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- PDB-9e78: 48-nm repeat of the Leishmania tarentolae doublet microtubule -

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Basic information

Entry
Database: PDB / ID: 9.0E+78
Title48-nm repeat of the Leishmania tarentolae doublet microtubule
Components
  • (DMIP24) x 2
  • ArcMAP1
  • ArcMAP2
  • ArcMAP3
  • ArcMAP4
  • CCDC81
  • CFAP106A
  • CFAP106B
  • CFAP107
  • CFAP115
  • CFAP127
  • CFAP141
  • CFAP143
  • CFAP161
  • CFAP20
  • CFAP21
  • CFAP210
  • CFAP45
  • CFAP52
  • CFAP53
  • CFAP67A
  • CFAP67B
  • CFAP96
  • CFAP97
  • DC5
  • DC6
  • DMAP1
  • DMAP2
  • DMAP7
  • DMIP1
  • DMIP10
  • DMIP11
  • DMIP12
  • DMIP13
  • DMIP14
  • DMIP15
  • DMIP16
  • DMIP17
  • DMIP18
  • DMIP19
  • DMIP2
  • DMIP20
  • DMIP21
  • DMIP22
  • DMIP23
  • DMIP25
  • DMIP26
  • DMIP27
  • DMIP3
  • DMIP4
  • DMIP5
  • DMIP6
  • DMIP7
  • DMIP8
  • DMIP9
  • PACRGA
  • PACRGB
  • RIB43
  • RIB72A
  • RIB72B
  • RIB72C
  • RIB72D
  • Tubulin alpha chain
  • Tubulin beta chain
  • distal DC1
  • distal DC2
  • distal DC4
KeywordsSTRUCTURAL PROTEIN / flagella / parasite / axoneme / doublet microtubule
Function / homology
Function and homology information


outer dynein arm assembly / cilium-dependent cell motility / cilium movement / axonemal microtubule / ciliary tip / ciliary rootlet / ciliary plasm / motile cilium / cyclosporin A binding / mitotic cytokinesis ...outer dynein arm assembly / cilium-dependent cell motility / cilium movement / axonemal microtubule / ciliary tip / ciliary rootlet / ciliary plasm / motile cilium / cyclosporin A binding / mitotic cytokinesis / axoneme / cilium assembly / alpha-tubulin binding / microtubule-based process / cytoplasmic microtubule / Hsp70 protein binding / mitotic spindle organization / meiotic cell cycle / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Hsp90 protein binding / structural constituent of cytoskeleton / mitotic spindle / kinase activity / protein folding / microtubule / cytoskeleton / calmodulin binding / hydrolase activity / cilium / ciliary basal body / ribosome / GTPase activity / calcium ion binding / centrosome / GTP binding / metal ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
Cilia- and flagella-associated protein 97 / Uncharacterized 22kDa protein in aldolase locus / Hemingway/CFA97 / : / Hemingway/CFA97 / : / Echinoderm microtubule-associated protein first beta-propeller / CCDC81, HU domain 1 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 ...Cilia- and flagella-associated protein 97 / Uncharacterized 22kDa protein in aldolase locus / Hemingway/CFA97 / : / Hemingway/CFA97 / : / Echinoderm microtubule-associated protein first beta-propeller / CCDC81, HU domain 1 / Protein of unknown function DUF4586 / Outer dynein arm-docking complex subunit 3 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / Cilia-and flagella-associated protein 96 / CCDC81 eukaryotic HU domain 2 / Sperm-tail PG-rich repeat / Sperm-tail PG-rich repeat / : / : / 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 / EF hand / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / EF-hand domain pair / : / Mir domain superfamily / Quinoprotein alcohol dehydrogenase-like superfamily / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Alpha tubulin / Peptidyl-prolyl cis-trans isomerase domain superfamily / 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 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 / Armadillo-type fold / 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
