[English] 日本語
Yorodumi
- PDB-8i7r: In situ structure of axonemal doublet microtubules in mouse sperm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8i7r
TitleIn situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat
Components
  • (Cilia- and flagella-associated protein ...) x 10
  • (EF-hand domain-containing family member ...) x 2
  • (Piercer of microtubule wall ...) x 2
  • Cilia and flagella-associated protein 77
  • Coiled-coil domain-containing protein 105
  • Detyrosinated tubulin alpha-3 chain
  • Dual specificity phosphatase 21
  • EF-hand calcium-binding domain-containing protein 6
  • EF-hand domain-containing protein 1
  • Enkurin
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase 7
  • Parkin coregulated gene protein homolog
  • Protein FAM166A
  • Protein FAM166C
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome-associated protein 9
  • Sperm-associated antigen 8
  • Tektin bundle-interacting protein 1
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tektin-5
  • Testis-expressed protein 43
  • Tubulin beta-4B chain
KeywordsSTRUCTURAL PROTEIN / microtubules / axoneme / sperm / filament
Function / homology
Function and homology information


protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly ...protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / protein polyglutamylation / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / Carboxyterminal post-translational modifications of tubulin / regulation of microtubule nucleation / Intraflagellar transport / positive regulation of feeding behavior / COPI-independent Golgi-to-ER retrograde traffic / MAP kinase tyrosine/serine/threonine phosphatase activity / inner dynein arm assembly / cilium-dependent cell motility / cerebrospinal fluid circulation / regulation of cilium beat frequency involved in ciliary motility / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / epithelial cilium movement involved in extracellular fluid movement / 9+2 motile cilium / COPI-mediated anterograde transport / cilium movement involved in cell motility / Aggrephagy / intraciliary transport / regulation of store-operated calcium entry / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / acrosomal membrane / axoneme assembly / left/right axis specification / cilium movement / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / microtubule sliding / Recycling pathway of L1 / calcium ion sensor activity / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / axonemal microtubule / Hedgehog 'off' state / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / cilium organization / AURKA Activation by TPX2 / gamma-tubulin ring complex / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of cilium assembly / MHC class II antigen presentation / flagellated sperm motility / 3'-5'-DNA exonuclease activity / UTP biosynthetic process / CTP biosynthetic process / motile cilium / determination of left/right symmetry / intermediate filament / DNA catabolic process / protein targeting to membrane / extrinsic component of membrane / nucleoside diphosphate kinase activity / positive regulation of cell motility / : / GTP biosynthetic process / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / tubulin complex / protein-serine/threonine phosphatase / AMP binding / ciliary base / regulation of neuron projection development / receptor clustering / ciliary transition zone / protein serine/threonine phosphatase activity / cerebral cortex cell migration / phosphatase activity / mitotic cytokinesis / microtubule organizing center / cellular response to UV-C / regulation of cell division / cilium assembly / cellular response to unfolded protein / spermatid development / negative regulation of protein binding
