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- PDB-8snb: atomic model of sea urchin sperm doublet microtubule (48-nm perio... -

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Basic information

Entry
Database: PDB / ID: 8snb
Titleatomic model of sea urchin sperm doublet microtubule (48-nm periodicity)
Components
  • (Cilia- and flagella-associated protein ...) x 6
  • (Coiled-coil domain-containing protein ...) x 2
  • (Meiosis-specific nuclear structural protein ...) x 2
  • (Outer dense fiber protein ...) x 2
  • (Trichohyalin-plectin-homology domain-containing ...) x 2
  • ATP6V1FNB
  • C20Orf85
  • C4orf45
  • CFA20 domain-containing protein
  • CFAP107
  • CFAP144(FAM183A)
  • CFAP21
  • CFAP276
  • CFAP68(UPF0686, C11orf1)
  • CFAP90(C5orf49)
  • CFAP96(C4orf47)
  • EF-hand domain-containing family member C2
  • Enkurin domain-containing protein
  • FAM166C
  • Flagellar FliJ protein
  • Flagellar protofilament ribbon protein rib74
  • HeLo_like_N(LOC577943)
  • Nucleoside diphosphate kinaseNucleoside-diphosphate kinase
  • PACRG
  • Pierce1
  • Protein FAM166B
  • Protein phosphatase 1 regulatory subunit 32
  • RIB35
  • RIB43A-like with coiled-coils protein 2
  • SAXO3(LOC115918676)
  • SPATA45
  • SPATA48
  • Sperm-associated antigen 8
  • TEPP protein
  • Tektin A1
  • Tektin B1
  • Tektin C1
  • Testicular haploid expressed gene protein-like
  • Tex26(LOC100888047)
  • Tex33
  • Tex36(CFAP95, C9orf135)
  • Tex43
  • Tex49
  • Tex49_homologue(LOC580808)
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / sperm / doublet microtubule / DMT / microtubule inner protein / cilia / flagella / FAP / CFAP / MIP / MAP / cytoskeleton / tublin / sea urchin / TEX / Tektin / SAXO / ODF / SPATA / RIB
Function / homology
Function and homology information


cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / : / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process ...cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / : / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / regulation of neuron projection development / axoneme / alpha-tubulin binding / mitotic cytokinesis / cilium assembly / sperm flagellum / phosphatase binding / microtubule-based process / Hsp70 protein binding / mitotic spindle organization / acrosomal vesicle / ciliary basal body / Hsp90 protein binding / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / protein-folding chaperone binding / microtubule binding / spermatogenesis / vesicle / microtubule / cytoskeleton / calmodulin binding / hydrolase activity / neuron projection / phosphorylation / GTPase activity / centrosome / calcium ion binding / GTP binding / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coiled-coil domain-containing protein 81 / Testicular haploid expressed repeat / Uncharacterised protein family C20orf85 / Protein of unknown function DUF4562 / Testis-expressed protein 33 / Protein of unknown function DUF4586 / Hemingway/CFA97 / CFAP97 domain-containing protein 1/2 / Testicular haploid expressed gene protein-like / Hemingway/CFA97 ...Coiled-coil domain-containing protein 81 / Testicular haploid expressed repeat / Uncharacterised protein family C20orf85 / Protein of unknown function DUF4562 / Testis-expressed protein 33 / Protein of unknown function DUF4586 / Hemingway/CFA97 / CFAP97 domain-containing protein 1/2 / Testicular haploid expressed gene protein-like / Hemingway/CFA97 / Testicular haploid expressed repeat / Normal lung function maintenance, Low in Lung Cancer 1 protein / Domain of unknown function (DUF4562) / Domain of unknown function (DUF4586) / Testis-expressed sequence 33 protein family / Repeats in THEG (testicular haploid expressed gene) and several fly proteins. / CCDC81, HU domain 1 / Protein phosphatase 1 regulatory subunit 32 / Testis, prostate and placenta-expressed protein / Testis-expressed protein 49 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / Protein phosphatase 1 regulatory subunit 32 / CCDC81 eukaryotic HU domain 2 / Protein of unknown function DUF1143 / Sperm-tail PG-rich repeat / Protein of unknown function DUF4541 / Protein of unknown function DUF4513 / Protein of unknown function (DUF1143) / Sperm-tail PG-rich repeat / Domain of unknown function (DUF4513) / Domain of unknown function (DUF4541) / FAM183 family / Coiled-coil domain-containing protein 105 / 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 / Tektin / Cilia- and flagella-associated protein 276 / Tektin family / Protein of unknown function (DUF3695) / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 77 / Uncharacterised protein FAM166/UPF0605 / Protein of unknown function (DUF2475) / Nucleoside diphosphate kinase 7 / Meiosis-specific nuclear structural protein 1 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Protein Flattop / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / 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, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / 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 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 97 / Uncharacterized protein / Uncharacterized protein / Protein FAM166B / Uncharacterized protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 97 / Uncharacterized protein / Uncharacterized protein / Protein FAM166B / Uncharacterized protein / Flagellar FliJ protein / TEPP protein / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 126 / Cilia- and flagella-associated protein 45 / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Tubulin beta chain / Cilia- and flagella-associated protein 52 / Protein phosphatase 1 regulatory subunit 32 / Coiled-coil domain-containing protein 81 / Cilia- and flagella-associated protein 161 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Coiled-coil domain-containing protein 105 / Outer dense fiber protein 3 / RIB43A-like with coiled-coils protein 2 / Uncharacterized protein / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Trichohyalin-plectin-homology domain-containing protein / Uncharacterized protein / EF-hand domain-containing protein / Uncharacterized protein / Testicular haploid expressed gene protein-like / Enkurin domain-containing protein / Tubulin alpha chain / Uncharacterized protein / Uncharacterized protein / Trichohyalin-plectin-homology domain-containing protein / EF-hand domain-containing family member C2 / Uncharacterized protein / Uncharacterized protein / Outer dense fiber protein 3 / CFA20 domain-containing protein / Nucleoside diphosphate kinase / Tektin / Uncharacterized protein / Cilia- and flagella-associated protein 77 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Tektin / Flagellar protofilament ribbon protein rib74 / Tektin
