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- PDB-7un1: 8-nm repeat of the human sperm tip singlet microtubule -

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Basic information

Entry
Database: PDB / ID: 7un1
Title8-nm repeat of the human sperm tip singlet microtubule
Components
  • Sperm acrosome-associated protein 9
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
KeywordsSTRUCTURAL PROTEIN / cilia / microtubule / sperm / cell motility
Function / homology
Function and homology information


axonemal microtubule doublet inner sheath / axoneme assembly / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis ...axonemal microtubule doublet inner sheath / axoneme assembly / Post-chaperonin tubulin folding pathway / organelle transport along microtubule / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis / glial cell differentiation / Intraflagellar transport / neuron projection arborization / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / flagellated sperm motility / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / centrosome cycle / Assembly and cell surface presentation of NMDA receptors / pyramidal neuron differentiation / motor behavior / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / smoothened signaling pathway / response to L-glutamate / regulation of synapse organization / ciliary base / startle response / MHC class I protein binding / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / sperm flagellum / response to tumor necrosis factor / RHO GTPases activate IQGAPs / microtubule-based process / intercellular bridge / Hedgehog 'off' state / response to mechanical stimulus / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule / COPI-mediated anterograde transport / condensed chromosome / homeostasis of number of cells within a tissue / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal vesicle / adult locomotory behavior / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / synapse organization / neuromuscular junction / visual learning / PKR-mediated signaling / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / neuron migration / Aggrephagy / calcium-dependent protein binding / mitotic spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / extracellular vesicle / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron apoptotic process / gene expression / microtubule / cytoskeleton / hydrolase activity / ciliary basal body / cilium / protein heterodimerization activity
Similarity search - Function
Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site ...Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / 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 / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta-4B chain / Tubulin alpha-1A chain / Sperm acrosome-associated protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å
AuthorsGui, M. / Croft, J.T. / Zabeo, D. / Acharya, V. / Kollman, J.M. / Burgoyne, T. / Hoog, J.L. / Brown, A.
Funding support United States, Sweden, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141109 United States
Swedish Research Council2015-05427 Sweden
Swedish Research Council2019-04004 Sweden
Smith Family Foundation United States
Pew Charitable Trusts United States
Charles A. King Trust Postdoctoral Research Fellowship United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.
Authors: Miao Gui / Jacob T Croft / Davide Zabeo / Vajradhar Acharya / Justin M Kollman / Thomas Burgoyne / Johanna L Höög / Alan Brown /
Abstract: The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins ...The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.
History
DepositionApr 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: 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_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sperm acrosome-associated protein 9
AB: Tubulin beta-4B chain
AC: Tubulin alpha-1A chain
AD: Tubulin beta-4B chain
AE: Tubulin alpha-1A chain
AF: Tubulin beta-4B chain
B: Sperm acrosome-associated protein 9
BA: Tubulin beta-4B chain
BC: Tubulin alpha-1A chain
BD: Tubulin beta-4B chain
BE: Tubulin alpha-1A chain
BF: Tubulin beta-4B chain
BG: Tubulin alpha-1A chain
C: Sperm acrosome-associated protein 9