Similarity search - Function
: / Atypical dual specificity phosphatase, subfamily B / Protein of unknown function DUF4513 / Sperm-associated microtubule inner protein 10 / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / Tektin bundle interacting protein 1 / : / DJBP, EF-hand domain / EF-hand domain ...: / Atypical dual specificity phosphatase, subfamily B / Protein of unknown function DUF4513 / Sperm-associated microtubule inner protein 10 / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / Tektin bundle interacting protein 1 / : / DJBP, EF-hand domain / EF-hand domain / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / : / Protein CFAP95 / Cilia- and flagella-associated protein 143 / Cilia and flagella associated protein 107 / Tektin / Cilia- and flagella-associated protein 276 / Sperm acrosome-associated protein 9 / : / Tektin family / Protein of unknown function (DUF3695) / Sperm acrosome-associated protein 9 / Uncharacterised protein FAM166/UPF0605 / Cilia- and flagella-associated protein 77 / Protein Flattop / Ciliary microtubule inner protein 2B-like / Cilia- and flagella-associated protein 77 / Flattop / Nucleoside diphosphate kinase 7 / Piercer of microtubule wall 1/2 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 161-like domain / : / : / EFHB C-terminal EF-hand domain / : / : / Nucleoside diphosphate kinase 7 N-terminal PH domain / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / RIB43A / RIB43A / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / Enkurin domain / : / Calmodulin-binding / Enkurin domain profile. / : / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Parkin co-regulated protein / Parkin co-regulated protein / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / EF hand / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / EF-hand domain pair / Mir domain superfamily / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Beta tubulin / Protein-tyrosine phosphatase-like / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 77 / Cilia- and flagella- associated protein 210 / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-3 chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 ...GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 77 / Cilia- and flagella- associated protein 210 / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-3 chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 / Piercer of microtubule wall 1 protein / Cilia- and flagella-associated protein 52 / Meiosis-specific nuclear structural protein 1 / EF-hand calcium-binding domain-containing protein 6 / Protein Flattop / Cilia- and flagella-associated protein 161 / Enkurin / Tektin-3 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 20 / EF-hand domain-containing family member B / Tektin-2 / Cilia- and flagella-associated protein 95 / Cilia- and