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- PDB-9ijj: In situ structure of the central apparatus in mouse sperm axoneme. -

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Basic information

Entry
Database: PDB / ID: 9ijj
TitleIn situ structure of the central apparatus in mouse sperm axoneme.
Components
  • (Cilia and flagella associated protein ...) x 2
  • (Cilia- and flagella-associated protein ...) x 8
  • (Leucine-rich repeat and ...) x 2
  • (Sperm-associated antigen ...) x 3
  • (Spermatogenesis-associated protein ...) x 2
  • Ankyrin repeat and MYND domain-containing protein 1
  • Calmodulin-1
  • Cilia and flagella-associated protein 47
  • Coiled-coil domain containing 180
  • Deleted in lung and esophageal cancer 1
  • G protein-coupled receptor kinase 3
  • Germ cell-less protein-like 1
  • Hydrocephalus-inducing protein
  • Kinesin-like protein KIF9
  • Leucine rich repeat containing 72
  • Leucine-rich repeat-containing protein 43
  • MORN repeat containing 2
  • MYCBP-associated protein
  • Microtubule-associated protein 1S
  • Protein FAM228B
  • Protein dpy-30 homolog
  • Putative aspartate aminotransferase, cytoplasmic 2
  • Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
  • Sperm acrosome-associated protein 9
  • Sperm flagellar protein 2
  • Tubulin alpha-3 chain
  • Tubulin beta-4B chain
  • Unknown1
  • Unknown2
  • Unknown3
  • Unknown4
  • Unknown5
  • Unknown6
KeywordsPROTEIN TRANSPORT / microtubules / axoneme / sperm / filament
Function / homology
Function and homology information