Similarity search - Component
Biological speciesStrongylocentrotus purpuratus (purple sea urchin)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZeng, J. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 United States
CitationJournal: Cell / Year: 2023
Title: Structural specializations of the sperm tail.
Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...Authors: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai /
Abstract: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1A: CFAP96(C4orf47)
1B: CFAP96(C4orf47)
1E: Coiled-coil domain-containing protein 105
1F: Coiled-coil domain-containing protein 105
1G: Coiled-coil domain-containing protein 105
1H: Coiled-coil domain-containing protein 105
1K: Coiled-coil domain-containing protein 81
1L: Coiled-coil domain-containing protein 81
1M: Coiled-coil domain-containing protein 81
1P: FAM166C
1Q: FAM166C
1T: Protein FAM166B
1U: Protein FAM166B
1V: Protein FAM166B
1W: Protein FAM166B
1Y: CFAP144(FAM183A)
1a: Outer dense fiber protein 3
1b: Outer dense fiber protein 3
1d: Tex33
1f: C20Orf85
1g: C20Orf85
1i: ATP6V1FNB
1j: ATP6V1FNB
1l: Tex26(LOC100888047)
1m: Tex26(LOC100888047)
1o: Meiosis-specific nuclear structural protein 1
1p: Meiosis-specific nuclear structural protein 1
1q: Meiosis-specific nuclear structural protein 1
1r: Meiosis-specific nuclear structural protein 1
1v: Coiled-coil domain-containing protein 81
1w: Coiled-coil domain-containing protein 81
1x: Coiled-coil domain-containing protein 81
1y: Coiled-coil domain-containing protein 81
1z: Coiled-coil domain-containing protein 81
2A: Enkurin domain-containing protein
2B: Enkurin domain-containing protein
2C: Enkurin domain-containing protein
2D: Enkurin domain-containing protein
2G: CFAP107
2J: Cilia- and flagella-associated protein 126
2K: Cilia- and flagella-associated protein 126
2L: Cilia- and flagella-associated protein 126
2O: Flagellar FliJ protein
2R: Meiosis-specific nuclear structural protein 1
2S: Meiosis-specific nuclear structural protein 1
2V: Cilia- and flagella-associated protein 161
2W: Cilia- and flagella-associated protein 161
2a: Coiled-coil domain-containing protein 81
3A: CFA20 domain-containing protein
3B: CFA20 domain-containing protein
3C: CFA20 domain-containing protein
3D: CFA20 domain-containing protein
3E: CFA20 domain-containing protein
3F: CFA20 domain-containing protein
3G: CFA20 domain-containing protein
3J: CFAP21
3K: CFAP21
3N: Trichohyalin-plectin-homology domain-containing protein
3O: Trichohyalin-plectin-homology domain-containing protein
3R: CFAP276
3S: CFAP276
3T: CFAP276
3W: Cilia- and flagella-associated protein 45
3X: Cilia- and flagella-associated protein 45
3Y: Cilia- and flagella-associated protein 45
3Z: Cilia- and flagella-associated protein 45
4A: Cilia- and flagella-associated protein 52
4B: Cilia- and flagella-associated protein 52
4C: Cilia- and flagella-associated protein 52
4F: Trichohyalin-plectin-homology domain-containing protein
4G: Trichohyalin-plectin-homology domain-containing protein
4J: Nucleoside diphosphate kinase
4K: Nucleoside diphosphate kinase
4N: Cilia- and flagella-associated protein 77
4O: Cilia- and flagella-associated protein 77
4P: Cilia- and flagella-associated protein 77
4Q: Cilia- and flagella-associated protein 77
4T: Cilia- and flagella-associated protein 97
4U: Cilia- and flagella-associated protein 97
4V: Cilia- and flagella-associated protein 97
4Y: HeLo_like_N(LOC577943)
5A: Outer dense fiber protein 3
5B: Outer dense fiber protein 3
5E: Outer dense fiber protein 3
5F: Outer dense fiber protein 3
5G: Outer dense fiber protein 3
5H: Outer dense fiber protein 3
5I: Outer dense fiber protein 3
5J: Outer dense fiber protein 3
5K: Outer dense fiber protein 3
5L: Outer dense fiber protein 3
5M: Outer dense fiber protein 3