flagella-associated protein 53 / EF-hand domain-containing family member C2 / Ciliary microtubule inner protein 2A / Tektin-like protein 1 / RIB43A-like with coiled-coils protein 2 / Dual specificity phosphatase 21 / Cilia- and flagella-associated protein 141 / Sperm-associated microtubule inner protein 10 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 45 / Cilia- and flagella-associated protein 276 / Tektin-1 / Parkin coregulated gene protein homolog / Ciliary microtubule inner protein 2C / Nucleoside diphosphate kinase 7 / Piercer of microtubule wall 2 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 6.5 Å
AuthorsZhu, Y. / Yin, G.L. / Tai, L.H. / Sun, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925026 China
CitationJournal: Cell Discov / Year: 2023
Title: In-cell structural insight into the stability of sperm microtubule doublet.
Authors: Linhua Tai / Guoliang Yin / Xiaojun Huang / Fei Sun / Yun Zhu /
Abstract: The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. ...The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
History
DepositionFeb 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.0Oct 11, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 11, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 11, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Oct 11, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 11, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 17, 2025Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: em_admin / pdbx_entry_details ...em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.1Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Group: Experimental summary / Data content type: EM metadata / Category: em_admin / Data content type: EM metadata / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Meiosis-specific nuclear structural protein 1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AB: Tubulin beta-4B chain
AC: Detyrosinated tubulin alpha-3 chain
AD: Tubulin beta-4B chain
AE: Detyrosinated tubulin alpha-3 chain
AF: Tubulin beta-4B chain
AG: Detyrosinated tubulin alpha-3 chain
AH: Tubulin beta-4B chain
AI: Detyrosinated tubulin alpha-3 chain
AJ: Tubulin beta-4B chain
AK: Detyrosinated tubulin alpha-3 chain
AL: Tubulin beta-4B chain
AM: Detyrosinated tubulin alpha-3 chain
B: Meiosis-specific nuclear structural protein 1
B1: Tektin-2
B2: Tektin-2
B3: Tektin-2
B4: Tektin-2
B5: Tektin-2
B6: Tektin-2
B7: Tektin-2
B8: Tektin-2
B9: Tektin-2
BB: Tubulin beta-4B chain
BC: Detyrosinated tubulin alpha-3 chain
BD: Tubulin beta-4B chain
BE: Detyrosinated tubulin alpha-3 chain
BF: Tubulin beta-4B chain
BG: Detyrosinated tubulin alpha-3 chain
BH: Tubulin beta-4B chain
BI: Detyrosinated tubulin alpha-3 chain
BJ: Tubulin beta-4B chain
BK: Detyrosinated tubulin alpha-3 chain
BL: Tubulin beta-4B chain
BM: Detyrosinated tubulin alpha-3 chain
C: Nucleoside diphosphate kinase 7
C1: Tektin-3
C2: Tektin-3
C3: Tektin-3
C4: Tektin-3
C5: Tektin-3
C6: Tektin-3
C7: Tektin-3
C8: Tektin-3
C9: Tektin-3
CB: Tubulin beta-4B chain
CC: Detyrosinated tubulin alpha-3 chain
CD: Tubulin beta-4B chain
CE: Detyrosinated tubulin alpha-3 chain
CF: Tubulin beta-4B chain
CG: Detyrosinated tubulin alpha-3 chain
CH: Tubulin beta-4B chain
CI: Detyrosinated tubulin alpha-3 chain
