhesion / endoplasmic reticulum lumen / focal adhesion / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / membrane
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 profile. / 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: 1.8 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 433 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • 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

Read more