5N: Outer dense fiber protein 3
5O: Outer dense fiber protein 3
6A: PACRG
6B: PACRG
6C: PACRG
6D: PACRG
6E: PACRG
6F: PACRG
6I: Pierce1
6J: Pierce1
6M: Protein phosphatase 1 regulatory subunit 32
6N: Protein phosphatase 1 regulatory subunit 32
6Q: RIB35
6R: RIB35
6U: RIB43A-like with coiled-coils protein 2
6V: RIB43A-like with coiled-coils protein 2
6W: RIB43A-like with coiled-coils protein 2
6X: RIB43A-like with coiled-coils protein 2
7A: EF-hand domain-containing family member C2
7B: EF-hand domain-containing family member C2
7C: EF-hand domain-containing family member C2
7D: EF-hand domain-containing family member C2
7G: Flagellar protofilament ribbon protein rib74
7H: Flagellar protofilament ribbon protein rib74
7I: Flagellar protofilament ribbon protein rib74
7M: SAXO3(LOC115918676)
7N: SAXO3(LOC115918676)
7Q: TEPP protein
7R: TEPP protein
7U: SPATA48
7V: SPATA48
7Y: Sperm-associated antigen 8
7Z: Sperm-associated antigen 8
8A: Testicular haploid expressed gene protein-like
8D: Tektin A1
8E: Tektin A1
8F: Tektin A1
8G: Tektin A1
8J: Tektin B1
8K: Tektin B1
8L: Tektin B1
8M: Tektin B1
8N: Tektin B1
8Q: Tektin C1
8R: Tektin C1
8S: Tektin C1
8T: Tektin C1
8U: Tektin C1
8X: Tex43
8Y: Tex43
8Z: Tex43
9A: Tex36(CFAP95, C9orf135)
9D: CFAP90(C5orf49)
9G: Tex49
9J: Tex49_homologue(LOC580808)
9M: ATP6V1FNB
9N: ATP6V1FNB
9O: ATP6V1FNB
9R: CFAP68(UPF0686, C11orf1)
9T: SPATA45
9V: C4orf45
9W: C4orf45
9Y: Outer dense fiber protein 3
9Z: Outer dense fiber protein 3
AA: Tubulin alpha chain
AB: Tubulin alpha chain
AC: Tubulin beta chain
AD: Tubulin beta chain
AE: Tubulin alpha chain
AF: Tubulin beta chain
AG: Tubulin alpha chain
AH: Tubulin beta chain
AI: Tubulin alpha chain
AJ: Tubulin beta chain
AK: Tubulin alpha chain
AL: Tubulin beta chain
AM: Tubulin alpha chain
BA: Tubulin alpha chain
BB: Tubulin alpha chain
BC: Tubulin beta chain
BD: Tubulin beta chain
BE: Tubulin alpha chain
BF: Tubulin beta chain
BG: Tubulin alpha chain
BH: Tubulin beta chain
BI: Tubulin alpha chain
BJ: Tubulin beta chain
BK: Tubulin alpha chain
BL: Tubulin beta chain
BM: Tubulin alpha chain
CA: Tubulin alpha chain
CB: Tubulin alpha chain
CC: Tubulin beta chain
CD: Tubulin beta chain
CE: Tubulin alpha chain
CF: Tubulin beta chain
CG: Tubulin alpha chain
CH: Tubulin beta chain
CI: Tubulin alpha chain
CJ: Tubulin beta chain
CK: Tubulin alpha chain
CL: Tubulin beta chain
CM: Tubulin alpha chain
DA: Tubulin alpha chain
DB: Tubulin alpha chain
DC: Tubulin beta chain
DD: Tubulin beta chain
DE: Tubulin alpha chain
DF: Tubulin beta chain
DG: Tubulin alpha chain
DH: Tubulin beta chain
DI: Tubulin alpha chain
DJ: Tubulin beta chain
DK: Tubulin alpha chain
DL: Tubulin beta chain
DM: Tubulin alpha chain
EA: Tubulin alpha chain
EB: Tubulin beta chain
EC: Tubulin alpha chain
ED: Tubulin beta chain
EE: Tubulin alpha chain
EF: Tubulin beta chain
EG: Tubulin alpha chain
EH: Tubulin beta chain
EI: Tubulin alpha chain
EJ: Tubulin beta chain
EK: Tubulin alpha chain
EL: Tubulin beta chain
EM: Tubulin beta chain
FA: Tubulin alpha chain
FB: Tubulin alpha chain
FC: Tubulin beta chain
FD: Tubulin beta chain
FE: Tubulin alpha chain
FF: Tubulin beta chain
FG: Tubulin alpha chain
FH: Tubulin beta chain
FI: Tubulin alpha chain
FJ: Tubulin beta chain
FK: Tubulin alpha chain
FL: Tubulin beta chain
FM: Tubulin beta chain
GA: Tubulin alpha chain
GB: Tubulin alpha chain
GC: Tubulin beta chain
GD: Tubulin beta chain
GE: Tubulin alpha chain
GF: Tubulin beta chain
GG: Tubulin alpha chain
GH: Tubulin beta chain
GI: Tubulin alpha chain
GJ: Tubulin beta chain
GK: Tubulin alpha chain
GL: Tubulin beta chain
GM: Tubulin beta chain
HA: Tubulin alpha chain
HB: Tubulin alpha chain
HC: Tubulin beta chain
HD: Tubulin beta chain
HE: Tubulin alpha chain
HF: Tubulin beta chain
HG: Tubulin alpha chain
HH: Tubulin beta chain
HI: Tubulin alpha chain
HJ: Tubulin beta chain
HK: Tubulin alpha chain
HL: Tubulin beta chain
HM: Tubulin beta chain
IA: Tubulin alpha chain
IB: Tubulin alpha chain
IC: Tubulin beta chain
ID: Tubulin beta chain
IE: Tubulin alpha chain
IF: Tubulin beta chain
IG: Tubulin alpha chain
IH: Tubulin beta chain
II: Tubulin alpha chain
IJ: Tubulin beta chain
IK: Tubulin alpha chain
IL: Tubulin beta chain
IM: Tubulin alpha chain
JA: Tubulin alpha chain
JB: Tubulin alpha chain
JC: Tubulin beta chain
JD: Tubulin beta chain
JE: Tubulin alpha chain
JF: Tubulin beta chain