cell motility in response to calcium ion / intramanchette transport / maintenance of cell number / substrate-dependent cell migration, cell attachment to substrate / axonemal central pair projection / male germ-line stem cell population maintenance / respiratory system development / organelle disassembly / regulation of cilium beat frequency / axonemal central apparatus ...cell motility in response to calcium ion / intramanchette transport / maintenance of cell number / substrate-dependent cell migration, cell attachment to substrate / axonemal central pair projection / male germ-line stem cell population maintenance / respiratory system development / organelle disassembly / regulation of cilium beat frequency / axonemal central apparatus / regulation of establishment of planar polarity / lateral wall of outer hair cell / axonemal microtubule doublet inner sheath / mucociliary clearance / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / sperm flagellum assembly / axonemal central apparatus assembly / manchette assembly / positive regulation of fertilization / radial spoke / axonemal B tubule inner sheath / CaMK IV-mediated phosphorylation of CREB / Cam-PDE 1 activation / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Glycogen breakdown (glycogenolysis) / Activation of RAC1 downstream of NMDARs / Sodium/Calcium exchangers / Activation of Ca-permeable Kainate Receptor / positive regulation of flagellated sperm motility / regulation of flagellated sperm motility / Synthesis of IP3 and IP4 in the cytosol / CLEC7A (Dectin-1) induces NFAT activation / RHO GTPases activate PAKs / Carboxyterminal post-translational modifications of tubulin / Calmodulin induced events / Inactivation, recovery and regulation of the phototransduction cascade / Intraflagellar transport / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / eNOS activation / protein polyglutamylation / trachea development / outer dynein arm / beta-adrenergic-receptor kinase / sperm axoneme assembly / positive regulation of feeding behavior / Reduction of cytosolic Ca++ levels / Unblocking of NMDA receptors, glutamate binding and activation / COPI-independent Golgi-to-ER retrograde traffic / Calcineurin activates NFAT / Ion transport by P-type ATPases / Protein methylation / sperm principal piece / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / olfactory behavior / regulation of cilium beat frequency involved in ciliary motility / cerebrospinal fluid circulation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / RAF activation / epithelial cilium movement involved in extracellular fluid movement / beta-adrenergic receptor kinase activity / G protein-coupled receptor kinase activity / cilium movement involved in cell motility / VEGFR2 mediated vascular permeability / response to odorant / COPI-mediated anterograde transport / sperm head-tail coupling apparatus / Aggrephagy / RAS processing / 9+2 motile cilium / G alpha (s) signalling events / microtubule anchoring at centrosome / Kinesins / PTW/PP1 phosphatase complex / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / metaphase chromosome alignment / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / acrosomal membrane / Ca2+ pathway / The role of GTSE1 in G2/M progression after G2 checkpoint / axoneme assembly / RHO GTPases activate IQGAPs / microtubule sliding / Recycling pathway of L1 / Extra-nuclear estrogen signaling / FCERI mediated Ca+2 mobilization / cilium movement / RAF/MAP kinase cascade / regulation of nucleocytoplasmic transport / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium assembly / PKA activation / RHO GTPases Activate Formins / regulation of podosome assembly / Separation of Sister Chromatids / cilium organization
Similarity search - Function
Germ cell-less protein-like / : / : / : / : / DLEC1 sixth Ig-like domain / Microtubule-associated protein 1B N-terminal / CFAP74 second Ig-like domain / CFAP65, eight Ig-like domain / MAP1B MBL-like domain ...Germ cell-less protein-like / : / : / : / : / DLEC1 sixth Ig-like domain / Microtubule-associated protein 1B N-terminal / CFAP74 second Ig-like domain / CFAP65, eight Ig-like domain / MAP1B MBL-like domain / Microtubule associated protein 1 / Hydin adenylate kinase-like domain / : / Hydin Adenylate kinase-like domain / Lrrd1 death domain / : / Kinesin-like protein KIF9 domain / Sperm-associated antigen 17 / Cilia- and flagella-associated protein 54 / Domain of unknown function DUF4456 / Domain of unknown function DUF4455 / Primary ciliary dyskinesia protein 1 / MYCBP-associated protein / Flagellar C1a complex subunit C1a-32 / Deleted in lung and esophageal cancer protein 1 / Cilia- and flagella-associated protein 99 / Cilia- and flagella-associated protein 46 / Protein FAM228 / Leucine-rich repeat-containing protein 72 / : / : / : / : / : / : / : / : / : / : / : / : / Domain of unknown function (DUF4455) / Domain of unknown function (DUF4456) / MYCBP-associated