[English] 日本語
Yorodumi
- EMDB-30766: Mouse radial spoke complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30766
TitleMouse radial spoke complex
Map dataMouse radial spoke head complex
Sample
  • Complex: Mouse radial spoke head complex
    • Protein or peptide: Radial spoke head protein 4 homolog A
    • Protein or peptide: Radial spoke head 1 homolog
    • Protein or peptide: Radial spoke head protein 9 homolog
KeywordsCilia / Complex / Signal transducer. / STRUCTURAL PROTEIN
Function / homology
Function and homology information


radial spoke assembly / maintenance of ciliary planar beating movement pattern / radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / axonemal central apparatus assembly / outer dense fiber / radial spoke head / radial spoke / mating ...radial spoke assembly / maintenance of ciliary planar beating movement pattern / radial spoke head 1 / radial spoke head 2 / radial spoke head 3 / axonemal central apparatus assembly / outer dense fiber / radial spoke head / radial spoke / mating / epithelial cilium movement involved in extracellular fluid movement / kinocilium / cilium movement involved in cell motility / 9+2 motile cilium / cilium movement / axoneme assembly / motile cilium assembly / flagellated sperm motility / motile cilium / meiotic spindle / axoneme / spermatid development / sperm flagellum / condensed nuclear chromosome / meiotic cell cycle / establishment of localization in cell / extracellular region / nucleus / cytoplasm
Similarity search - Function
Radial spokehead-like protein / Radial spokehead-like protein / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / MORN motif / MORN repeat
Similarity search - Domain/homology
Radial spoke head protein 4 homolog A / Radial spoke head 1 homolog / Radial spoke head protein 9 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZheng W / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Distinct architecture and composition of mouse axonemal radial spoke head revealed by cryo-EM.
Authors: Wei Zheng / Fan Li / Zhanyu Ding / Hao Liu / Lei Zhu / Cong Xu / Jiawei Li / Qi Gao / Yanxing Wang / Zhenglin Fu / Chao Peng / Xiumin Yan / Xueliang Zhu / Yao Cong /
Abstract: The radial spoke (RS) heads of motile cilia and flagella contact projections of the central pair (CP) apparatus to coordinate motility, but the morphology is distinct for protozoa and metazoa. Here ...The radial spoke (RS) heads of motile cilia and flagella contact projections of the central pair (CP) apparatus to coordinate motility, but the morphology is distinct for protozoa and metazoa. Here we show the murine RS head is compositionally distinct from that of Our reconstituted murine RS head core complex consists of Rsph1, Rsph3b, Rsph4a, and Rsph9, lacking Rsph6a and Rsph10b, whose orthologs exist in the protozoan RS head. We resolve its cryo-electron microscopy (cryo-EM) structure at 3.2-Å resolution. Our atomic model further reveals a twofold symmetric brake pad-shaped structure, in which Rsph4a and Rsph9 form a compact body extended laterally with two long arms of twisted Rsph1 β-sheets and potentially connected dorsally via Rsph3b to the RS stalk. Furthermore, our modeling suggests that the core complex contacts the periodic CP projections either rigidly through its tooth-shaped Rsph4a regions or elastically through both arms for optimized RS-CP interactions and mechanosignal transduction.
History
DepositionDec 5, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7dmp
  • Surface level: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dmp
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30766.png

Downloads & links

-
Map

FileDownload / File: emd_30766.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse radial spoke head complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 400 pix.
= 408. Å		1.02 Å/pix.
x 400 pix.
= 408. Å		1.02 Å/pix.
x 400 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.050901692 - 0.11381518
Average (Standard dev.)0.000047719943 (±0.0012573777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0510.1140.000

-
Supplemental data

-
Sample components

-
Entire : Mouse radial spoke head complex

EntireName: Mouse radial spoke head complex
Components
  • Complex: Mouse radial spoke head complex
    • Protein or peptide: Radial spoke head protein 4 homolog A
    • Protein or peptide: Radial spoke head 1 homolog
    • Protein or peptide: Radial spoke head protein 9 homolog

-
Supramolecule #1: Mouse radial spoke head complex

SupramoleculeName: Mouse radial spoke head complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Radial spoke head protein 4 homolog A