CJ: Tubulin beta-4B chain
CK: Detyrosinated tubulin alpha-3 chain
CL: Tubulin beta-4B chain
CM: Detyrosinated tubulin alpha-3 chain
Ca: Tektin-3
Cb: Tektin-3
Cc: Tektin-3
Cd: Tektin-3
D: Nucleoside diphosphate kinase 7
D1: Tektin-4
D2: Tektin-4
D3: Tektin-4
D4: Tektin-4
D5: Tektin-4
D6: Tektin-4
D7: Tektin-4
D8: Tektin-4
D9: Tektin-4
DA: Detyrosinated tubulin alpha-3 chain
DB: Tubulin beta-4B chain
DC: Detyrosinated tubulin alpha-3 chain
DD: Tubulin beta-4B chain
DE: Detyrosinated tubulin alpha-3 chain
DF: Tubulin beta-4B chain
DG: Detyrosinated tubulin alpha-3 chain
DH: Tubulin beta-4B chain
DI: Detyrosinated tubulin alpha-3 chain
DJ: Tubulin beta-4B chain
DK: Detyrosinated tubulin alpha-3 chain
DL: Tubulin beta-4B chain
Da: Tektin-4
E: EF-hand domain-containing family member B
E1: Tektin bundle-interacting protein 1
E2: Tektin bundle-interacting protein 1
E3: Tektin bundle-interacting protein 1
E4: Tektin bundle-interacting protein 1
EA: Detyrosinated tubulin alpha-3 chain
EB: Tubulin beta-4B chain
EC: Detyrosinated tubulin alpha-3 chain
ED: Tubulin beta-4B chain
EE: Detyrosinated tubulin alpha-3 chain
EF: Tubulin beta-4B chain
EG: Detyrosinated tubulin alpha-3 chain
EH: Tubulin beta-4B chain
EI: Detyrosinated tubulin alpha-3 chain
EJ: Tubulin beta-4B chain
EK: Detyrosinated tubulin alpha-3 chain
EL: Tubulin beta-4B chain
F: EF-hand domain-containing family member B
F1: Tektin-5
F2: Tektin-5
F3: Tektin-5
F4: Tektin-5
F5: Tektin-5
F6: Tektin-5
F7: Tektin-5
F8: Tektin-5
F9: Tektin-5
FA: Detyrosinated tubulin alpha-3 chain
FB: Tubulin beta-4B chain
FC: Detyrosinated tubulin alpha-3 chain
FD: Tubulin beta-4B chain
FE: Detyrosinated tubulin alpha-3 chain
FF: Tubulin beta-4B chain
FG: Detyrosinated tubulin alpha-3 chain
FH: Tubulin beta-4B chain
FI: Detyrosinated tubulin alpha-3 chain
FJ: Tubulin beta-4B chain
FK: Detyrosinated tubulin alpha-3 chain
FL: Tubulin beta-4B chain
Fa: Tektin-5
Fb: Tektin-5
Fc: Tektin-5
Fd: Tektin-5
Fe: Tektin-5
Ff: Tektin-5
Fg: Tektin-5
Fh: Tektin-5
Fi: Tektin-5
Fj: Tektin-5
Fk: Tektin-5
Fl: Tektin-5
Fm: Tektin-5
G: Cilia- and flagella-associated protein 53
G1: EF-hand domain-containing protein 1
G2: EF-hand domain-containing protein 1
G3: EF-hand domain-containing protein 1
G4: EF-hand domain-containing family member C2
G5: EF-hand domain-containing family member C2
G6: EF-hand domain-containing family member C2
GA: Detyrosinated tubulin alpha-3 chain
GB: Tubulin beta-4B chain
GC: Detyrosinated tubulin alpha-3 chain
GD: Tubulin beta-4B chain
GE: Detyrosinated tubulin alpha-3 chain
GF: Tubulin beta-4B chain
GG: Detyrosinated tubulin alpha-3 chain
GH: Tubulin beta-4B chain
GI: Detyrosinated tubulin alpha-3 chain
GJ: Tubulin beta-4B chain
GK: Detyrosinated tubulin alpha-3 chain
GL: Tubulin beta-4B chain
H: Cilia- and flagella-associated protein 53
H1: Protein FAM166A
H2: Protein FAM166A
H3: Protein FAM166A
H4: Protein FAM166A
H5: Protein FAM166A
H6: Protein FAM166A
HA: Detyrosinated tubulin alpha-3 chain
HB: Tubulin beta-4B chain
HC: Detyrosinated tubulin alpha-3 chain
HD: Tubulin beta-4B chain
HE: Detyrosinated tubulin alpha-3 chain
HF: Tubulin beta-4B chain
HG: Detyrosinated tubulin alpha-3 chain
HH: Tubulin beta-4B chain
HI: Detyrosinated tubulin alpha-3 chain
HJ: Tubulin beta-4B chain
HK: Detyrosinated tubulin alpha-3 chain