protein family / Flagellar C1a complex subunit C1a-32 / Cilia- and flagella-associated protein 54 / Flagellar-associated PapD-like / Cilia- and flagella-associated protein 69, ARM repeat / CPC1/SPEF2 domain D5 / Deleted in lung and esophageal cancer protein 1 Ig domain / SPEF2 C-terminal domain / Cilia- and flagella-associated protein 65-like, Ig-like domain / Cilia- and flagella-associated protein 47 domain / CFAP74 first Ig-like domain / CFAP74 third Ig-like domain / CFAP74 forth Ig-like domain / CFAP65, seventh Ig-like domain / CFAP46, N-terminal TPR repeats / : / Hydrocephalus-inducing-like / Cilia- and flagella-associated protein 65-like, Ig-like domain / : / HYDIN/CFA65/VesB-like, Ig-like domain / : / CFAP65, fourth Ig-like domain / CH-like domain in sperm protein / : / CH-like domain in sperm protein / : / Sperm acrosome-associated protein 9 / : / Sperm acrosome-associated protein 9 / Sdc1/DPY30 / Dpy-30 motif / Dpy-30 motif / Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / MORN motif / MORN repeat / GPCR kinase / PapD-like superfamily / Adenylate kinase / : / MYND finger / Zinc finger MYND-type signature. / Zinc finger, MYND-type / Zinc finger MYND-type profile. / Aspartate/other aminotransferase / Regulator of G protein signaling domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS domain superfamily / Leucine-rich repeat / Serine/threonine specific protein phosphatases signature.
Similarity search - Domain/homology
Cilia and flagella-associated protein 47 / Cilia and flagella associated protein 99 / Leucine rich repeat containing 72 / MORN repeat containing 2 / Cilia- and flagella-associated protein 221 / Cilia- and flagella-associated protein 70 / Cilia and flagella associated protein 46 / Deleted in lung and esophageal cancer 1 / Coiled-coil domain containing 180 / Tubulin alpha-3 chain ...Cilia and flagella-associated protein 47 / Cilia and flagella associated protein 99 / Leucine rich repeat containing 72 / MORN repeat containing 2 / Cilia- and flagella-associated protein 221 / Cilia- and flagella-associated protein 70 / Cilia and flagella associated protein 46 / Deleted in lung and esophageal cancer 1 / Coiled-coil domain containing 180 / Tubulin alpha-3 chain / Calmodulin-1 / Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / Tubulin beta-4B chain / Cilia- and flagella-associated protein 74 / G protein-coupled receptor kinase 3 / Cilia- and flagella-associated protein 65 / Leucine-rich repeat-containing protein 43 / Protein FAM228B / Sperm-associated antigen 17 / MYCBP-associated protein / Cilia- and flagella-associated protein 119 / Sperm acrosome-associated protein 9 / Putative aspartate aminotransferase, cytoplasmic 2 / Hydrocephalus-inducing protein / Cilia- and flagella-associated protein 69 / Cilia- and flagella-associated protein 20 / Microtubule-associated protein 1S / Leucine-rich repeat and death domain-containing protein 1 / Ankyrin repeat and MYND domain-containing protein 1 / Cilia- and flagella-associated protein 54 / Sperm flagellar protein 2 / Spermatogenesis-associated protein 4 / Sperm-associated antigen 16 protein / Germ cell-less protein-like 1 / Protein dpy-30 homolog / Spermatogenesis-associated protein 17 / Leucine-rich repeat and guanylate kinase domain-containing protein / Sperm-associated antigen 6 / Kinesin-like protein KIF9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.7 Å
AuthorsZhu, Y. / Yin, G. / Sun, F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31925026 China
CitationJournal: Cell Res / Year: 2025
Title: In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.
Authors: Yun Zhu / Tingting Lin / Guoliang Yin / Linhua Tai / Lianwan Chen / Jing Ma / Guoning Huang / Yi Lu / Zhiyong Zhang / Binbin Wang / Suren Chen / Fei Sun /
Abstract: The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron ...The central apparatus (CA) within the sperm axoneme is vital for sperm motility, yet its molecular architecture and functional mechanisms remain incompletely understood. Combining cryo-electron tomography and AlphaFold2, we resolved the in-cell structure of mouse sperm CA at a subnanometer resolution and built a near-complete atomic model. Our analysis identified 39 CA-associated proteins, including eight previously unreported components. By presenting the full-length structures of CFAP47 and HYDIN, we elucidate their molecular roles in tethering the C1 and C2 microtubules within the CA. Specifically, HYDIN forms a semicircular chain that encircles C1 and C2, with its N-terminal half driving the C1-C2 connection and its C-terminal half providing axial support in C2. CFAP47, the core structural component of the bridge, binds C1 through its N-terminal domains, interacts with HYDIN via its central CFAP47-ring, and anchors to C2 through its C-terminal region. The significantly reduced sperm motility and impaired CA structure observed in Cfap47-knockout mice confirmed the important role of CFAP47. Furthermore, genetic analysis of infertile Chinese men with asthenozoospermia identified previously unreported mutations in the CFAP47. The CA structural model elucidates the pathogenic mechanisms of these mutations, establishing a direct link between CFAP47 dysfunction and impaired sperm motility. Therefore, our study provides mechanistic insights into CA-related fertility disorders.