MacromoleculeName: Radial spoke head protein 4 homolog A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 80.214102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENSTSLKQE KENQEPGEAE RLWQGESDVS PQEPGPPSPE YREEEQRTDT EPAPRMSPSW SHQSRVSLST GDLTAGPEVS SSPPPPPLQ FHSTPLNTET TQDPVAASPT EKTANGIADT GTPYSDPWES SSAAKQSTSH YTSHAEESTF PQSQTPQPDL C GLRDASRN ...String:
MENSTSLKQE KENQEPGEAE RLWQGESDVS PQEPGPPSPE YREEEQRTDT EPAPRMSPSW SHQSRVSLST GDLTAGPEVS SSPPPPPLQ FHSTPLNTET TQDPVAASPT EKTANGIADT GTPYSDPWES SSAAKQSTSH YTSHAEESTF PQSQTPQPDL C GLRDASRN KSKHKGLRFD LLQEEGSDSN CDPDQPEVGA SEAAQSMLEV AIQNAKAYLL STSSKSGLNL YDHLSKVLTK IL DERPADA VDIIENISQD VKMAHFNKKL DTLHNEYEML PAYEIAETQK ALFLQGHLEG ADSELEEEMA ESSLPNVMES AYY FEQAGV GLGTDETYRV FLALKQLTDT HPIQRCRFWG KILGLEMNYI VAEVEFRDGE DEEEVEEEGI AEERDNGGSE AGEE EEEEL PKSLYKAPQV IPKEESRTGA NKYVYFVCNV PGRPWVRLPS VTPAQIVTAR KIKKFFTGRL DAAVISYPPF PGNES NYLR AQIARISAGT HVSPLGFYQF GEEEGEEEEV EGGRDSYEEN PDFEGIQVID LVESLSNWVH HVQYILPQGR CNWFNP IQK DEDEEEEEEE DEEKGEEPDY IEQEVGPPLL TPISEDLGIQ NIPSWTTQLS SNLIPQYAIA VLRSNLWPGA YAFSNGK KF ENFYIGWGHK YCVENYTPPS PPPVYQEYPS GPEITEMNDP SVEEEQAFRM TQEPVALSTE ENEGTEDEDE DDED

UniProtKB: Radial spoke head protein 4 homolog A

-
Macromolecule #2: Radial spoke head 1 homolog

MacromoleculeName: Radial spoke head 1 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 34.218254 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSDLGSEELE EEGENDLGEY EGERNEVGER HGHGKARLPN GDTYEGSYEF GKRHGQGTYK FKNGARYTGD YVKNKKHGQG TFIYPDGSR YEGEWADDQR HGQGVYYYVN NDTYTGEWFN HQRHGQGTYL YAETGSKYVG TWVHGQQEGA AELIHLNHRY Q GKFMNKNP ...String:
MSDLGSEELE EEGENDLGEY EGERNEVGER HGHGKARLPN GDTYEGSYEF GKRHGQGTYK FKNGARYTGD YVKNKKHGQG TFIYPDGSR YEGEWADDQR HGQGVYYYVN NDTYTGEWFN HQRHGQGTYL YAETGSKYVG TWVHGQQEGA AELIHLNHRY Q GKFMNKNP VGPGKYVFDI GCEQHGEYRL TDTERGEEEE EEETLVNIVP KWKALNITEL ALWTPTLSEE QPPPEGQGQE EP QGLTGVG DPSEDIQAEG FEGELEPRGA DEDVDTFRQE SQENSYDIDQ GNLNFDEEPS DLQD

UniProtKB: Radial spoke head 1 homolog

-
Macromolecule #3: Radial spoke head protein 9 homolog

MacromoleculeName: Radial spoke head protein 9 homolog / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 31.365902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDADSLLLSL ELASGSGQGL SPDRRASLLT SLMLVKRDYR FARVLFWGRI LGLVADYYIA QGLSEDQLAP RKTLYSLNCT EWSLLPPAT EEMAMQISVV SGRFMGDPSH EYEHTELQKV NEGEKVFDEE VVVQIKEETR LVSIIDQIDK AVAIIPRGAL F KTPFGVTH ...String:
MDADSLLLSL ELASGSGQGL SPDRRASLLT SLMLVKRDYR FARVLFWGRI LGLVADYYIA QGLSEDQLAP RKTLYSLNCT EWSLLPPAT EEMAMQISVV SGRFMGDPSH EYEHTELQKV NEGEKVFDEE VVVQIKEETR LVSIIDQIDK AVAIIPRGAL F KTPFGVTH VNRTFEGLPL SEVRKLSSYF HFREAIDLKN KTLLEKSDLE PSLDFLDSLE YDIPRGSWSI QMERGNALVV LR SLLWPGL TFYHAPRTKN YGYIYVGTGE KNMDLPFML

UniProtKB: Radial spoke head protein 9 homolog

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 302573
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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