JG: Tubulin alpha chain
JH: Tubulin beta chain
JI: Tubulin alpha chain
JJ: Tubulin beta chain
JK: Tubulin alpha chain
JL: Tubulin beta chain
JM: Tubulin beta chain
KA: Tubulin alpha chain
KB: Tubulin alpha chain
KC: Tubulin beta chain
KD: Tubulin beta chain
KE: Tubulin alpha chain
KF: Tubulin beta chain
KG: Tubulin alpha chain
KH: Tubulin beta chain
KI: Tubulin alpha chain
KJ: Tubulin beta chain
KK: Tubulin alpha chain
KL: Tubulin beta chain
KM: Tubulin beta chain
LA: Tubulin alpha chain
LB: Tubulin alpha chain
LC: Tubulin beta chain
LD: Tubulin beta chain
LE: Tubulin alpha chain
LF: Tubulin beta chain
LG: Tubulin alpha chain
LH: Tubulin beta chain
LI: Tubulin alpha chain
LJ: Tubulin beta chain
LK: Tubulin alpha chain
LL: Tubulin beta chain
LM: Tubulin beta chain
MA: Tubulin alpha chain
MB: Tubulin alpha chain
MC: Tubulin beta chain
MD: Tubulin beta chain
ME: Tubulin alpha chain
MF: Tubulin beta chain
MG: Tubulin alpha chain
MH: Tubulin beta chain
MI: Tubulin alpha chain
MJ: Tubulin beta chain
MK: Tubulin alpha chain
ML: Tubulin alpha chain
MM: Tubulin beta chain
NA: Tubulin alpha chain
NB: Tubulin alpha chain
NC: Tubulin beta chain
ND: Tubulin beta chain
NE: Tubulin alpha chain
NF: Tubulin beta chain
NG: Tubulin alpha chain
NH: Tubulin beta chain
NI: Tubulin alpha chain
NJ: Tubulin beta chain
NK: Tubulin beta chain
NL: Tubulin alpha chain
NM: Tubulin beta chain
OA: Tubulin alpha chain
OB: Tubulin alpha chain
OC: Tubulin beta chain
OD: Tubulin beta chain
OE: Tubulin alpha chain
OF: Tubulin beta chain
OG: Tubulin alpha chain
OH: Tubulin beta chain
OI: Tubulin alpha chain
OJ: Tubulin beta chain
OK: Tubulin alpha chain
OL: Tubulin alpha chain
OM: Tubulin beta chain
PA: Tubulin alpha chain
PB: Tubulin alpha chain
PC: Tubulin beta chain
PD: Tubulin beta chain
PE: Tubulin alpha chain
PF: Tubulin beta chain
PG: Tubulin alpha chain
PH: Tubulin beta chain
PI: Tubulin alpha chain
PJ: Tubulin beta chain
PK: Tubulin alpha chain
PL: Tubulin alpha chain
PM: Tubulin beta chain
QA: Tubulin alpha chain
QB: Tubulin alpha chain
QC: Tubulin beta chain
QD: Tubulin beta chain
QE: Tubulin alpha chain
QF: Tubulin beta chain
QG: Tubulin alpha chain
QH: Tubulin beta chain
QI: Tubulin alpha chain
QJ: Tubulin beta chain
QK: Tubulin alpha chain
QL: Tubulin alpha chain
QM: Tubulin beta chain
RA: Tubulin alpha chain
RB: Tubulin alpha chain
RC: Tubulin beta chain
RD: Tubulin beta chain
RE: Tubulin alpha chain
RF: Tubulin beta chain
RG: Tubulin alpha chain
RH: Tubulin beta chain
RI: Tubulin alpha chain
RJ: Tubulin beta chain
RK: Tubulin alpha chain
RL: Tubulin alpha chain
RM: Tubulin beta chain
SA: Tubulin alpha chain
SB: Tubulin alpha chain
SC: Tubulin beta chain
SD: Tubulin beta chain
SE: Tubulin alpha chain
SF: Tubulin beta chain
SG: Tubulin alpha chain
SH: Tubulin beta chain
SI: Tubulin alpha chain
SJ: Tubulin beta chain
SK: Tubulin alpha chain
SL: Tubulin beta chain
SM: Tubulin beta chain
TA: Tubulin alpha chain
TB: Tubulin alpha chain
TC: Tubulin beta chain
TD: Tubulin beta chain
TE: Tubulin alpha chain
TF: Tubulin beta chain
TG: Tubulin alpha chain
TH: Tubulin beta chain
TI: Tubulin alpha chain
TJ: Tubulin beta chain
TK: Tubulin alpha chain
TL: Tubulin beta chain
TM: Tubulin beta chain
UA: Tubulin alpha chain
UB: Tubulin alpha chain
UC: Tubulin beta chain
UD: Tubulin beta chain
UE: Tubulin alpha chain
UF: Tubulin beta chain
UG: Tubulin alpha chain
UH: Tubulin beta chain
UI: Tubulin alpha chain
UJ: Tubulin beta chain
UK: Tubulin alpha chain
UL: Tubulin beta chain
UM: Tubulin beta chain
VA: Tubulin alpha chain
VB: Tubulin alpha chain
VC: Tubulin beta chain
VD: Tubulin beta chain
VE: Tubulin alpha chain
VF: Tubulin beta chain
VG: Tubulin alpha chain
VH: Tubulin beta chain
VI: Tubulin alpha chain
VJ: Tubulin beta chain
VK: Tubulin alpha chain
VL: Tubulin beta chain
VM: Tubulin beta chain
WA: Tubulin alpha chain
WB: Tubulin alpha chain
WC: Tubulin beta chain
WD: Tubulin beta chain
WE: Tubulin alpha chain
WF: Tubulin beta chain
WG: Tubulin alpha chain
WH: Tubulin beta chain
WI: Tubulin alpha chain
WJ: Tubulin beta chain
WK: Tubulin alpha chain
WL: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,164,643900
Polymers21,017,135454
Non-polymers147,508446
Water0
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 , 41 types, 395 molecules 1A1B1P1Q1T1U1V1W1Y1d1f1g1i1j9M9N9O1l1m2A2B2C2D2G2O3A3B3C3D3E...