History
DepositionJun 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
b: Spermatogenesis-associated protein 4
c: Kinesin-like protein KIF9
d: Kinesin-like protein KIF9
e: Kinesin-like protein KIF9
f: Kinesin-like protein KIF9
g: Kinesin-like protein KIF9
h: Cilia- and flagella-associated protein 65
i: Cilia- and flagella-associated protein 65
j: Cilia- and flagella-associated protein 65
k: Cilia- and flagella-associated protein 70
a: Spermatogenesis-associated protein 4
n: Cilia- and flagella-associated protein 70
o: Cilia- and flagella-associated protein 70
p: Cilia- and flagella-associated protein 70
q: Protein FAM228B
r: Protein FAM228B
s: Protein FAM228B
t: Cilia- and flagella-associated protein 20
u: Cilia- and flagella-associated protein 20
v: MYCBP-associated protein
w: MYCBP-associated protein
m: Cilia- and flagella-associated protein 70
A: Cilia and flagella associated protein 46
B: Cilia and flagella associated protein 46
C: Cilia- and flagella-associated protein 74
D: Cilia- and flagella-associated protein 74
E: Cilia- and flagella-associated protein 74
F: Coiled-coil domain containing 180
G: Coiled-coil domain containing 180
H: Cilia- and flagella-associated protein 54
I: Cilia- and flagella-associated protein 54
L: Cilia- and flagella-associated protein 221
M: Leucine rich repeat containing 72
O: Deleted in lung and esophageal cancer 1
P: Deleted in lung and esophageal cancer 1
Q: Sperm-associated antigen 16 protein
R: Sperm-associated antigen 16 protein
S: Sperm-associated antigen 16 protein
T: Sperm-associated antigen 16 protein
U: Sperm-associated antigen 16 protein
V: Sperm-associated antigen 16 protein
W: Spermatogenesis-associated protein 4
X: Spermatogenesis-associated protein 4
Y: Spermatogenesis-associated protein 4
Z: Spermatogenesis-associated protein 4
x: Sperm-associated antigen 17
y: Sperm-associated antigen 17
z: Sperm-associated antigen 17
l: Cilia- and flagella-associated protein 70
Ab: Tubulin beta-4B chain
Ac: Tubulin alpha-3 chain
Ad: Tubulin beta-4B chain
Ae: Tubulin alpha-3 chain
Af: Tubulin beta-4B chain
Ag: Tubulin alpha-3 chain
Ah: Tubulin beta-4B chain
Ai: Tubulin alpha-3 chain
Aj: Tubulin beta-4B chain
Ak: Tubulin alpha-3 chain
Bb: Tubulin beta-4B chain
Bc: Tubulin alpha-3 chain
Bd: Tubulin beta-4B chain
Be: Tubulin alpha-3 chain
Bf: Tubulin beta-4B chain
Bg: Tubulin alpha-3 chain
Bh: Tubulin beta-4B chain
Bi: Tubulin alpha-3 chain
Bj: Tubulin beta-4B chain
Bk: Tubulin alpha-3 chain
Cb: Tubulin beta-4B chain
Cc: Tubulin alpha-3 chain
Cd: Tubulin beta-4B chain
Ce: Tubulin alpha-3 chain
Cf: Tubulin beta-4B chain
Cg: Tubulin alpha-3 chain
Ch: Tubulin beta-4B chain
Ci: Tubulin alpha-3 chain
Cj: Tubulin beta-4B chain
Ck: Tubulin alpha-3 chain
Db: Tubulin beta-4B chain
Dc: Tubulin alpha-3 chain
Dd: Tubulin beta-4B chain
De: Tubulin alpha-3 chain
Df: Tubulin beta-4B chain
Dg: Tubulin alpha-3 chain
Dh: Tubulin beta-4B chain
Di: Tubulin alpha-3 chain
Dj: Tubulin beta-4B chain
Dk: Tubulin alpha-3 chain
Eb: Tubulin beta-4B chain
Ec: Tubulin alpha-3 chain
Ed: Tubulin beta-4B chain
Ee: Tubulin alpha-3 chain
Ef: Tubulin beta-4B chain
Eg: Tubulin alpha-3 chain
Eh: Tubulin beta-4B chain
Ei: Tubulin alpha-3 chain
Ej: Tubulin beta-4B chain
Ek: Tubulin alpha-3 chain
Fa: Tubulin alpha-3 chain
Fb: Tubulin beta-4B chain
Fc: Tubulin alpha-3 chain
Fd: Tubulin beta-4B chain
Fe: Tubulin alpha-3 chain
Ff: Tubulin beta-4B chain
Fg: Tubulin alpha-3 chain
Fh: Tubulin beta-4B chain
Fi: Tubulin alpha-3 chain
Fj: Tubulin beta-4B chain
Ga: Tubulin alpha-3 chain
Gb: Tubulin beta-4B chain
Gc: Tubulin alpha-3 chain
Gd: Tubulin beta-4B chain
Ge: Tubulin alpha-3 chain
Gf: Tubulin beta-4B chain
Gg: Tubulin alpha-3 chain
Gh: Tubulin beta-4B chain
Gi: Tubulin alpha-3 chain
Gj: Tubulin beta-4B chain
Ha: Tubulin alpha-3 chain
Hb: Tubulin beta-4B chain
Hc: Tubulin alpha-3 chain
Hd: Tubulin beta-4B chain
He: Tubulin alpha-3 chain
Hf: Tubulin beta-4B chain
Hg: Tubulin alpha-3 chain
Hh: Tubulin beta-4B chain
Hi: Tubulin alpha-3 chain
Hj: Tubulin beta-4B chain
Ia: Tubulin alpha-3 chain
Ib: Tubulin beta-4B chain
Ic: Tubulin alpha-3 chain
Id: Tubulin beta-4B chain
Ie: Tubulin alpha-3 chain
If: Tubulin beta-4B chain
Ig: Tubulin alpha-3 chain
Ih: Tubulin beta-4B chain
Ii: Tubulin alpha-3 chain
Ij: Tubulin beta-4B chain
Ja: Tubulin alpha-3 chain
Jb: Tubulin beta-4B chain
Jc: Tubulin alpha-3 chain
Jd: Tubulin beta-4B chain
Je: Tubulin alpha-3 chain
Jf: Tubulin beta-4B chain
Jg: Tubulin alpha-3 chain
Jh: Tubulin beta-4B chain
Ji: Tubulin alpha-3 chain
Jj: Tubulin beta-4B chain
