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- PDB-7ung: 48-nm repeat of the human respiratory doublet microtubule -

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Basic information

Entry
Database: PDB / ID: 7ung
Title48-nm repeat of the human respiratory doublet microtubule
Components
  • (Cilia- and flagella-associated protein ...) x 5
  • (EF-hand domain-containing family member ...) x 2
  • (Uncharacterized protein ...) x 2
  • EF-hand domain-containing protein 1
  • Enkurin
  • Isoform 2 of Cilia- and flagella-associated protein 77
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase 7
  • Parkin coregulated gene protein
  • Protein CFAP107
  • Protein CFAP141
  • Protein CFAP210
  • Protein CFAP276
  • Protein CFAP95
  • Protein FAM166B
  • Protein FAM166C
  • Protein FAM183A
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome-associated protein 9
  • Sperm-associated antigen 8
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
  • UPF0686 protein C11orf1
  • UPF0691 protein C9orf116
KeywordsSTRUCTURAL PROTEIN / cilia / microtubule / sperm / cell motility
Function / homology
Function and homology information


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 ...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 / protein polyglutamylation / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / sperm axoneme assembly / regulation of microtubule nucleation / positive regulation of feeding behavior / cilium-dependent cell motility / Transferases; Transferring phosphorus-containing groups / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / 9+2 motile cilium / regulation of store-operated calcium entry / intraciliary transport / acrosomal membrane / axoneme assembly / microtubule sliding / cilium movement / ciliary transition zone / left/right axis specification / Post-chaperonin tubulin folding pathway / calcium ion sensor activity / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / cilium organization / Carboxyterminal post-translational modifications of tubulin / forebrain morphogenesis / gamma-tubulin ring complex / manchette / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / positive regulation of cilium assembly / Formation of tubulin folding intermediates by CCT/TriC / glial cell differentiation / dentate gyrus development / neuron projection arborization / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / UTP biosynthetic process / CTP biosynthetic process / Kinesins / COPI-independent Golgi-to-ER retrograde traffic / determination of left/right symmetry / Assembly and cell surface presentation of NMDA receptors / response to L-glutamate / intermediate filament / pyramidal neuron differentiation / centrosome cycle / positive regulation of cell motility / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium / GTP biosynthetic process / smoothened signaling pathway / natural killer cell mediated cytotoxicity / AMP binding / ciliary base / regulation of synapse organization / receptor clustering / regulation of neuron projection development / startle response / motor behavior / cerebral cortex cell migration / response to tumor necrosis factor / Recycling pathway of L1 / locomotory exploration behavior / microtubule polymerization / MHC class I protein binding / regulation of cell division / microtubule organizing center / mitotic cytokinesis / cellular response to UV-C / axoneme / cilium assembly / glial cell projection / spermatid development / cellular response to unfolded protein / response to mechanical stimulus / single fertilization / sperm flagellum / alpha-tubulin binding / RHO GTPases activate IQGAPs / beta-tubulin binding / microtubule-based process
Similarity search - Function
Protein of unknown function DUF1143 / Cilia- and flagella-associated protein 68 / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / : / FAM183 family / FAM183A and FAM183B related / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain ...Protein of unknown function DUF1143 / Cilia- and flagella-associated protein 68 / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / : / FAM183 family / FAM183A and FAM183B related / 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 / 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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 90 / Ciliary microtubule inner protein 2C / Cilia- and flagella-associated protein 144 / Ciliary microtubule inner protein 2B / Piercer of microtubule wall 2 protein / Tubulin beta-4B chain / Cilia- and flagella- associated protein 210 / Piercer of microtubule wall 1 protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 90 / Ciliary microtubule inner protein 2C / Cilia- and flagella-associated protein 144 / Ciliary microtubule inner protein 2B / Piercer of microtubule wall 2 protein / Tubulin beta-4B chain / Cilia- and flagella- associated protein 210 / Piercer of microtubule wall 1 protein / EF-hand domain-containing family member C2 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 276 / Protein Flattop / Cilia- and flagella-associated protein 95 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 161 / Cilia- and flagella-associated protein 77 / Tubulin alpha-1A chain / Cilia- and flagella-associated protein 107 / Cilia- and flagella-associated protein 52 / EF-hand domain-containing family member B / Meiosis-specific nuclear structural protein 1 / Enkurin / Tektin-4 / Tektin-1 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 53 / Parkin coregulated gene protein / Sperm-associated antigen 8 / Tektin-3 / RIB43A-like with coiled-coils protein 2 / Cilia- and flagella-associated protein 68 / Tektin-2 / Cilia- and flagella-associated protein 45 / Nucleoside diphosphate kinase homolog 7 / Cilia- and flagella-associated protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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 TrustPostdoctoral 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 11, 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