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Enkurin domain-containing protein / Kinesin / EF-hand domain-containing protein / Uncharacterized protein / EF-hand domain-containing family member C2 / Cilia- and flagella-associated protein 45 / Tubulin alpha chain ...ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Enkurin domain-containing protein / Kinesin / EF-hand domain-containing protein / Uncharacterized protein / EF-hand domain-containing family member C2 / Cilia- and flagella-associated protein 45 / Tubulin alpha chain / Uncharacterized protein / HMG box domain-containing protein / EF-hand domain-containing protein / Trichohyalin-plectin-homology domain-containing protein / Uncharacterized protein / Cyclophilin, putative / Uncharacterized protein / Axonemal dynein intermediate chain protein / Calcyphosin / Enkurin domain-containing protein / CFA20 domain-containing protein / Cilia-and flagella-associated protein 96 / Flagellar protofilament ribbon protein-like protein / Cilia- and flagella-associated protein 53 / EF-hand domain-containing protein / Enkurin domain-containing protein / peptidylprolyl isomerase / DM10 domain-containing protein / Uncharacterized protein / Cilia- and flagella-associated protein 52 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / EF-hand domain-containing family member C2 / Uncharacterized protein / Calpain-like cysteine peptidase, putative / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Calcium-binding protein, putative / Sperm-tail PG-rich repeat / Calcium-binding protein, putative / DM10 domain-containing protein / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Nucleoside diphosphate kinase, putative / Uncharacterized protein / Uncharacterized protein / EF-hand domain-containing protein / Uncharacterized protein / CCDC81 HU domain-containing protein / Flagella associated protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Tubulin beta chain / Flagellar protofilament ribbon protein-like protein / Rib72 protein-like protein / EF-hand domain-containing protein
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDoran, M.H. / Ren, P. / Hoog, J.L. / Brown, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141109 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM143183 United States
National Science Foundation (NSF, United States)MCB-2434879 United States
CitationJournal: Science / Year: 2025
Title: Evolutionary adaptations of doublet microtubules in trypanosomatid parasites.
Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J ...Authors: Matthew H Doran / Qingwei Niu / Jianwei Zeng / Tom Beneke / James Smith / Peter Ren / Sophia Fochler / Adrian Coscia / Johanna L Höög / Shimi Meleppattu / Polina V Lishko / Richard J Wheeler / Eva Gluenz / Rui Zhang / Alan Brown /
Abstract: The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet ...The movement and pathogenicity of trypanosomatid species, the causative agents of trypanosomiasis and leishmaniasis, are dependent on a flagellum that contains an axoneme of dynein-bound doublet microtubules (DMTs). In this work, we present cryo-electron microscopy structures of DMTs from two trypanosomatid species, and , at resolutions up to 2.7 angstrom. The structures revealed 27 trypanosomatid-specific microtubule inner proteins, a specialized dynein-docking complex, and the presence of paralogous proteins that enable higher-order periodicities or proximal-distal patterning. Leveraging the genetic tractability of trypanosomatid species, we quantified the location and contribution of each structure-identified protein to swimming behavior. Our study shows that proper B-tubule closure is critical for flagellar motility, exemplifying how integrating structural identification with systematic gene deletion can dissect individual protein contributions to flagellar motility.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin beta chain
AA: Tubulin alpha chain
AB: Tubulin beta chain
AC: Tubulin alpha 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
AN: Tubulin beta chain
B: Tubulin beta chain
BA: Tubulin alpha chain
BB: Tubulin beta chain