HL: Tubulin beta-4B chain
I: Cilia- and flagella-associated protein 95
I1: Protein FAM166C
I2: Protein FAM166C
I3: Protein FAM166C
IA: Detyrosinated tubulin alpha-3 chain
IB: Tubulin beta-4B chain
IC: Detyrosinated tubulin alpha-3 chain
ID: Tubulin beta-4B chain
IE: Detyrosinated tubulin alpha-3 chain
IF: Tubulin beta-4B chain
IG: Detyrosinated tubulin alpha-3 chain
IH: Tubulin beta-4B chain
II: Detyrosinated tubulin alpha-3 chain
IJ: Tubulin beta-4B chain
IK: Detyrosinated tubulin alpha-3 chain
IL: Tubulin beta-4B chain
IM: Detyrosinated tubulin alpha-3 chain
J: Cilia- and flagella-associated protein 107
J1: Dual specificity phosphatase 21
J2: Dual specificity phosphatase 21
J3: Dual specificity phosphatase 21
JA: Detyrosinated tubulin alpha-3 chain
JB: Tubulin beta-4B chain
JC: Detyrosinated tubulin alpha-3 chain
JD: Tubulin beta-4B chain
JE: Detyrosinated tubulin alpha-3 chain
JF: Tubulin beta-4B chain
JG: Detyrosinated tubulin alpha-3 chain
JH: Tubulin beta-4B chain
JI: Detyrosinated tubulin alpha-3 chain
JJ: Tubulin beta-4B chain
JK: Detyrosinated tubulin alpha-3 chain
JL: Tubulin beta-4B chain
K: Cilia- and flagella-associated protein 161
K1: Coiled-coil domain-containing protein 105
K2: Coiled-coil domain-containing protein 105
K3: Coiled-coil domain-containing protein 105
K4: Coiled-coil domain-containing protein 105
K5: Coiled-coil domain-containing protein 105
KA: Detyrosinated tubulin alpha-3 chain
KB: Tubulin beta-4B chain
KC: Detyrosinated tubulin alpha-3 chain
KD: Tubulin beta-4B chain
KE: Detyrosinated tubulin alpha-3 chain
KF: Tubulin beta-4B chain
KG: Detyrosinated tubulin alpha-3 chain
KH: Tubulin beta-4B chain
KI: Detyrosinated tubulin alpha-3 chain
KJ: Tubulin beta-4B chain
KK: Detyrosinated tubulin alpha-3 chain
KL: Tubulin beta-4B chain
L: Cilia- and flagella-associated protein 161
L1: Enkurin
L2: Enkurin
L3: Enkurin
L4: Enkurin
LA: Detyrosinated tubulin alpha-3 chain
LB: Tubulin beta-4B chain
LC: Detyrosinated tubulin alpha-3 chain
LD: Tubulin beta-4B chain
LE: Detyrosinated tubulin alpha-3 chain
LF: Tubulin beta-4B chain
LG: Detyrosinated tubulin alpha-3 chain
LH: Tubulin beta-4B chain
LI: Detyrosinated tubulin alpha-3 chain
LJ: Tubulin beta-4B chain
LK: Detyrosinated tubulin alpha-3 chain
LL: Tubulin beta-4B chain
M: Piercer of microtubule wall 1 protein
M1: Testis-expressed protein 43
M2: Testis-expressed protein 43
M3: Testis-expressed protein 43
MB: Tubulin beta-4B chain
MC: Detyrosinated tubulin alpha-3 chain
MD: Tubulin beta-4B chain
ME: Detyrosinated tubulin alpha-3 chain
MF: Tubulin beta-4B chain
MG: Detyrosinated tubulin alpha-3 chain
MH: Tubulin beta-4B chain
MI: Detyrosinated tubulin alpha-3 chain
MJ: Tubulin beta-4B chain
MK: Detyrosinated tubulin alpha-3 chain
ML: Tubulin beta-4B chain
MM: Detyrosinated tubulin alpha-3 chain
N: Piercer of microtubule wall 2 protein
N1: Cilia- and flagella-associated protein 276
N2: Cilia- and flagella-associated protein 276
N3: Cilia- and flagella-associated protein 276
N4: Cilia- and flagella-associated protein 276
NA: Detyrosinated tubulin alpha-3 chain
NB: Tubulin beta-4B chain
NC: Detyrosinated tubulin alpha-3 chain
ND: Tubulin beta-4B chain
NE: Detyrosinated tubulin alpha-3 chain
NF: Tubulin beta-4B chain
NG: Detyrosinated tubulin alpha-3 chain
