[English] 日本語
Yorodumi
- PDB-9r5y: Crystal structure of the C-terminal domain of human TNC in comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9r5y
TitleCrystal structure of the C-terminal domain of human TNC in complex with Adhiron 52
Components
  • Adhiron
  • Tenascin
KeywordsSIGNALING PROTEIN / Complex / protein protein interaction / Inhibitor / extracellular matrix
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 / cellular response to prostaglandin D stimulus / response to fibroblast growth factor ...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 / cellular response to prostaglandin D stimulus / 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 / Post-translational protein phosphorylation / regulation of cell growth / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / integrin binding / 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-like EGF domain / : / 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. ...Tenascin, EGF-like domain / Tenascin EGF domain / Teneurin-like EGF domain / : / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsGaule, T.G. / Trinh, C. / Simmons, K.J. / Tomlinson, D.C. / Maqbool, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/17/72/33255 United Kingdom
CitationJournal: To Be Published
Title: Targeting Tenascin-C-Toll-like Receptor 4 signalling with Adhiron-derived small molecules - a viable strategy for reducing fibrosis in Systemic Sclerosis
Authors: Gaule, T.G. / Simmons, K.J. / Walker, K. / DelGaldo, F. / Ross, R.L. / Viswambharan, H. / Krishnappa, J. / Pacey, J. / McPhillie, M. / Tomlinson, D.C. / Maqbool, A.
History
DepositionMay 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tenascin
B: Adhiron
C: Adhiron
D: Tenascin


Theoretical massNumber of molelcules
Total (without water)71,1164
Polymers71,1164
Non-polymers00
Water6,107339
1
A: Tenascin
B: Adhiron


Theoretical massNumber of molelcules
Total (without water)35,5582
Polymers35,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Adhiron
D: Tenascin


Theoretical massNumber of molelcules
Total (without water)35,5582
Polymers35,5582
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.535, 90.152, 104.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
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: 25127.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNC, HXB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24821
#2: Protein Adhiron


Mass: 10430.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.02 M sodium formate, 0.02 M ammonium acetate, 0.02 M trisodium citrate, 0.02 M sodium potassium l-tartrate, 0.02 M sodium oxamate, 0.1 M bicine/Trizma base pH 8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.399→58.854 Å / Num. obs: 143762 / % possible obs: 99.61 % / Redundancy: 12.6 % / Biso Wilson estimate: 13.5 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.8
Reflection shellResolution: 1.399→1.436 Å / Rmerge(I) obs: 0.823 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 9572 / CC1/2: 0.825 / Rpim(I) all: 0.313 / Rrim(I) all: 0.884

-
Processing

Software
NameVersionClassification
xia2data reduction
PHASERphasing
Coot0.9.6model building
REFMAC5.8.0267refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.399→58.854 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.676 / SU ML: 0.03 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.05
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.185 7047 4.902 %
Rwork0.1608 136715 -
all0.162 --
obs-143762 99.617 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.037 Å2
Baniso -1Baniso -2Baniso -3
1-0.565 Å20 Å20 Å2
2--0.076 Å2-0 Å2
3----0.641 Å2
Refinement stepCycle: LAST / Resolution: 1.399→58.854 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4605 0 0 339 4944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134754
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154195
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.6386421
X-RAY DIFFRACTIONr_angle_other_deg1.3651.5879596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2335571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.74422.289284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.02615754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7111529
X-RAY DIFFRACTIONr_chiral_restr0.0660.2570
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025528
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021254
X-RAY DIFFRACTIONr_nbd_refined0.190.2725
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23836
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22187
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22106
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.2234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.080.27
X-RAY DIFFRACTIONr_nbd_other0.1890.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0890.28
X-RAY DIFFRACTIONr_mcbond_it1.4752.0732299
X-RAY DIFFRACTIONr_mcbond_other1.4742.0722298
X-RAY DIFFRACTIONr_mcangle_it1.8673.1082865
X-RAY DIFFRACTIONr_mcangle_other1.8673.1082866
X-RAY DIFFRACTIONr_scbond_it1.6562.3072455
X-RAY DIFFRACTIONr_scbond_other1.6562.3072456
X-RAY DIFFRACTIONr_scangle_it2.0943.3863556
X-RAY DIFFRACTIONr_scangle_other2.0943.3863557
X-RAY DIFFRACTIONr_lrange_it2.58523.1815185
X-RAY DIFFRACTIONr_lrange_other2.52122.965126
X-RAY DIFFRACTIONr_rigid_bond_restr0.90638949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.399-1.4360.2535350.2279579X-RAY DIFFRACTION95.4781
1.436-1.4750.2184940.1889720X-RAY DIFFRACTION99.4257
1.475-1.5180.2034760.1589544X-RAY DIFFRACTION100
1.518-1.5650.1634910.1329264X-RAY DIFFRACTION100
1.565-1.6160.1394700.1198964X-RAY DIFFRACTION100
1.616-1.6720.1564510.1148695X-RAY DIFFRACTION99.9891
1.672-1.7360.1453980.1128448X-RAY DIFFRACTION100
1.736-1.8060.164290.1178100X-RAY DIFFRACTION99.9883
1.806-1.8870.154070.1217774X-RAY DIFFRACTION100
1.887-1.9790.1613640.1297416X-RAY DIFFRACTION100
1.979-2.0860.1763670.1487113X-RAY DIFFRACTION99.9866
2.086-2.2120.1763240.156716X-RAY DIFFRACTION100
2.212-2.3650.1773270.1456340X-RAY DIFFRACTION100
2.365-2.5540.192930.1575903X-RAY DIFFRACTION100
2.554-2.7980.1842910.1655411X-RAY DIFFRACTION100
2.798-3.1280.2152560.1764967X-RAY DIFFRACTION100
3.128-3.6110.1982160.1894403X-RAY DIFFRACTION100
3.611-4.4220.1812080.1613709X-RAY DIFFRACTION100
4.422-6.2480.1851620.1922939X-RAY DIFFRACTION100
6.248-58.8540.263880.2551711X-RAY DIFFRACTION99.7781

+
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