#1: Protein CFAP96(C4orf47)


Mass: 33406.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7TH36
#4: Protein FAM166C


Mass: 23728.354 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHZ2
#5: Protein
Protein FAM166B


Mass: 48701.172 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7HL38
#6: Protein CFAP144(FAM183A)


Mass: 16431.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7GGZ7
#8: Protein Tex33


Mass: 40544.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NRA7
#9: Protein C20Orf85


Mass: 23738.551 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7HL88
#10: Protein
ATP6V1FNB


Mass: 21973.307 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7GIN5
#11: Protein Tex26(LOC100888047)


Mass: 19625.033 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7GGC2
#13: Protein
Enkurin domain-containing protein


Mass: 30122.543 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RFW1
#14: Protein CFAP107


Mass: 27343.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RF95
#16: Protein Flagellar FliJ protein


Mass: 14037.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7LW98
#19: Protein
CFA20 domain-containing protein


Mass: 22892.596 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7SUA7
#20: Protein CFAP21


Mass: 66165.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RFU1
#22: Protein CFAP276


Mass: 19508.793 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RBR2
#26: Protein Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase


Mass: 42906.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7SX53
#29: Protein HeLo_like_N(LOC577943)


Mass: 34673.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHW6
#31: Protein
PACRG


Mass: 26652.809 Da / Num. of mol.: 6 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7REU1
#32: Protein Pierce1


Mass: 13920.258 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7GRL1
#33: Protein Protein phosphatase 1 regulatory subunit 32


Mass: 52795.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7P181
#34: Protein RIB35


Mass: 34957.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7THB5
#35: Protein
RIB43A-like with coiled-coils protein 2


Mass: 45162.070 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RDQ5
#36: Protein
EF-hand domain-containing family member C2


Mass: 85763.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHU7
#37: Protein Flagellar protofilament ribbon protein rib74


Mass: 74127.648 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: Q6TXM2
#38: Protein SAXO3(LOC115918676)