NH: Tubulin beta-4B chain
NI: Detyrosinated tubulin alpha-3 chain
NJ: Tubulin beta-4B chain
NK: Detyrosinated tubulin alpha-3 chain
NL: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
O1: Protein Flattop
O2: Protein Flattop
O3: Protein Flattop
OA: Detyrosinated tubulin alpha-3 chain
OB: Tubulin beta-4B chain
OC: Detyrosinated tubulin alpha-3 chain
OD: Tubulin beta-4B chain
OE: Detyrosinated tubulin alpha-3 chain
OF: Tubulin beta-4B chain
OG: Detyrosinated tubulin alpha-3 chain
OH: Tubulin beta-4B chain
OI: Detyrosinated tubulin alpha-3 chain
OJ: Tubulin beta-4B chain
OK: Detyrosinated tubulin alpha-3 chain
OL: Tubulin beta-4B chain
P: RIB43A-like with coiled-coils protein 2
P1: Cilia- and flagella-associated protein 52
P2: Cilia- and flagella-associated protein 52
P3: Cilia- and flagella-associated protein 52
PA: Detyrosinated tubulin alpha-3 chain
PB: Tubulin beta-4B chain
PC: Detyrosinated tubulin alpha-3 chain
PD: Tubulin beta-4B chain
PE: Detyrosinated tubulin alpha-3 chain
PF: Tubulin beta-4B chain
PG: Detyrosinated tubulin alpha-3 chain
PH: Tubulin beta-4B chain
PI: Detyrosinated tubulin alpha-3 chain
PJ: Tubulin beta-4B chain
PK: Detyrosinated tubulin alpha-3 chain
PL: Tubulin beta-4B chain
PM: Detyrosinated tubulin alpha-3 chain
Q: RIB43A-like with coiled-coils protein 2
Q1: EF-hand calcium-binding domain-containing protein 6
Q2: EF-hand calcium-binding domain-containing protein 6
Q3: EF-hand calcium-binding domain-containing protein 6
QB: Tubulin beta-4B chain
QC: Detyrosinated tubulin alpha-3 chain
QD: Tubulin beta-4B chain
QE: Detyrosinated tubulin alpha-3 chain
QF: Tubulin beta-4B chain
QG: Detyrosinated tubulin alpha-3 chain
QH: Tubulin beta-4B chain
QI: Detyrosinated tubulin alpha-3 chain
QJ: Tubulin beta-4B chain
QK: Detyrosinated tubulin alpha-3 chain
QL: Tubulin beta-4B chain
QM: Detyrosinated tubulin alpha-3 chain
R: RIB43A-like with coiled-coils protein 2
R1: Cilia and flagella-associated protein 77
R2: Cilia and flagella-associated protein 77
R3: Cilia and flagella-associated protein 77
RB: Tubulin beta-4B chain
RC: Detyrosinated tubulin alpha-3 chain
RD: Tubulin beta-4B chain
RE: Detyrosinated tubulin alpha-3 chain
RF: Tubulin beta-4B chain
RG: Detyrosinated tubulin alpha-3 chain
RH: Tubulin beta-4B chain
RI: Detyrosinated tubulin alpha-3 chain
RJ: Tubulin beta-4B chain
RK: Detyrosinated tubulin alpha-3 chain
RL: Tubulin beta-4B chain
RM: Detyrosinated tubulin alpha-3 chain
S: Sperm-associated antigen 8
SB: Tubulin beta-4B chain
SC: Detyrosinated tubulin alpha-3 chain
SD: Tubulin beta-4B chain
SE: Detyrosinated tubulin alpha-3 chain
SF: Tubulin beta-4B chain
SG: Detyrosinated tubulin alpha-3 chain
SH: Tubulin beta-4B chain
SI: Detyrosinated tubulin alpha-3 chain
SJ: Tubulin beta-4B chain
SK: Detyrosinated tubulin alpha-3 chain
SL: Tubulin beta-4B chain
SM: Detyrosinated tubulin alpha-3 chain
T: Sperm-associated antigen 8
TB: Tubulin beta-4B chain
TC: Detyrosinated tubulin alpha-3 chain
TD: Tubulin beta-4B chain
TE: Detyrosinated tubulin alpha-3 chain
TF: Tubulin beta-4B chain
TG: Detyrosinated tubulin alpha-3 chain
TH: Tubulin beta-4B chain
TI: Detyrosinated tubulin alpha-3 chain
TJ: Tubulin beta-4B chain
TK: Detyrosinated tubulin alpha-3 chain
TL: Tubulin beta-4B chain
TM: Detyrosinated tubulin alpha-3 chain