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Assembly

Deposited unit
0: Protein CFAP95
1: EF-hand domain-containing family member B
2: EF-hand domain-containing family member B
3: Cilia- and flagella-associated protein 53
4: Cilia- and flagella-associated protein 53
5: Nucleoside diphosphate kinase 7
6: Nucleoside diphosphate kinase 7
7: Protein CFAP95
8: Protein CFAP107
9: Protein CFAP107
A: Protein CFAP141
A0: Tektin-1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AA: Tubulin alpha-1A chain
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
AG: Tubulin alpha-1A chain
AH: Tubulin beta-4B chain
AI: Tubulin alpha-1A chain
AJ: Tubulin beta-4B chain
AK: Tubulin alpha-1A chain
AL: Tubulin beta-4B chain
AM: Tubulin alpha-1A chain
B: Meiosis-specific nuclear structural protein 1
B0: Tektin-2
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
BA: Tubulin alpha-1A chain
BB: 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
BH: Tubulin beta-4B chain
BI: Tubulin alpha-1A chain
BJ: Tubulin beta-4B chain
BK: Tubulin alpha-1A chain
BL: Tubulin beta-4B chain
BM: Tubulin alpha-1A chain
C: Meiosis-specific nuclear structural protein 1
C0: Tektin-3
C1: Tektin-3
C2: Tektin-3
C3: Tektin-3
C4: Tektin-3
CA: Tubulin alpha-1A chain
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
CH: Tubulin beta-4B chain
CI: Tubulin alpha-1A chain
CJ: Tubulin beta-4B chain
CK: Tubulin alpha-1A chain
CL: Tubulin beta-4B chain
CM: Tubulin alpha-1A chain
D: Sperm-associated antigen 8
D0: Tektin-4
D1: Tektin-4
D2: Tektin-4
D3: Tektin-4
D5: Tektin-4
D6: Tektin-4
D7: Tektin-4
D8: Tektin-4
DA: Tubulin alpha-1A chain
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
DH: Tubulin beta-4B chain
DI: Tubulin alpha-1A chain
DJ: Tubulin beta-4B chain
DK: Tubulin alpha-1A chain
DL: Tubulin beta-4B chain
DM: Tubulin alpha-1A chain
E: Cilia- and flagella-associated protein 161
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
EH: Tubulin beta-4B chain
EI: Tubulin alpha-1A chain
EJ: Tubulin beta-4B chain
EK: Tubulin alpha-1A chain
EL: Tubulin beta-4B chain
EM: Tubulin alpha-1A chain
EN: Tubulin beta-4B chain
F: Cilia- and flagella-associated protein 161
F0: Sperm acrosome-associated protein 9
F1: Sperm acrosome-associated protein 9
F2: Sperm acrosome-associated protein 9
F3: Sperm acrosome-associated protein 9
F4: Sperm acrosome-associated protein 9
F5: Sperm acrosome-associated protein 9
F6: Sperm acrosome-associated protein 9
F7: Sperm acrosome-associated protein 9
F8: Sperm acrosome-associated protein 9
FB: Tubulin beta-4B chain
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
FI: Tubulin alpha-1A chain
FJ: Tubulin beta-4B chain