CB: Tubulin beta-4B chain
CC: Tubulin alpha-1A chain
CD: Tubulin beta-4B chain
CE: Tubulin alpha-1A chain
CF: Tubulin beta-4B chain
CG: Tubulin alpha-1A chain
D: Sperm acrosome-associated protein 9
DB: Tubulin beta-4B chain
DC: Tubulin alpha-1A chain
DD: Tubulin beta-4B chain
DE: Tubulin alpha-1A chain
DF: Tubulin beta-4B chain
DG: Tubulin alpha-1A chain
E: Sperm acrosome-associated protein 9
EB: Tubulin beta-4B chain
EC: Tubulin alpha-1A chain
ED: Tubulin beta-4B chain
EE: Tubulin alpha-1A chain
EF: Tubulin beta-4B chain
EG: Tubulin alpha-1A chain
F: Sperm acrosome-associated protein 9
FC: Tubulin alpha-1A chain
FD: Tubulin beta-4B chain
FE: Tubulin alpha-1A chain
FF: Tubulin beta-4B chain
FG: Tubulin alpha-1A chain
FH: Tubulin beta-4B chain
G: Sperm acrosome-associated protein 9
GC: Tubulin alpha-1A chain
GD: Tubulin beta-4B chain
GE: Tubulin alpha-1A chain
GF: Tubulin beta-4B chain
GG: Tubulin alpha-1A chain
GH: Tubulin beta-4B chain
H: Sperm acrosome-associated protein 9
HC: Tubulin alpha-1A chain
HD: Tubulin beta-4B chain
HE: Tubulin alpha-1A chain
HF: Tubulin beta-4B chain
HG: Tubulin alpha-1A chain
HH: Tubulin beta-4B chain
I: Sperm acrosome-associated protein 9
IC: Tubulin alpha-1A chain
ID: Tubulin beta-4B chain
IE: Tubulin alpha-1A chain
IF: Tubulin beta-4B chain
IG: Tubulin alpha-1A chain
IH: Tubulin beta-4B chain
J: Sperm acrosome-associated protein 9
JC: Tubulin alpha-1A chain
JD: Tubulin beta-4B chain
JE: Tubulin alpha-1A chain
JF: Tubulin beta-4B chain
JG: Tubulin alpha-1A chain
K: Sperm acrosome-associated protein 9
KC: Tubulin alpha-1A chain
KD: Tubulin beta-4B chain
KE: Tubulin alpha-1A chain
KF: Tubulin beta-4B chain
KG: Tubulin alpha-1A chain
KH: Tubulin beta-4B chain
L: Sperm acrosome-associated protein 9
LA: Tubulin alpha-1A chain
LB: Tubulin beta-4B chain
LC: Tubulin alpha-1A chain
LD: Tubulin beta-4B chain
LE: Tubulin alpha-1A chain
LF: Tubulin beta-4B chain
M: Sperm acrosome-associated protein 9
MA: Tubulin alpha-1A chain
MB: Tubulin beta-4B chain
MC: Tubulin alpha-1A chain
MD: Tubulin beta-4B chain
ME: Tubulin alpha-1A chain
MF: Tubulin beta-4B chain
N: Sperm acrosome-associated protein 9
O: Sperm acrosome-associated protein 9
P: Sperm acrosome-associated protein 9
Q: Sperm acrosome-associated protein 9
R: Sperm acrosome-associated protein 9
S: Sperm acrosome-associated protein 9
T: Sperm acrosome-associated protein 9
U: Sperm acrosome-associated protein 9
V: Sperm acrosome-associated protein 9
W: Sperm acrosome-associated protein 9
X: Sperm acrosome-associated protein 9
d: Sperm acrosome-associated protein 9
e: Sperm acrosome-associated protein 9
f: Sperm acrosome-associated protein 9
g: Sperm acrosome-associated protein 9
h: Sperm acrosome-associated protein 9
i: Sperm acrosome-associated protein 9
j: Sperm acrosome-associated protein 9
k: Sperm acrosome-associated protein 9
l: Sperm acrosome-associated protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,672,060223
Polymers4,634,414109
Non-polymers37,646114
Water00
1


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

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Components

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Protein , 3 types, 109 molecules ABCDEFGHIJKLMNOPQRSTUVWXdefghi...

#1: Protein ...
Sperm acrosome-associated protein 9


Mass: 25208.977 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96E40
#2: Protein ...
Tubulin beta-4B chain / Tubulin beta-2 chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68371
#3: Protein ...
Tubulin alpha-1A chain / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


Mass: 50188.441 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q71U36

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Non-polymers , 3 types, 114 molecules

#4: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Singlet microtubule and associated SPACA9 / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Filaments
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: EMS Lacey Carbon
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
12RELION43D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21990 / Symmetry type: POINT

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