TN: Tubulin beta-4B chain
U: Cilia- and flagella-associated protein 45
UA: Detyrosinated tubulin alpha-3 chain
UB: Tubulin beta-4B chain
UC: Detyrosinated tubulin alpha-3 chain
UD: Tubulin beta-4B chain
UE: Detyrosinated tubulin alpha-3 chain
UF: Tubulin beta-4B chain
UG: Detyrosinated tubulin alpha-3 chain
UH: Tubulin beta-4B chain
UI: Detyrosinated tubulin alpha-3 chain
UJ: Tubulin beta-4B chain
UK: Detyrosinated tubulin alpha-3 chain
UL: Tubulin beta-4B chain
V: Cilia- and flagella-associated protein 45
VA: Detyrosinated tubulin alpha-3 chain
VB: Tubulin beta-4B chain
VC: Detyrosinated tubulin alpha-3 chain
VD: Tubulin beta-4B chain
VE: Detyrosinated tubulin alpha-3 chain
VF: Tubulin beta-4B chain
VG: Detyrosinated tubulin alpha-3 chain
VH: Tubulin beta-4B chain
VI: Detyrosinated tubulin alpha-3 chain
VJ: Tubulin beta-4B chain
VK: Detyrosinated tubulin alpha-3 chain
VL: Tubulin beta-4B chain
W: Cilia- and flagella-associated protein 45
WA: Detyrosinated tubulin alpha-3 chain
WB: Tubulin beta-4B chain
WC: Detyrosinated tubulin alpha-3 chain
WD: Tubulin beta-4B chain
WE: Detyrosinated tubulin alpha-3 chain
WF: Tubulin beta-4B chain
WG: Detyrosinated tubulin alpha-3 chain
WH: Tubulin beta-4B chain
WI: Detyrosinated tubulin alpha-3 chain
WJ: Tubulin beta-4B chain
WK: Detyrosinated tubulin alpha-3 chain
WL: Tubulin beta-4B chain
X: Cilia- and flagella-associated protein 45
XA: Cilia- and flagella-associated protein 20
XB: Cilia- and flagella-associated protein 20
XC: Cilia- and flagella-associated protein 20
XD: Cilia- and flagella-associated protein 20
XE: Cilia- and flagella-associated protein 20
XF: Cilia- and flagella-associated protein 20
XG: Cilia- and flagella-associated protein 20
XH: Parkin coregulated gene protein homolog
XI: Parkin coregulated gene protein homolog
XJ: Parkin coregulated gene protein homolog
XK: Parkin coregulated gene protein homolog
XL: Parkin coregulated gene protein homolog
XM: Parkin coregulated gene protein homolog
Y: Cilia- and flagella-associated protein 210
YA: Sperm acrosome-associated protein 9
YB: Sperm acrosome-associated protein 9
YC: Sperm acrosome-associated protein 9
YD: Sperm acrosome-associated protein 9
YE: Sperm acrosome-associated protein 9
YF: Sperm acrosome-associated protein 9
YG: Sperm acrosome-associated protein 9
YH: Sperm acrosome-associated protein 9
YI: Sperm acrosome-associated protein 9
YJ: Sperm acrosome-associated protein 9
YK: Sperm acrosome-associated protein 9
YL: Sperm acrosome-associated protein 9
YM: Sperm acrosome-associated protein 9
YN: Sperm acrosome-associated protein 9
YO: Sperm acrosome-associated protein 9
YP: Sperm acrosome-associated protein 9
YQ: Sperm acrosome-associated protein 9
YR: Sperm acrosome-associated protein 9
YS: Sperm acrosome-associated protein 9
YT: Sperm acrosome-associated protein 9
YU: Sperm acrosome-associated protein 9
YV: Sperm acrosome-associated protein 9
YW: Sperm acrosome-associated protein 9
Z: Cilia- and flagella-associated protein 210
a: Cilia- and flagella-associated protein 141
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,412,304729
Polymers21,266,337450
Non-polymers145,967279
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 24 types, 416 molecules ABA1A2A3A4ABADAFAHAJALBBBDBFBHBJBLCBCDCFCHCJCLDBDDDFDHDJDL...