Mass: 37032.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7THD0
#39: Protein TEPP protein


Mass: 21414.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7N5A5
#40: Protein SPATA48


Mass: 23009.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
#41: Protein Sperm-associated antigen 8 /


Mass: 23161.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7N7W6
#42: Protein Testicular haploid expressed gene protein-like


Mass: 30135.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RFU8
#43: Protein
Tektin A1


Mass: 53036.789 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: Q9U0E3
#44: Protein
Tektin B1


Mass: 49845.398 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7SXG5
#45: Protein
Tektin C1


Mass: 46691.652 Da / Num. of mol.: 5 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: Q26623
#46: Protein Tex43


Mass: 14191.163 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7G0R8
#47: Protein Tex36(CFAP95, C9orf135)


Mass: 25701.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RBC4
#48: Protein CFAP90(C5orf49)


Mass: 19712.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7SYJ8
#49: Protein Tex49


Mass: 17482.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RDT3
#50: Protein Tex49_homologue(LOC580808)


Mass: 20695.467 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RFU3
#51: Protein CFAP68(UPF0686, C11orf1)


Mass: 17679.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RBK2
#52: Protein SPATA45


Mass: 9870.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHE9
#53: Protein C4orf45


Mass: 32467.586 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHI6
#54: Protein ...
Tubulin alpha chain


Mass: 50184.496 Da / Num. of mol.: 148 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RGW6
#55: Protein ...
Tubulin beta chain


Mass: 50097.988 Da / Num. of mol.: 150 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NS69

-
Coiled-coil domain-containing protein ... , 2 types, 13 molecules 1E1F1G1H1K1L1M1v1w1x1y1z2a

#2: Protein
Coiled-coil domain-containing protein 105


Mass: 49945.527 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RBY5
#3: Protein
Coiled-coil domain-containing protein 81


Mass: 79691.844 Da / Num. of mol.: 9 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7PGM9

-
Outer dense fiber protein ... , 2 types, 17 molecules 1a1b5E5F5G5H5I5J5K5L5M5N5O5A5B9Y9Z

#7: Protein
Outer dense fiber protein 3


Mass: 27280.830 Da / Num. of mol.: 13 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RI41
#30: Protein
Outer dense fiber protein 3


Mass: 30624.738 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RDG4

-
Meiosis-specific nuclear structural protein ... , 2 types, 6 molecules 1o1p1q1r2R2S

#12: Protein
Meiosis-specific nuclear structural protein 1


Mass: 17323.562 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NFX5
#17: Protein Meiosis-specific nuclear structural protein 1


Mass: 61705.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7REB1

-
Cilia- and flagella-associated protein ... , 6 types, 19 molecules 2J2K2L2V2W3W3X3Y3Z4A4B4C4N4O4P4Q4T4U4V

#15: Protein Cilia- and flagella-associated protein 126


Mass: 15883.667 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NA77
#18: Protein Cilia- and flagella-associated protein 161


Mass: 32480.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RAY9
#23: Protein
Cilia- and flagella-associated protein 45


Mass: 64116.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NFL8
#24: Protein Cilia- and flagella-associated protein 52


Mass: 70455.148 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7NV05
#27: Protein
Cilia- and flagella-associated protein 77


Mass: 27690.299 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7TG06
#28: Protein Cilia- and flagella-associated protein 97


Mass: 27701.848 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7GHD6

-
Trichohyalin-plectin-homology domain-containing ... , 2 types, 4 molecules 3N3O4F4G

#21: Protein Trichohyalin-plectin-homology domain-containing protein


Mass: 65783.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7REW2
#25: Protein Trichohyalin-plectin-homology domain-containing protein


Mass: 62040.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Strongylocentrotus purpuratus (purple sea urchin)
References: UniProt: A0A7M7RHS4

-
Non-polymers , 3 types, 446 molecules

#56: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 148 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#57: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 148 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#58: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 150 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: sea urchin sperm doublet microtubule / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#55 / Source: NATURAL
Source (natural)Organism: Strongylocentrotus purpuratus (purple sea urchin)
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

SoftwareName: UCSF ChimeraX / Version: 1.5/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127673 / Symmetry type: POINT

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