FK: Tubulin alpha-1A chain
FL: Tubulin beta-4B chain
FM: Tubulin alpha-1A chain
FN: Tubulin beta-4B chain
G: Uncharacterized protein C15orf65
G0: Sperm acrosome-associated protein 9
G1: Sperm acrosome-associated protein 9
G2: Sperm acrosome-associated protein 9
G3: Sperm acrosome-associated protein 9
G4: Sperm acrosome-associated protein 9
G5: Sperm acrosome-associated protein 9
G6: Sperm acrosome-associated protein 9
G7: Sperm acrosome-associated protein 9
G8: Sperm acrosome-associated protein 9
GB: Tubulin beta-4B chain
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
GI: Tubulin alpha-1A chain
GJ: Tubulin beta-4B chain
GK: Tubulin alpha-1A chain
GL: Tubulin beta-4B chain
GM: Tubulin alpha-1A chain
GN: Tubulin beta-4B chain
H: Protein FAM166B
H0: Sperm acrosome-associated protein 9
H1: Sperm acrosome-associated protein 9
H2: Sperm acrosome-associated protein 9
HB: Tubulin beta-4B chain
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
HI: Tubulin alpha-1A chain
HJ: Tubulin beta-4B chain
HK: Tubulin alpha-1A chain
HL: Tubulin beta-4B chain
HM: Tubulin alpha-1A chain
HN: Tubulin beta-4B chain
HO: Tubulin alpha-1A chain
I: Protein FAM166B
I1: UPF0686 protein C11orf1
IB: Tubulin beta-4B chain
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
II: Tubulin alpha-1A chain
IJ: Tubulin beta-4B chain
IK: Tubulin alpha-1A chain
IL: Tubulin beta-4B chain
IM: Tubulin alpha-1A chain
IN: Tubulin beta-4B chain
IO: Tubulin alpha-1A chain
J: Protein FAM166B
J1: Isoform 2 of Cilia- and flagella-associated protein 77
J2: Isoform 2 of Cilia- and flagella-associated protein 77
J3: Isoform 2 of Cilia- and flagella-associated protein 77
J4: Isoform 2 of Cilia- and flagella-associated protein 77
J5: Isoform 2 of Cilia- and flagella-associated protein 77
JB: Tubulin beta-4B chain
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
JH: Tubulin beta-4B chain
JI: Tubulin alpha-1A chain
JJ: Tubulin beta-4B chain
JK: Tubulin alpha-1A chain
JL: Tubulin beta-4B chain
JM: Tubulin alpha-1A chain
JN: Tubulin beta-4B chain
K: Protein FAM166B
K1: Protein FAM183A
KB: Tubulin beta-4B chain
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
KI: Tubulin alpha-1A chain
KJ: Tubulin beta-4B chain
KK: Tubulin alpha-1A chain
KL: Tubulin beta-4B chain
KM: Tubulin alpha-1A chain
KN: Tubulin beta-4B chain
KO: Tubulin alpha-1A chain
L: Protein FAM166B
L1: Uncharacterized protein C5orf49
L2: Uncharacterized protein C5orf49
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
LG: Tubulin alpha-1A chain
LH: Tubulin beta-4B chain
LI: Tubulin alpha-1A chain
LJ: Tubulin beta-4B chain
LK: Tubulin alpha-1A chain
LL: Tubulin beta-4B chain
LM: Tubulin alpha-1A chain