#1: Protein Meiosis-specific nuclear structural protein 1


Mass: 60353.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q61884
#2: Protein
Tektin-1


Mass: 48713.035 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAJ2
#3: Protein ...
Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 47897.918 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#4: Protein ...
Detyrosinated tubulin alpha-3 chain


Mass: 48689.090 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P05214
#5: Protein
Tektin-2 / Tektin-t / Testicular tektin


Mass: 50385.066 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q922G7
#6: Protein Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7 / nm23-M7


Mass: 44489.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9QXL8, nucleoside-diphosphate kinase
#7: Protein
Tektin-3


Mass: 56754.777 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6X6Z7
#8: Protein
Tektin-4 / Testicular microtubules-related protein 4


Mass: 52121.449 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q149S1
#10: Protein
Tektin bundle-interacting protein 1


Mass: 23987.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A6H6Q4
#11: Protein ...
Tektin-5


Mass: 62817.535 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G5E8A8
#13: Protein EF-hand domain-containing protein 1 / Myoclonin-1


Mass: 75235.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9T8
#15: Protein
Protein FAM166A


Mass: 36659.566 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4K5
#17: Protein Protein FAM166C


Mass: 23097.957 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAS2
#19: Protein Dual specificity phosphatase 21


Mass: 21527.574 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q9D9D8, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#21: Protein
Coiled-coil domain-containing protein 105


Mass: 57406.484 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4K7
#22: Protein
Enkurin


Mass: 29587.521 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6SP97
#24: Protein Testis-expressed protein 43


Mass: 16305.608 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9I1
#27: Protein
RIB43A-like with coiled-coils protein 2


Mass: 45328.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D4Q1
#28: Protein Protein Flattop / Cilia- and flagella-associated protein 126


Mass: 20575.123 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8X9
#30: Protein EF-hand calcium-binding domain-containing protein 6 / DJ-1-binding protein / DJBP


Mass: 176028.312 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P1E8
#31: Protein Cilia and flagella-associated protein 77


Mass: 32786.020 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A087WRI3
#32: Protein Sperm-associated antigen 8 / Sperm membrane protein 1 / SMP-1 / Sperm membrane protein BS-84


Mass: 50591.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V0Q6
#35: Protein
Parkin coregulated gene protein homolog / Hypertension-related protein 1-like protein / PARK2 coregulated gene protein


Mass: 27763.268 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAK2
#37: Protein ...
Sperm acrosome-associated protein 9 / Acrosome and sperm tail protein / MAST


Mass: 19512.373 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TPM5

-
EF-hand domain-containing family member ... , 2 types, 5 molecules EFG4G5G6

#9: Protein EF-hand domain-containing family member B / Cilia- and flagella-associated protein 21


Mass: 95891.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8CDU5
#14: Protein EF-hand domain-containing family member C2


Mass: 87758.023 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D485

-
Cilia- and flagella-associated protein ... , 10 types, 27 molecules GHIJKLN1N2N3N4P1P2P3UVWXXAXBXCXDXEXFXGYZa

#12: Protein Cilia- and flagella-associated protein 53 / Coiled-coil domain-containing protein 11


Mass: 62036.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D439
#16: Protein Cilia- and flagella-associated protein 95


Mass: 26633.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQC3
#18: Protein Cilia- and flagella-associated protein 107


Mass: 23062.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q4KKZ1
#20: Protein Cilia- and flagella-associated protein 161


Mass: 34433.383 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6P8Y0
#26: Protein
Cilia- and flagella-associated protein 276


Mass: 18960.092 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAD0
#29: Protein Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16


Mass: 68322.164 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5F201
#33: Protein
Cilia- and flagella-associated protein 45 / Coiled-coil domain-containing protein 19 / Nasopharyngeal epithelium-specific protein 1


Mass: 65962.016 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9U9
#34: Protein
Cilia- and flagella-associated protein 20 / Gene trap locus 3 protein


Mass: 22781.389 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1
#36: Protein Cilia- and flagella-associated protein 210 / Coiled-coil domain-containing protein 173


Mass: 65266.520 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0JLY1
#38: Protein Cilia- and flagella-associated protein 141


Mass: 12278.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D9D9

-
Piercer of microtubule wall ... , 2 types, 2 molecules MN

#23: Protein Piercer of microtubule wall 1 protein / Pierce1 / p53-induced expression in RB-null cells protein 1


Mass: 18862.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5BN45
#25: Protein Piercer of microtubule wall 2 protein


Mass: 13728.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: V9GXK1

-
Non-polymers , 1 types, 279 molecules

#39: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 279 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: mouse sperm / Type: CELL / Entity ID: #1-#38 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 3 e/Å2 / Avg electron dose per subtomogram: 117 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.6/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17450 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 689 / Num. of volumes extracted: 17450

+
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