[English] 日本語
Yorodumi
- SASDFW4: Conformation of R8-15 human dystrophin fragment (Human dystrophin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDFW4
SampleConformation of R8-15 human dystrophin fragment
  • Human dystrophin central domain R8-15 fragment (protein)
Function / homology
Function and homology information


regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / dystrophin-associated glycoprotein complex / cell-substrate junction / peptide biosynthetic process / motile cilium assembly ...regulation of muscle system process / regulation of cellular response to growth factor stimulus / regulation of skeletal muscle contraction / syntrophin complex / synaptic signaling / cardiac muscle cell action potential / dystrophin-associated glycoprotein complex / cell-substrate junction / peptide biosynthetic process / motile cilium assembly / dystroglycan binding / regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion / vinculin binding / Formation of the dystrophin-glycoprotein complex (DGC) / regulation of sodium ion transmembrane transport / costamere / muscle cell development / regulation of calcium ion transmembrane transport / neuron projection terminus / Striated Muscle Contraction / filopodium membrane / structural constituent of muscle / maintenance of blood-brain barrier / muscle organ development / muscle cell cellular homeostasis / myosin binding / nitric-oxide synthase binding / Non-integrin membrane-ECM interactions / neuron development / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / skeletal muscle tissue development / cardiac muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle stretch / positive regulation of neuron differentiation / regulation of heart rate / filopodium / sarcolemma / positive regulation of neuron projection development / structural constituent of cytoskeleton / Z disc / intracellular protein localization / actin binding / protein-containing complex assembly / postsynaptic membrane / cytoskeleton / membrane raft / synapse / cell surface / protein-containing complex / zinc ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats ...Dystrophin/utrophin / EF-hand domain, type 1 / EF-hand domain, type 2 / EF hand / EF-hand / : / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Zinc finger ZZ-type signature. / Calponin homology (CH) domain / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ type / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / EF-hand domain pair
Similarity search - Domain/homology
Contact author
  • Raphael Dos Santos Morais (University of Lorraine)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2888
Type: atomic / Chi-square value: 1.819
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Conformation of R8-15 human dystrophin fragment
BufferName: NaP 10 mM, NaCl 500 mM, EDTA 1 mM, Glycerol 2% / pH: 7.5
Entity #1554Type: protein / Description: Human dystrophin central domain R8-15 fragment / Formula weight: 100.208 / Num. of mol.: 1 / References: UniProt: P11532
Sequence: MSYYHHHHHH DYDIPTTENL YFQGAMDPEF DCGSRKEALK GGLEKTVSLQ KDLSEMHEWM TQAEEEYLER DFEYKTPDEL QKAVEEMKRA KEEAQQKEAK VKLLTESVNS VIAQAPPVAQ EALKKELETL TTNYQWLCTR LNGKCKTLEE VWACWHELLS YLEKANKWLN ...Sequence:
MSYYHHHHHH DYDIPTTENL YFQGAMDPEF DCGSRKEALK GGLEKTVSLQ KDLSEMHEWM TQAEEEYLER DFEYKTPDEL QKAVEEMKRA KEEAQQKEAK VKLLTESVNS VIAQAPPVAQ EALKKELETL TTNYQWLCTR LNGKCKTLEE VWACWHELLS YLEKANKWLN EVEFKLKTTE NIPGGAEEIS EVLDSLENLM RHSEDNPNQI RILAQTLTDG GVMDELINEE LETFNSRWRE LHEEAVRRQK LLEQSIQSAQ ETEKSLHLIQ ESLTFIDKQL AAYIADKVDA AQMPQEAQKI QSDLTSHEIS LEEMKKHNQG KEAAQRVLSQ IDVAQKKLQD VSMKFRLFQK PANFELRLQE SKMILDEVKM HLPALETKSV EQEVVQSQLN HCVNLYKSLS EVKSEVEMVI KTGRQIVQKK QTENPKELDE RVTALKLHYN ELGAKVTERK QQLEKCLKLS RKMRKEMNVL TEWLAATDME LTKRSAVEGM PSNLDSEVAW GKATQKEIEK QKVHLKSITE VGEALKTVLG KKETLVEDKL SLLNSNWIAV TSRAEEWLNL LLEYQKHMET FDQNVDHITK WIIQADTLLD ESEKKKPQQK EDVLKRLKAE LNDIRPKVDS TRDQAANLMA NRGDHCRKLV EPQISELNHR FAAISHRIKT GKASIPLKEL EQFNSDIQKL LEPLEAEIQQ GVNLKEEDFN KDMNEDNEGT VKELLQRGDN LQQRITDERK REEIKIKQQL LQTKHNALKD LRSQRRKKAL EISHQWYQYK RQADDLLKCL DDIEKKLASL PEPRDERKIK EIDRELQKKK EELNAVRRQA EGLSEDGAAM AVEPTQIQLS KRWREIESKF AQFRRLNFAQ

-
Experimental information

BeamInstrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 1.8 mm
DetectorName: AVIEX PCCD170170 / Type: CCD
Scan
Title: Conformation of R8-15 human dystrophin fragment / Measurement date: Sep 23, 2015 / Cell temperature: 15 °C / Exposure time: 1.5 sec. / Number of frames: 38 / Unit: 1/A /
MinMax
Q0.0062 0.6145
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 478 /
MinMax
Q0.00735 0.2768
P(R) point3 480
R0 360
Result
Experimental MW: 88 kDa / Type of curve: sec
Comments: SEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500Å (4.6 mm id * 300 mm); Flow rate: 0.2 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: ...Comments: SEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500Å (4.6 mm id * 300 mm); Flow rate: 0.2 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: 60μL. The data were collected through the SEC peak of the protein as a series of 38 x 1.5 second exposures. The experimental molecular weight was determined from the volume of correlation, Vc.
P(R)Guinier
Forward scattering, I00.03204 0.0327
Radius of gyration, Rg9.93 nm10.06 nm

MinMax
D-36
Guinier point1 9

+
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