LN: Tubulin beta-4B chain
M: Protein FAM166B
M1: Protein FAM166C
M2: Protein FAM166C
M3: Protein FAM166C
M4: Protein FAM166C
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
MG: Tubulin alpha-1A chain
MH: Tubulin beta-4B chain
MI: Tubulin alpha-1A chain
MJ: Tubulin beta-4B chain
MK: Tubulin alpha-1A chain
ML: Tubulin beta-4B chain
MM: Tubulin alpha-1A chain
MN: Tubulin beta-4B chain
N: Protein FAM166B
NB: Tubulin beta-4B chain
NC: Tubulin alpha-1A chain
ND: Tubulin beta-4B chain
NE: Tubulin alpha-1A chain
NF: Tubulin beta-4B chain
NG: Tubulin alpha-1A chain
NH: Tubulin beta-4B chain
NI: Tubulin alpha-1A chain
NJ: Tubulin beta-4B chain
NK: Tubulin alpha-1A chain
NL: Tubulin beta-4B chain
NM: Tubulin alpha-1A chain
NN: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
OB: Tubulin beta-4B chain
OC: Tubulin alpha-1A chain
OD: Tubulin beta-4B chain
OE: Tubulin alpha-1A chain
OF: Tubulin beta-4B chain
OG: Tubulin alpha-1A chain
OH: Tubulin beta-4B chain
OI: Tubulin alpha-1A chain
OJ: Tubulin beta-4B chain
OK: Tubulin alpha-1A chain
OL: Tubulin beta-4B chain
OM: Tubulin alpha-1A chain
ON: Tubulin beta-4B chain
OO: Tubulin alpha-1A chain
P: RIB43A-like with coiled-coils protein 2
PC: Tubulin alpha-1A chain
PD: Tubulin beta-4B chain
PE: Tubulin alpha-1A chain
PF: Tubulin beta-4B chain
PG: Tubulin alpha-1A chain
PH: Tubulin beta-4B chain
PI: Tubulin alpha-1A chain
PJ: Tubulin beta-4B chain
PK: Tubulin alpha-1A chain
PL: Tubulin beta-4B chain
PM: Tubulin alpha-1A chain
PN: Tubulin beta-4B chain
PO: Tubulin alpha-1A chain
Q: RIB43A-like with coiled-coils protein 2
QC: Tubulin alpha-1A chain
QD: Tubulin beta-4B chain
QE: Tubulin alpha-1A chain
QF: Tubulin beta-4B chain
QG: Tubulin alpha-1A chain
QH: Tubulin beta-4B chain
QI: Tubulin alpha-1A chain
QJ: Tubulin beta-4B chain
QK: Tubulin alpha-1A chain
QL: Tubulin beta-4B chain
QM: Tubulin alpha-1A chain
QN: Tubulin beta-4B chain
QO: Tubulin alpha-1A chain
R: RIB43A-like with coiled-coils protein 2
RC: Tubulin alpha-1A chain
RD: Tubulin beta-4B chain
RE: Tubulin alpha-1A chain
RF: Tubulin beta-4B chain
RG: Tubulin alpha-1A chain
RH: Tubulin beta-4B chain
RI: Tubulin alpha-1A chain
RJ: Tubulin beta-4B chain
RK: Tubulin alpha-1A chain
RL: Tubulin beta-4B chain
RM: Tubulin alpha-1A chain
RN: Tubulin beta-4B chain
RO: Tubulin alpha-1A chain
S: RIB43A-like with coiled-coils protein 2
SD: Tubulin beta-4B chain
SE: Tubulin alpha-1A chain
SF: Tubulin beta-4B chain
SG: Tubulin alpha-1A chain
SH: Tubulin beta-4B chain
SI: Tubulin alpha-1A chain
SJ: Tubulin beta-4B chain
SK: Tubulin alpha-1A chain
SL: Tubulin beta-4B chain
SM: Tubulin alpha-1A chain
SN: Tubulin beta-4B chain
SO: Tubulin alpha-1A chain
