[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructures of sperm flagellar doublet microtubules expand the genetic spectrum of male infertility.
Journal, issue, pagesCell, Vol. 186, Issue 13, Page 2897-2910.e19, Year 2023
Publish dateJun 22, 2023
AuthorsLunni Zhou / Haobin Liu / Siyu Liu / Xiaoyu Yang / Yue Dong / Yun Pan / Zhuang Xiao / Beihong Zheng / Yan Sun / Pengyu Huang / Xixi Zhang / Jin Hu / Rui Sun / Shan Feng / Yi Zhu / Mingxi Liu / Miao Gui / Jianping Wu /
PubMed AbstractSperm motility is crucial for successful fertilization. Highly decorated doublet microtubules (DMTs) form the sperm tail skeleton, which propels the movement of spermatozoa. Using cryo-electron ...Sperm motility is crucial for successful fertilization. Highly decorated doublet microtubules (DMTs) form the sperm tail skeleton, which propels the movement of spermatozoa. Using cryo-electron microscopy (cryo-EM) and artificial intelligence (AI)-based modeling, we determined the structures of mouse and human sperm DMTs and built an atomic model of the 48-nm repeat of the mouse sperm DMT. Our analysis revealed 47 DMT-associated proteins, including 45 microtubule inner proteins (MIPs). We identified 10 sperm-specific MIPs, including seven classes of Tektin5 in the lumen of the A tubule and FAM166 family members that bind the intra-tubulin interfaces. Interestingly, the human sperm DMT lacks some MIPs compared with the mouse sperm DMT. We also discovered variants in 10 distinct MIPs associated with a subtype of asthenozoospermia characterized by impaired sperm motility without evident morphological abnormalities. Our study highlights the conservation and tissue/species specificity of DMTs and expands the genetic spectrum of male infertility.
External linksCell / PubMed:37295417
MethodsEM (single particle)
Resolution3.07 - 4.34 Å
Structure data

EMDB-35810: Cryo-EM structure of the 48-nm repeat doublet microtubule from human sperm
Method: EM (single particle) / Resolution: 4.3 Å

EMDB-35823, PDB-8iyj:
Cryo-EM structure of the 48-nm repeat doublet microtubule from mouse sperm
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-36458: Local map of the mouse sperm doublet microtubule (Middel01)
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-36498: Overall consensus map of the mouse sperm doublet microtubule
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-36499: Local map of the mouse sperm doublet microtubule (Lower01)
Method: EM (single particle) / Resolution: 3.26 Å

EMDB-36500: Local map of the mouse sperm doublet microtubule (Upper10)
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-36501: Local map of the mouse sperm doublet microtubule (Middle02)
Method: EM (single particle) / Resolution: 3.28 Å

EMDB-36502: Local map of the mouse sperm doublet microtubule (Lower02)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-36503: Local map of the mouse sperm doublet microtubule (Upper09)
Method: EM (single particle) / Resolution: 3.87 Å

EMDB-36504: Local map of the mouse sperm doublet microtubule (Middle03)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-36509: Local map of the mouse sperm doublet microtubule (Lower03)
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-36510: Local map of the mouse sperm doublet microtubule (Middle04)
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-36511: Local map of the mouse sperm doublet microtubule (Upper08)
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-36513: Local map of the mouse sperm doublet microtubule (Lower04)
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-36514: Local map of the mouse sperm doublet microtubule (Upper07)
Method: EM (single particle) / Resolution: 3.62 Å

EMDB-36515: Local map of the mouse sperm doublet microtubule (Middle05)
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-36516: Local map of the mouse sperm doublet microtubule (Lower05)
Method: EM (single particle) / Resolution: 3.35 Å

EMDB-36517: Local map of the mouse sperm doublet microtubule (Upper06)
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-36518: Local map of the mouse sperm doublet microtubule (Middle06)
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-36519: Local map of the mouse sperm doublet microtubule (Lower06)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-36520: Local map of the mouse sperm doublet microtubule (Upper05)
Method: EM (single particle) / Resolution: 3.36 Å

EMDB-36521: Local map of the mouse sperm doublet microtubule (Middle07)
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-36523: Local map of the mouse sperm doublet microtubule (Upper04)
Method: EM (single particle) / Resolution: 3.44 Å

EMDB-36524: Local map of the mouse sperm doublet microtubule (Middle08)
Method: EM (single particle) / Resolution: 3.59 Å

EMDB-36525: Local map of the mouse sperm doublet microtubule (Lower07)
Method: EM (single particle) / Resolution: 3.65 Å

EMDB-36526: Local map of the mouse sperm doublet microtubule (Upper03)
Method: EM (single particle) / Resolution: 3.45 Å

EMDB-36527: Local map of the mouse sperm doublet microtubule (Middle09)
Method: EM (single particle) / Resolution: 3.79 Å

EMDB-36528: Local map of the mouse sperm doublet microtubule (Lower08)
Method: EM (single particle) / Resolution: 3.65 Å

EMDB-36529: Local map of the mouse sperm doublet microtubule (Upper02)
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-36530: Local map of the mouse sperm doublet microtubule (Middle10)
Method: EM (single particle) / Resolution: 3.55 Å

EMDB-36531: Local map of the mouse sperm doublet microtubule (Lower09)
Method: EM (single particle) / Resolution: 3.89 Å

EMDB-36532: Local map of the mouse sperm doublet microtubule (Upper01)
Method: EM (single particle) / Resolution: 3.33 Å

EMDB-36533: Local map of the mouse sperm doublet microtubule (Lower10)
Method: EM (single particle) / Resolution: 3.53 Å