Kb: Tubulin beta-4B chain
Kc: Tubulin alpha-3 chain
Kd: Tubulin beta-4B chain
Ke: Tubulin alpha-3 chain
Kf: Tubulin beta-4B chain
Kg: Tubulin alpha-3 chain
Kh: Tubulin beta-4B chain
Ki: Tubulin alpha-3 chain
Kj: Tubulin beta-4B chain
Kk: Tubulin alpha-3 chain
Lb: Tubulin beta-4B chain
Lc: Tubulin alpha-3 chain
Ld: Tubulin beta-4B chain
Le: Tubulin alpha-3 chain
Lf: Tubulin beta-4B chain
Lg: Tubulin alpha-3 chain
Lh: Tubulin beta-4B chain
Li: Tubulin alpha-3 chain
Lj: Tubulin beta-4B chain
Lk: Tubulin alpha-3 chain
Mb: Tubulin beta-4B chain
Mc: Tubulin alpha-3 chain
Md: Tubulin beta-4B chain
Me: Tubulin alpha-3 chain
Mf: Tubulin beta-4B chain
Mg: Tubulin alpha-3 chain
Mh: Tubulin beta-4B chain
Mi: Tubulin alpha-3 chain
Mj: Tubulin beta-4B chain
Mk: Tubulin alpha-3 chain
An: Tubulin beta-4B chain
Ao: Tubulin alpha-3 chain
Ap: Tubulin beta-4B chain
Aq: Tubulin alpha-3 chain
Ar: Tubulin beta-4B chain
As: Tubulin alpha-3 chain
At: Tubulin beta-4B chain
Au: Tubulin alpha-3 chain
Av: Tubulin beta-4B chain
Aw: Tubulin alpha-3 chain
Bn: Tubulin beta-4B chain
Bo: Tubulin alpha-3 chain
Bp: Tubulin beta-4B chain
Bq: Tubulin alpha-3 chain
Br: Tubulin beta-4B chain
Bs: Tubulin alpha-3 chain
Bt: Tubulin beta-4B chain
Bu: Tubulin alpha-3 chain
Bv: Tubulin beta-4B chain
Bm: Tubulin alpha-3 chain
Cn: Tubulin beta-4B chain
Co: Tubulin alpha-3 chain
Cp: Tubulin beta-4B chain
Cq: Tubulin alpha-3 chain
Cr: Tubulin beta-4B chain
Cs: Tubulin alpha-3 chain
Ct: Tubulin beta-4B chain
Cu: Tubulin alpha-3 chain
Cv: Tubulin beta-4B chain
Cm: Tubulin alpha-3 chain
Dn: Tubulin beta-4B chain
Do: Tubulin alpha-3 chain
Dp: Tubulin beta-4B chain
Dq: Tubulin alpha-3 chain
Dr: Tubulin beta-4B chain
Ds: Tubulin alpha-3 chain
Dt: Tubulin beta-4B chain
Du: Tubulin alpha-3 chain
Dv: Tubulin beta-4B chain
Dm: Tubulin alpha-3 chain
En: Tubulin beta-4B chain
Eo: Tubulin alpha-3 chain
Ep: Tubulin beta-4B chain
Eq: Tubulin alpha-3 chain
Er: Tubulin beta-4B chain
Es: Tubulin alpha-3 chain
Et: Tubulin beta-4B chain
Eu: Tubulin alpha-3 chain
Ev: Tubulin beta-4B chain
Em: Tubulin alpha-3 chain
Fo: Tubulin alpha-3 chain
Fp: Tubulin beta-4B chain
Fq: Tubulin alpha-3 chain
Fr: Tubulin beta-4B chain
Fs: Tubulin alpha-3 chain
Ft: Tubulin beta-4B chain
Fu: Tubulin alpha-3 chain
Fv: Tubulin beta-4B chain
Fw: Tubulin alpha-3 chain
Fn: Tubulin beta-4B chain
Go: Tubulin alpha-3 chain
Gp: Tubulin beta-4B chain
Gq: Tubulin alpha-3 chain
Gr: Tubulin beta-4B chain
Gs: Tubulin alpha-3 chain
Gt: Tubulin beta-4B chain
Gu: Tubulin alpha-3 chain
Gv: Tubulin beta-4B chain
Gw: Tubulin alpha-3 chain
Gn: Tubulin beta-4B chain
Ho: Tubulin alpha-3 chain
Hp: Tubulin beta-4B chain
Hq: Tubulin alpha-3 chain
Hr: Tubulin beta-4B chain
Hs: Tubulin alpha-3 chain
Ht: Tubulin beta-4B chain
Hu: Tubulin alpha-3 chain
Hv: Tubulin beta-4B chain
Hw: Tubulin alpha-3 chain
Hn: Tubulin beta-4B chain
Io: Tubulin alpha-3 chain
Ip: Tubulin beta-4B chain
Iq: Tubulin alpha-3 chain
Ir: Tubulin beta-4B chain
Is: Tubulin alpha-3 chain
It: Tubulin beta-4B chain
Iu: Tubulin alpha-3 chain
Iv: Tubulin beta-4B chain
Iw: Tubulin alpha-3 chain
In: Tubulin beta-4B chain
Jo: Tubulin alpha-3 chain
Jp: Tubulin beta-4B chain
Jq: Tubulin alpha-3 chain
Jr: Tubulin beta-4B chain
Js: Tubulin alpha-3 chain
Jt: Tubulin beta-4B chain
Ju: Tubulin alpha-3 chain
Jv: Tubulin beta-4B chain
Jw: Tubulin alpha-3 chain
Jn: Tubulin beta-4B chain
Kn: Tubulin beta-4B chain
Ko: Tubulin alpha-3 chain
Kp: Tubulin beta-4B chain
Kq: Tubulin alpha-3 chain
Kr: Tubulin beta-4B chain
Ks: Tubulin alpha-3 chain
Kt: Tubulin beta-4B chain
Ku: Tubulin alpha-3 chain
Kv: Tubulin beta-4B chain
Km: Tubulin alpha-3 chain
Ln: Tubulin beta-4B chain
Lo: Tubulin alpha-3 chain
Lp: Tubulin beta-4B chain
Lq: Tubulin alpha-3 chain
Lr: Tubulin beta-4B chain
Ls: Tubulin alpha-3 chain
Lt: Tubulin beta-4B chain
Lu: Tubulin alpha-3 chain
Lv: Tubulin beta-4B chain
Lm: Tubulin alpha-3 chain
Mn: Tubulin beta-4B chain
Mo: Tubulin alpha-3 chain
Mp: Tubulin beta-4B chain
Mq: Tubulin alpha-3 chain
Mr: Tubulin beta-4B chain
Ms: Tubulin alpha-3 chain
Mt: Tubulin beta-4B chain
Mu: Tubulin alpha-3 chain
Mv: Tubulin beta-4B chain
Mm: Tubulin alpha-3 chain
AA: Sperm-associated antigen 6
AB: Sperm-associated antigen 6
AC: Sperm-associated antigen 6
AD: Sperm-associated antigen 6
AE: Sperm-associated antigen 6
AF: Sperm-associated antigen 6
AG: Sperm-associated antigen 6
AH: Sperm-associated antigen 6
AI: Sperm-associated antigen 6
AJ: Sperm-associated antigen 6
AK: Sperm-associated antigen 6
AL: Sperm-associated antigen 6
AM: Sperm-associated antigen 6
AN: Sperm-associated antigen 6
AO: Sperm-associated antigen 6
AP: Sperm-associated antigen 6
AQ: Sperm-associated antigen 6
AR: Sperm-associated antigen 6
AS: Sperm-associated antigen 6
AT: Sperm-associated antigen 6
AU: Sperm-associated antigen 6
AV: Sperm-associated antigen 6
AW: Sperm-associated antigen 6
3D: Calmodulin-1
AX: Sperm-associated antigen 6
AY: Sperm-associated antigen 6
