[English] 日本語
Yorodumi
- SASDCR9: Kif2A-tubulin-DARPin complex in presence of AMP-PNP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDCR9
SampleKif2A-tubulin-DARPin complex in presence of AMP-PNP
  • Designed Ankyrin Repeat Protein D1 (protein), DARPin D1, synthetic construct
  • Kinesin-like protein KIF2A (protein), Kif2A, Homo sapiens
  • Tubulin alpha-1B chain (protein), alpha tubulin, Bos taurus
  • Tubulin beta-2B chain (protein), beta tubulin, Bos taurus
Biological speciessynthetic construct (others)
Homo sapiens (human)
Bos taurus (cattle)

-
Structure visualization

Downloads & links

-
Models

-
Sample

SampleName: Kif2A-tubulin-DARPin complex in presence of AMP-PNP / Specimen concentration: 3.7 mg/ml / Entity id: 875 / 890 / 902 / 903
BufferName: HEPES 20 mM, MgCl2 1mM, NaCl 150mM / pH: 7.2
Entity #875Name: DARPin D1 / Type: protein / Description: Designed Ankyrin Repeat Protein D1 / Formula weight: 17.886 / Num. of mol.: 1 / Source: synthetic construct
Sequence:
MGSHHHHHHG SDLGKKLLEA ARAGQDDEVR ILMANGADVN ATDASGLTPL HLAATYGHLE IVEVLLKHGA DVNAIDIMGS TPLHLAALIG HLEIVEVLLK HGADVNAVDT WGDTPLHLAA IMGHLEIVEV LLKHGADVNA QDKFGKTAFD ISIDNGNEDL AEILQKLN
Entity #890Name: Kif2A / Type: protein / Description: Kinesin-like protein KIF2A / Formula weight: 47.834 / Num. of mol.: 1 / Source: Homo sapiens
Sequence: MGSSHHHHHH SSGLVPRGSS RRKSNCVKEV EKLQEKREKR RLQQQELREK RAQDVDATNP NYEIMCMIRD FRGSLDYRPL TTADPIDEHR ICVCVRKRPL NKKETQMKDL DVITIPSKDV VMVHEPKQKV DLTRYLENQT FRFDYAFDDS APNEMVYRFT ARPLVETIFE ...Sequence:
MGSSHHHHHH SSGLVPRGSS RRKSNCVKEV EKLQEKREKR RLQQQELREK RAQDVDATNP NYEIMCMIRD FRGSLDYRPL TTADPIDEHR ICVCVRKRPL NKKETQMKDL DVITIPSKDV VMVHEPKQKV DLTRYLENQT FRFDYAFDDS APNEMVYRFT ARPLVETIFE RGMATCFAYG QTGSGKTHTM GGDFSGKNQD CSKGIYALAA RDVFLMLKKP NYKKLELQVY ATFFEIYSGK VFDLLNRKTK LRVLEDGKQQ VQVVGLQERE VKCVEDVLKL IDIGNSCRTS GQTSANAHSS RSHAVFQIIL RRKGKLHGKF SLIDLAGNER GADTSSADRQ TRLEGAEINK SLLALKECIR ALGRNKPHTP FRASKLTQVL RDSFIGENSR TCMIATISPG MASCENTLNT LRYANRVKEL
Entity #902Name: alpha tubulin / Type: protein / Description: Tubulin alpha-1B chain / Formula weight: 50.151 / Num. of mol.: 2 / Source: Bos taurus
Sequence: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...Sequence:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL ISQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y
Entity #903Name: beta tubulin / Type: protein / Description: Tubulin beta-2B chain / Formula weight: 49.936 / Num. of mol.: 2 / Source: Bos taurus
Sequence: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVM ...Sequence:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVM PSPKVSDTVV EPYNATLSVH QLVENTDETY SIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDSKNMM AACDPRHGRY LTVAAIFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMSATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEQGEFEEEE GEDEA

-
Experimental information

BeamInstrument name: Cornell High Energy Synchrotron Source (CHESS) G1
City: Ithaca, NY / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.1267 Å / Dist. spec. to detc.: 1.47 mm
DetectorName: Finger Lakes CCD / Type: CCD
ScanTitle: Kif2A-tubulin-DARPin complex in presence of AMP-PNP / Measurement date: May 16, 2016 / Storage temperature: 4 °C / Cell temperature: 22 °C / Exposure time: 2 sec. / Number of frames: 1200 / Unit: 1/A /
MinMax
Q0.0086 0.2735
ResultType of curve: sec
Comments: For the SEC-SAXS analysis, a mixture of Kif2A, tubulin and DARPin was passed continuously through an X-ray sample cell via an in-line size exclusion column (GE Superdex 200 10/300 GL) at a ...Comments: For the SEC-SAXS analysis, a mixture of Kif2A, tubulin and DARPin was passed continuously through an X-ray sample cell via an in-line size exclusion column (GE Superdex 200 10/300 GL) at a flow rate of 1 ml/min. The column was pre-equilibrated with running buffer consisting of 20 mM HEPES, 150 mM NaCl, 1 mM MgCl2 pH 7.2. The protein sample was prepared at 25 μM tubulin, 27 μM DARP in and 20 μM Kif2A and injected into a 100 μL loop. Approximately 1200 two-second exposures were collected per sample, and 100 buffer profiles preceding the elution peaks were averaged and used for background subtraction.
ExperimentalPorod
MW258.5 kDa279.7 kDa
Volume-374 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.0298 0.00029 0.02949 0.0002
Radius of gyration, Rg5.6 nm0.03 5.41 nm0.05

MinMax
D-19.5
Guinier point4 26

+
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://pdbjlvh1.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