T: EF-hand domain-containing protein 1
TD: Tubulin beta-4B chain
TE: Tubulin alpha-1A chain
TF: Tubulin beta-4B chain
TG: Tubulin alpha-1A chain
TH: Tubulin beta-4B chain
TI: Tubulin alpha-1A chain
TJ: Tubulin beta-4B chain
TK: Tubulin alpha-1A chain
TL: Tubulin beta-4B chain
TM: Tubulin alpha-1A chain
TN: Tubulin beta-4B chain
TO: Tubulin alpha-1A chain
TP: Tubulin beta-4B chain
U: EF-hand domain-containing protein 1
UD: Tubulin beta-4B chain
UE: Tubulin alpha-1A chain
UF: Tubulin beta-4B chain
UG: Tubulin alpha-1A chain
UH: Tubulin beta-4B chain
UI: Tubulin alpha-1A chain
UJ: Tubulin beta-4B chain
UK: Tubulin alpha-1A chain
UL: Tubulin beta-4B chain
UM: Tubulin alpha-1A chain
UN: Tubulin beta-4B chain
UO: Tubulin alpha-1A chain
UP: Tubulin beta-4B chain
V: EF-hand domain-containing protein 1
VD: Tubulin beta-4B chain
VE: Tubulin alpha-1A chain
VF: Tubulin beta-4B chain
VG: Tubulin alpha-1A chain
VH: Tubulin beta-4B chain
VI: Tubulin alpha-1A chain
VJ: Tubulin beta-4B chain
VK: Tubulin alpha-1A chain
VL: Tubulin beta-4B chain
VM: Tubulin alpha-1A chain
VN: Tubulin beta-4B chain
VO: Tubulin alpha-1A chain
VP: Tubulin beta-4B chain
W: EF-hand domain-containing family member C2
WD: Tubulin beta-4B chain
WE: Tubulin alpha-1A chain
WF: Tubulin beta-4B chain
WG: Tubulin alpha-1A chain
WH: Tubulin beta-4B chain
WI: Tubulin alpha-1A chain
WJ: Tubulin beta-4B chain
WK: Tubulin alpha-1A chain
WL: Tubulin beta-4B chain
WM: Tubulin alpha-1A chain
WN: Tubulin beta-4B chain
WO: Tubulin alpha-1A chain
WP: Tubulin beta-4B chain
X: EF-hand domain-containing family member C2
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
Y: EF-hand domain-containing family member C2
YB: Parkin coregulated gene protein
YC: Parkin coregulated gene protein
YD: Parkin coregulated gene protein
YE: Parkin coregulated gene protein
YF: Parkin coregulated gene protein
YG: Parkin coregulated gene protein
Z: EF-hand domain-containing family member C2
a: Cilia- and flagella-associated protein 45
b: Cilia- and flagella-associated protein 45
c: Cilia- and flagella-associated protein 45
d: Cilia- and flagella-associated protein 45
e: Cilia- and flagella-associated protein 52
f: Cilia- and flagella-associated protein 52
g: Cilia- and flagella-associated protein 52
h: Enkurin
i: Enkurin
j: Enkurin
k: Enkurin
l: Protein Flattop
m: Protein Flattop
n: Protein Flattop
o: Protein CFAP210
o1: Protein CFAP210
p: Protein CFAP210
q: Protein CFAP276
r: Protein CFAP276
s: Protein CFAP276
y: UPF0691 protein C9orf116
z: UPF0691 protein C9orf116
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,589,726886
Polymers20,440,341435
Non-polymers149,385451
Water00
1