AZ: Sperm-associated antigen 6
A1: Sperm-associated antigen 6
A2: Cilia- and flagella-associated protein 69
A3: Cilia- and flagella-associated protein 69
A4: Cilia- and flagella-associated protein 69
1A: Sperm acrosome-associated protein 9
1B: Sperm acrosome-associated protein 9
1C: Sperm acrosome-associated protein 9
1D: Sperm acrosome-associated protein 9
1G: Sperm acrosome-associated protein 9
1I: Sperm acrosome-associated protein 9
1E: Sperm acrosome-associated protein 9
1F: Sperm acrosome-associated protein 9
1J: Sperm acrosome-associated protein 9
1K: Sperm acrosome-associated protein 9
1L: Sperm acrosome-associated protein 9
1M: Sperm acrosome-associated protein 9
1N: Sperm acrosome-associated protein 9
1O: Sperm acrosome-associated protein 9
1P: Sperm acrosome-associated protein 9
1Q: Sperm acrosome-associated protein 9
1R: Sperm acrosome-associated protein 9
1S: Sperm acrosome-associated protein 9
1T: Sperm acrosome-associated protein 9
1U: Sperm acrosome-associated protein 9
1V: Sperm acrosome-associated protein 9
1W: Sperm acrosome-associated protein 9
1X: Sperm acrosome-associated protein 9
1Y: Sperm acrosome-associated protein 9
1Z: Sperm acrosome-associated protein 9
1a: Sperm acrosome-associated protein 9
1b: Sperm acrosome-associated protein 9
1c: Sperm acrosome-associated protein 9
1d: Sperm acrosome-associated protein 9
3X: Protein dpy-30 homolog
3Y: Protein dpy-30 homolog
3V: Protein dpy-30 homolog
3W: Protein dpy-30 homolog
3T: Protein dpy-30 homolog
3U: Protein dpy-30 homolog
3A: Unknown1
3B: Spermatogenesis-associated protein 17
3E: Calmodulin-1
3F: Calmodulin-1
3G: Calmodulin-1
3K: Cilia- and flagella-associated protein 119
3L: Cilia- and flagella-associated protein 119
3Q: MORN repeat containing 2
3C: Spermatogenesis-associated protein 17
3H: Calmodulin-1
3I: Calmodulin-1
3J: Calmodulin-1
3M: Cilia- and flagella-associated protein 119
3N: Cilia- and flagella-associated protein 119
3R: MORN repeat containing 2
3O: Cilia- and flagella-associated protein 119
3P: Cilia- and flagella-associated protein 119
3S: MORN repeat containing 2
3Z: Unknown2
3a: Unknown2
3b: Unknown3
3c: Unknown3
3d: Unknown3
3e: Unknown4
3f: Unknown5
3g: Unknown6
4A: Cilia and flagella-associated protein 47
4B: Cilia and flagella-associated protein 47
4G: Hydrocephalus-inducing protein
4H: Hydrocephalus-inducing protein
4I: Hydrocephalus-inducing protein
4J: Hydrocephalus-inducing protein
4K: Hydrocephalus-inducing protein
4C: Germ cell-less protein-like 1
4D: Germ cell-less protein-like 1
4E: Germ cell-less protein-like 1
4F: Germ cell-less protein-like 1
4M: Sperm flagellar protein 2
4P: Leucine-rich repeat and guanylate kinase domain-containing protein
4N: Sperm flagellar protein 2
4Q: Leucine-rich repeat and guanylate kinase domain-containing protein
4L: Sperm flagellar protein 2
4O: Leucine-rich repeat and guanylate kinase domain-containing protein
4R: Putative aspartate aminotransferase, cytoplasmic 2
4S: Putative aspartate aminotransferase, cytoplasmic 2
4T: Putative aspartate aminotransferase, cytoplasmic 2
4U: Putative aspartate aminotransferase, cytoplasmic 2
4V: Putative aspartate aminotransferase, cytoplasmic 2
4W: Putative aspartate aminotransferase, cytoplasmic 2
4X: Leucine-rich repeat and death domain-containing protein 1
4Y: Leucine-rich repeat and death domain-containing protein 1
4Z: G protein-coupled receptor kinase 3
4a: Serine/threonine-protein phosphatase PP1-gamma catalytic subunit
2A: Sperm acrosome-associated protein 9
2D: Sperm acrosome-associated protein 9
2B: Sperm acrosome-associated protein 9
2C: Sperm acrosome-associated protein 9
2F: Sperm acrosome-associated protein 9
2E: Sperm acrosome-associated protein 9
2G: Sperm acrosome-associated protein 9
2H: Sperm acrosome-associated protein 9
2I: Sperm acrosome-associated protein 9
2J: Sperm acrosome-associated protein 9
2K: Sperm acrosome-associated protein 9
2L: Sperm acrosome-associated protein 9
2M: Sperm acrosome-associated protein 9
2N: Sperm acrosome-associated protein 9
2O: Sperm acrosome-associated protein 9
2P: Sperm acrosome-associated protein 9
2Q: Sperm acrosome-associated protein 9
2R: Sperm acrosome-associated protein 9
2S: Sperm acrosome-associated protein 9
2T: Sperm acrosome-associated protein 9
2U: Sperm acrosome-associated protein 9
2V: Sperm acrosome-associated protein 9
4b: Microtubule-associated protein 1S
4c: Microtubule-associated protein 1S
1e: Sperm acrosome-associated protein 9
1f: Sperm acrosome-associated protein 9
1g: Sperm acrosome-associated protein 9
1h: Sperm acrosome-associated protein 9
1i: Sperm acrosome-associated protein 9
1j: Sperm acrosome-associated protein 9
1k: Sperm acrosome-associated protein 9
J: Cilia and flagella associated protein 99
K: Cilia and flagella associated protein 99
5A: Cilia and flagella associated protein 99
5B: Ankyrin repeat and MYND domain-containing protein 1
5C: Leucine-rich repeat-containing protein 43