EMDB-36534: Overall consensus map of the human sperm doublet microtubule
Method: EM (single particle) / Resolution: 4.34 Å

EMDB-36536: Local map of the human sperm doublet microtubule (Lower01)
Method: EM (single particle) / Resolution: 4.07 Å

EMDB-36537: Local map of the human sperm doublet microtubule (Lower02)
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-36538: Local map of the human sperm doublet microtubule (Lower03)
Method: EM (single particle) / Resolution: 4.15 Å

EMDB-36539: Local map of the human sperm doublet microtubule (Lower04)
Method: EM (single particle) / Resolution: 4.12 Å

EMDB-36540: Local map of the human sperm doublet microtubule (Lower05)
Method: EM (single particle) / Resolution: 3.91 Å

EMDB-36542: Local map of the human sperm doublet microtubule (Lower06)
Method: EM (single particle) / Resolution: 3.7 Å

EMDB-36543: Local map of the human sperm doublet microtubule (Lower07)
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-36544: Local map of the human sperm doublet microtubule (Lower08)
Method: EM (single particle) / Resolution: 4.27 Å

EMDB-36545: Local map of the human sperm doublet microtubule (Lower09)
Method: EM (single particle) / Resolution: 4.29 Å

EMDB-36546: Local map of the human sperm doublet microtubule (Lower10)
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-36547: Local map of the human sperm doublet microtubule (Middle01)
Method: EM (single particle) / Resolution: 3.77 Å

EMDB-36549: Local map of the human sperm doublet microtubule (Middle02)
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-36550: Local map of the human sperm doublet microtubule (Middle03)
Method: EM (single particle) / Resolution: 4.0 Å

EMDB-36551: Local map of the human sperm doublet microtubule (Middle04)
Method: EM (single particle) / Resolution: 3.93 Å

EMDB-36552: Local map of the human sperm doublet microtubule (Middle05)
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-36553: Local map of the human sperm doublet microtubule (Middle06)
Method: EM (single particle) / Resolution: 3.56 Å

EMDB-36554: Local map of the human sperm doublet microtubule (Middle07)
Method: EM (single particle) / Resolution: 3.98 Å

EMDB-36555: Local map of the human sperm doublet microtubule (Middle08)
Method: EM (single particle) / Resolution: 4.14 Å

EMDB-36556: Local map of the human sperm doublet microtubule (Middle09)
Method: EM (single particle) / Resolution: 4.25 Å

EMDB-36557: Local map of the human sperm doublet microtubule (Middle10)
Method: EM (single particle) / Resolution: 3.95 Å

EMDB-36558: Local map of the human sperm doublet microtubule (Upper01)
Method: EM (single particle) / Resolution: 3.83 Å

EMDB-36559: Local map of the human sperm doublet microtubule (Upper02)
Method: EM (single particle) / Resolution: 3.94 Å

EMDB-36560: Local map of the human sperm doublet microtubule (Upper03)
Method: EM (single particle) / Resolution: 4.2 Å

EMDB-36561: Local map of the human sperm doublet microtubule (Upper04)
Method: EM (single particle) / Resolution: 4.07 Å

EMDB-36562: Local map of the human sperm doublet microtubule (Upper05)
Method: EM (single particle) / Resolution: 3.92 Å

EMDB-36564: Local map of the human sperm doublet microtubule (Upper06)
Method: EM (single particle) / Resolution: 3.71 Å

EMDB-36565: Local map of the human sperm doublet microtubule (Upper07)
Method: EM (single particle) / Resolution: 4.06 Å

EMDB-36566: Local map of the human sperm doublet microtubule (Upper08)
Method: EM (single particle) / Resolution: 4.21 Å

EMDB-36567: Local map of the human sperm doublet microtubule (Upper09)
Method: EM (single particle) / Resolution: 4.33 Å

EMDB-36568: Local map of the human sperm doublet microtubule (Upper10)
Method: EM (single particle) / Resolution: 4.04 Å

EMDB-36580: Local map of the mouse sperm doublet microtubule (Upper_ODF3A)
Method: EM (single particle) / Resolution: 3.43 Å

EMDB-36581: Local map of the mouse sperm doublet microtubule (Middle_ODF3A)
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-36582: Local map of the mouse sperm doublet microtubule (Lower_ODF3A)
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-36583: Local map of the mouse sperm doublet microtubule (Middle_A13)
Method: EM (single particle) / Resolution: 3.21 Å

EMDB-36584: Local map of the mouse sperm doublet microtubule (Upper_A13)
Method: EM (single particle) / Resolution: 3.27 Å

EMDB-36585: Local map of the mouse sperm doublet microtubule (TSSK6)
Method: EM (single particle) / Resolution: 3.52 Å

EMDB-36586: Local map of the mouse sperm doublet microtubule (A07_A08)
Method: EM (single particle) / Resolution: 3.65 Å

EMDB-36587: Local map of the mouse sperm doublet microtubule (DUSP21_TEX37)
Method: EM (single particle) / Resolution: 3.22 Å

EMDB-36588: Local map of the mouse sperm doublet microtubule (A09_A10)
Method: EM (single particle) / Resolution: 3.41 Å

EMDB-36591: Local map of the mouse sperm doublet microtubule (A13_A01_A02)
Method: EM (single particle) / Resolution: 3.23 Å

Chemicals

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

Source
  • Homo sapiens (human)
  • mus musculus (house mouse)
KeywordsSTRUCTURAL PROTEIN / doublet microtubule

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more