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

-
Components

+
Protein , 26 types, 408 molecules 075689AA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCECG...

#1: Protein Protein CFAP95 / Cilia- and flagella-associated protein 95


Mass: 26483.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VTT2
#4: Protein Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7 / nm23-H7


Mass: 42545.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y5B8, nucleoside-diphosphate kinase
#5: Protein Protein CFAP107 / Cilia- and flagella-associated protein 107


Mass: 23105.348 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1D5
#6: Protein Protein CFAP141 / Cilia- and flagella-associated protein 141


Mass: 12151.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VU69
#7: Protein
Tektin-1


Mass: 48360.113 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q969V4
#8: Protein ...
Tubulin alpha-1A chain / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


Mass: 50188.441 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q71U36
#9: Protein ...
Tubulin beta-4B chain / Tubulin beta-2 chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68371
#10: Protein Meiosis-specific nuclear structural protein 1


Mass: 60687.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8NEH6
#11: Protein
Tektin-2 / Tektin-t / Testicular tektin / Testicular tektin B1-like protein / TEKTB1 / Tektin-B1


Mass: 49743.176 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UIF3
#12: Protein
Tektin-3


Mass: 56717.902 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BXF9
#13: Protein Sperm-associated antigen 8 / HSD-1 / Sperm membrane protein 1 / SMP-1 / Sperm membrane protein BS-84


Mass: 51187.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99932
#14: Protein
Tektin-4


Mass: 50725.926 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8WW24
#16: Protein ...
Sperm acrosome-associated protein 9


Mass: 25208.977 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96E40
#18: Protein
Protein FAM166B


Mass: 30610.637 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A8MTA8
#19: Protein UPF0686 protein C11orf1


Mass: 17806.924 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H5F2
#20: Protein
Isoform 2 of Cilia- and flagella-associated protein 77


Mass: 33037.211 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6ZQR2
#21: Protein Protein FAM183A


Mass: 16028.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A6NL82
#23: Protein
Protein FAM166C / Family with sequence similarity 166 member C


Mass: 23457.842 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A6NJV1
#24: Protein
RIB43A-like with coiled-coils protein 2


Mass: 45510.234 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H4K1
#25: Protein EF-hand domain-containing protein 1 / Myoclonin-1


Mass: 74084.102 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JVL4
#28: Protein
Parkin coregulated gene protein / Molecular chaperone/chaperonin-binding protein / PARK2 coregulated gene protein


Mass: 29352.184 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96M98
#31: Protein
Enkurin


Mass: 29510.348 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8TC29
#32: Protein Protein Flattop / Cilia- and flagella-associated protein 126


Mass: 19320.871 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5VTH2
#33: Protein Protein CFAP210 / Cilia- and flagella- associated protein 210 / Coiled-coil domain-containing protein 173


Mass: 66544.008 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q0VFZ6
#34: Protein Protein CFAP276 / Cilia- and flagella-associated protein 276


Mass: 19376.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5T5A4
#35: Protein UPF0691 protein C9orf116 / p53-induced expression in RB-null cells protein 1 / Pierce1


Mass: 15278.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5BN46

-
EF-hand domain-containing family member ... , 2 types, 6 molecules 12WXYZ

#2: Protein EF-hand domain-containing family member B


Mass: 93940.008 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N7U6
#26: Protein
EF-hand domain-containing family member C2


Mass: 87516.828 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q5JST6

-
Cilia- and flagella-associated protein ... , 5 types, 18 molecules 34EFXAXBXCXDXEXFXGabcdefg

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


Mass: 61960.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96M91
#15: Protein Cilia- and flagella-associated protein 161


Mass: 34339.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6P656
#27: Protein
Cilia- and flagella-associated protein 20 / Basal body up-regulated protein 22 / Transcription factor IIB


Mass: 22807.469 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y6A4
#29: Protein
Cilia- and flagella-associated protein 45 / Coiled-coil domain-containing protein 19 / Nasopharyngeal epithelium-specific protein 1


Mass: 65858.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UL16
#30: Protein Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16 / WD40-repeat protein up-regulated in HCC


Mass: 68379.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N1V2

-
Uncharacterized protein ... , 2 types, 3 molecules GL1L2

#17: Protein Uncharacterized protein C15orf65


Mass: 13778.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: H3BRN8
#22: Protein Uncharacterized protein C5orf49


Mass: 17019.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: A4QMS7

-
Non-polymers , 3 types, 451 molecules

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


Mass: 523.180 Da / Num. of mol.: 149 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#37: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 149 / Source method: obtained synthetically / Formula: Mg
#38: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 153 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Doublet microtubule and associated proteins / Type: COMPLEX / Entity ID: #1-#35 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE / Humidity: 100 %

-
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 magnification: 64000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameVersionCategory
2SerialEM3.7image acquisition
13PHENIX1.19model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208558 / Symmetry type: POINT

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