Theoretical massNumber of molelcules
Total (without water)28,871,569464
Polymers28,871,569464
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Spermatogenesis-associated protein ... , 2 types, 8 molecules baWXYZ3B3C

#1: Protein
Spermatogenesis-associated protein 4 / Spermatogenesis-related gene 2 protein / Testis and spermatogenesis cell-related protein 2 / Testis ...Spermatogenesis-related gene 2 protein / Testis and spermatogenesis cell-related protein 2 / Testis spermatocyte apoptosis-related gene 2 protein


Mass: 33629.938 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V1
#25: Protein Spermatogenesis-associated protein 17 / Spermatogenesis-related protein 11


Mass: 45579.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D552

+
Protein , 26 types, 382 molecules cdefgqrsvwFGMOPAbAdAfAhAjBbBdBfBhBjCbCdCfChCj...

#2: Protein
Kinesin-like protein KIF9


Mass: 90023.070 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WV04
#5: Protein Protein FAM228B


Mass: 27875.152 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q497Q6
#7: Protein MYCBP-associated protein / AMAM-1 / AMY-1-binding protein 1 / AMAP-1


Mass: 106611.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5SUV2
#10: Protein Coiled-coil domain containing 180


Mass: 196116.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: J3QNE4
#13: Protein Leucine rich repeat containing 72


Mass: 33759.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A1Y7VMI0
#14: Protein Deleted in lung and esophageal cancer 1


Mass: 194002.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q8C0
#17: Protein ...
Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#18: Protein ...
Tubulin alpha-3 chain / Alpha-tubulin 3/7 / Alpha-tubulin isotype M-alpha-3/7 / Tubulin alpha-3/alpha-7 chain


