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- PDB-6qnv: Fibrinogen-like globe domain of Human Tenascin-C -

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Basic information

Entry
Database: PDB / ID: 6qnv
TitleFibrinogen-like globe domain of Human Tenascin-C
ComponentsTenascin
KeywordsIMMUNE SYSTEM / Fibrinogen-related protein (FReP) / pro-inflammatory / damage-associated molecular pattern (DAMP) / Structural Genomics / Structural Genomics Consortium / SGC
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 / regulation of cell adhesion / response to mechanical stimulus / cellular response to retinoic acid / regulation of cell migration / morphogenesis of an epithelium / regulation of cell growth / 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 / response to ethanol / collagen-containing extracellular matrix / 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 / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / 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 ...Tenascin, EGF-like domain / Tenascin EGF domain / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / 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 / Few Secondary Structures / Irregular / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCoker, J.A. / Bezerra, G.A. / Bradshaw, W.J. / Zhang, M. / Yosaatmadja, Y. / Fernandez-Cid, A. / Shrestha, L. / Burgess-Brown, N. / Gileadi, O. / Arrowsmith, C.H. ...Coker, J.A. / Bezerra, G.A. / Bradshaw, W.J. / Zhang, M. / Yosaatmadja, Y. / Fernandez-Cid, A. / Shrestha, L. / Burgess-Brown, N. / Gileadi, O. / Arrowsmith, C.H. / Bountra, C. / Midwood, K.S. / Yue, W.W. / Marsden, B.D. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative115766 United Kingdom
CitationJournal: To Be Published
Title: Fibrinogen-like globe domain of Human Tenascin-C
Authors: Coker, J.A. / Bezerra, G.A. / Bradshaw, W.J. / Zhang, M. / Yosaatmadja, Y. / Fernandez-Cid, A. / Shrestha, L. / Burgess-Brown, N. / Gileadi, O. / Arrowsmith, C.H. / Bountra, C. / Midwood, K. ...Authors: Coker, J.A. / Bezerra, G.A. / Bradshaw, W.J. / Zhang, M. / Yosaatmadja, Y. / Fernandez-Cid, A. / Shrestha, L. / Burgess-Brown, N. / Gileadi, O. / Arrowsmith, C.H. / Bountra, C. / Midwood, K.S. / Yue, W.W. / Marsden, B.D.
History
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tenascin


Theoretical massNumber of molelcules
Total (without water)25,1841
Polymers25,1841
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Native mass spectrometry confirms folded monomer, in agreement with size-exclusion chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.829, 77.829, 71.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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: 25183.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNC, HXB / Production host: Escherichia coli (E. coli) / Strain (production host): CyDisCo / References: UniProt: P24821
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: Morpheus 0.09M NPS, 0.1M Buffer System 3 pH = 8.5, 50% v/v Precipitant Mix 1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→71.93 Å / Num. obs: 69462 / % possible obs: 100 % / Redundancy: 23.4 % / Biso Wilson estimate: 13.127 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.078 / Net I/σ(I): 18.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) all% possible all
1.2-1.2213.1133910.7692.80799.2
3.26-72.0623.771.237860.0080.038100

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FID

1fid


Resolution: 1.4→55.04 Å / Cross valid method: FREE R-VALUE
Details: Truncated to 1.4 angstroms (from 1.2A) during refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2141 4.9 %Random selection
Rwork0.164 ---
obs-41929 100 %-
Displacement parametersBiso max: 84.41 Å2 / Biso mean: 21.6135 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: LAST / Resolution: 1.4→55.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1677 0 0 175 1852

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