Mass: 50012.359 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P05214, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#20: Protein
Calmodulin-1


Mass: 16852.545 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0DP26
#22: Protein ...
Sperm acrosome-associated protein 9 / Acrosome and sperm tail protein / MAST


Mass: 19512.373 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TPM5
#23: Protein
Protein dpy-30 homolog / Dpy-30-like protein / Dpy-30L


Mass: 11224.607 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LT0
#24: Protein Unknown1


Mass: 4868.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#27: Protein MORN repeat containing 2


Mass: 16815.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A2I3BRK9
#28: Protein Unknown2


Mass: 8698.714 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#29: Protein Unknown3


Mass: 12188.016 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#30: Protein Unknown4


Mass: 4613.678 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#33: Protein Cilia and flagella-associated protein 47


Mass: 360784.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A0G2JEB6
#34: Protein
Hydrocephalus-inducing protein / Protein Hy-3


Mass: 582208.875 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q80W93
#35: Protein
Germ cell-less protein-like 1 / mGcl-1 / DP-interacting protein / DIP


Mass: 59722.980 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q920G9
#36: Protein Sperm flagellar protein 2 / Protein KPL2


Mass: 198248.422 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C9J3
#38: Protein
Putative aspartate aminotransferase, cytoplasmic 2 / Glutamate oxaloacetate transaminase 1-like protein 1 / Transaminase A-like protein 1


Mass: 45505.746 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TSV6, aspartate transaminase
#40: Protein G protein-coupled receptor kinase 3 / Beta-adrenergic receptor kinase 2 / Beta-ARK-2


Mass: 79774.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q3UYH7, beta-adrenergic-receptor kinase
#41: Protein Serine/threonine-protein phosphatase PP1-gamma catalytic subunit / PP-1G / Protein phosphatase 1C catalytic subunit


Mass: 37030.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P63087, protein-serine/threonine phosphatase
#42: Protein Microtubule-associated protein 1S / MAP-1S / BPY2-interacting protein 1 / Microtubule-associated protein 8


Mass: 103058.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C052
#44: Protein Ankyrin repeat and MYND domain-containing protein 1


Mass: 102124.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C0W1
#45: Protein Leucine-rich repeat-containing protein 43


Mass: 75038.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V0L5

-
Cilia- and flagella-associated protein ... , 8 types, 26 molecules hijknopmltuCDEHILA2A3A43K3L3M3N3O3P

#3: Protein Cilia- and flagella-associated protein 65 / Coiled-coil domain-containing protein 108


Mass: 209372.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V0B4
#4: Protein
Cilia- and flagella-associated protein 70 / Tetratricopeptide repeat protein 18 / TPR repeat protein 18


Mass: 128422.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: D3YVL2
#6: Protein Cilia- and flagella-associated protein 20 / Gene trap locus 3 protein


Mass: 22781.389 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BTU1
#9: Protein Cilia- and flagella-associated protein 74


Mass: 179171.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3UY96
#11: Protein Cilia- and flagella-associated protein 54


Mass: 354209.125 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C6S9
#12: Protein Cilia- and flagella-associated protein 221 / Primary ciliary dyskinesia protein 1


Mass: 97096.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A9Q751
#21: Protein Cilia- and flagella-associated protein 69


Mass: 106368.562 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BH53
#26: Protein
Cilia- and flagella-associated protein 119 / Coiled-coil domain-containing protein 189


Mass: 37912.082 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6NZQ0

-
Cilia and flagella associated protein ... , 2 types, 5 molecules ABJK5A

#8: Protein Cilia and flagella associated protein 46


Mass: 302995.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q2C0
#43: Protein Cilia and flagella associated protein 99


Mass: 76053.766 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A140LIX9

-
Sperm-associated antigen ... , 3 types, 36 molecules QRSTUVxyzAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAU...

#15: Protein
Sperm-associated antigen 16 protein / Pf20 protein homolog


Mass: 71570.812 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K450
#16: Protein Sperm-associated antigen 17 / Projection protein PF6 homolog


Mass: 263465.531 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5S003
#19: Protein ...
Sperm-associated antigen 6 / Axoneme central apparatus protein / Protein PF16 homolog


Mass: 55329.016 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9JLI7

-
Protein/peptide , 2 types, 2 molecules 3f3g

#31: Protein/peptide Unknown5


Mass: 1549.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#32: Protein/peptide Unknown6


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

-
Leucine-rich repeat and ... , 2 types, 5 molecules 4P4Q4O4X4Y

#37: Protein Leucine-rich repeat and guanylate kinase domain-containing protein


Mass: 93304.680 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D5S7
#39: Protein Leucine-rich repeat and death domain-containing protein 1


Mass: 97243.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C0R9

-
Details

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: all / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19000 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 1889 / Num. of volumes extracted: 105000

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