BC: Tubulin alpha 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
BN: Tubulin beta chain
C: Tubulin alpha chain
CA: Tubulin beta chain
CB: Tubulin alpha chain
CC: Tubulin beta chain
CD: Tubulin alpha chain
CE: Tubulin beta chain
CF: Tubulin alpha chain
CG: Tubulin beta chain
CH: Tubulin alpha chain
CI: Tubulin beta chain
CJ: Tubulin alpha chain
CK: Tubulin beta chain
CL: Tubulin alpha chain
CM: Tubulin beta chain
D: Tubulin alpha chain
DA: Tubulin beta chain
DB: Tubulin alpha chain
DC: Tubulin beta chain
DD: Tubulin alpha chain
DE: Tubulin beta chain
DF: Tubulin alpha chain
DG: Tubulin beta chain
DH: Tubulin alpha chain
DI: Tubulin beta chain
DJ: Tubulin alpha chain
DK: Tubulin beta chain
DL: Tubulin alpha chain
DM: Tubulin beta chain
E: Tubulin beta 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
F: Tubulin beta chain
FA: Tubulin alpha chain
FB: Tubulin beta chain
FC: Tubulin alpha 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
G: Tubulin beta chain
GA: Tubulin alpha chain
GB: Tubulin beta chain
GC: Tubulin alpha 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
H: Tubulin beta chain
HA: Tubulin alpha chain
HB: Tubulin beta chain
HC: Tubulin alpha 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 alpha chain
I: Tubulin beta chain
IA: Tubulin alpha chain
IB: Tubulin beta chain
IC: Tubulin alpha 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
J: Tubulin alpha chain
JA: Tubulin beta chain
JB: Tubulin alpha chain
JC: Tubulin beta chain
JD: Tubulin alpha chain
JE: Tubulin beta chain
JF: Tubulin alpha chain
JG: Tubulin beta chain
JH: Tubulin alpha chain
JI: Tubulin beta chain
JJ: Tubulin alpha chain
JK: Tubulin beta chain
JL: Tubulin alpha chain
JM: Tubulin beta chain
JN: Tubulin alpha chain
K: Tubulin alpha chain
KA: Tubulin beta chain
KB: Tubulin alpha chain
KC: Tubulin beta chain
KD: Tubulin alpha chain
KE: Tubulin beta chain
KF: Tubulin alpha chain
KG: Tubulin beta chain
KH: Tubulin alpha chain
KI: Tubulin beta chain
KJ: Tubulin alpha chain
KK: Tubulin beta chain
KL: Tubulin alpha chain
KM: Tubulin beta chain
KN: Tubulin alpha chain
L: Tubulin alpha chain
LA: Tubulin beta chain
LB: Tubulin alpha chain
LC: Tubulin beta chain
LD: Tubulin alpha chain
LE: Tubulin beta chain
LF: Tubulin alpha chain
LG: Tubulin beta chain
LH: Tubulin alpha chain
LI: Tubulin beta chain
LJ: Tubulin alpha chain
LK: Tubulin beta chain
LL: Tubulin alpha chain
LM: Tubulin beta chain
LN: Tubulin alpha chain
LO: Tubulin beta chain
M: Tubulin beta chain
MA: Tubulin alpha chain
MB: Tubulin beta chain
MC: Tubulin alpha 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 beta chain
MM: Tubulin alpha chain
MN: Tubulin beta chain
N: Tubulin beta chain
NA: Tubulin alpha chain
NB: Tubulin beta chain
NC: Tubulin alpha 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 alpha chain
NL: Tubulin beta chain
NM: Tubulin alpha chain
O: Tubulin beta chain
OA: Tubulin alpha chain
OB: Tubulin beta chain
OC: Tubulin alpha 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 beta chain
OM: Tubulin alpha chain
P: Tubulin beta chain
PA: Tubulin alpha chain
PB: Tubulin beta chain
PC: Tubulin alpha 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 beta chain
PM: Tubulin alpha chain
Q: Tubulin alpha chain
QA: Tubulin beta chain
QB: Tubulin alpha chain
QC: Tubulin beta chain
QD: Tubulin alpha chain
QE: Tubulin beta chain
QF: Tubulin alpha chain
QG: Tubulin beta chain
QH: Tubulin alpha chain
QI: Tubulin beta chain
QJ: Tubulin alpha chain
QK: Tubulin beta chain
QL: Tubulin alpha chain
R: Tubulin alpha chain
RA: Tubulin beta chain
RB: Tubulin alpha chain
RC: Tubulin beta chain
RD: Tubulin alpha chain
RE: Tubulin beta chain
RF: Tubulin alpha chain
RG: Tubulin beta chain
RH: Tubulin alpha chain
RI: Tubulin beta chain
RJ: Tubulin alpha chain
RK: Tubulin beta chain
RL: Tubulin alpha chain
S: Tubulin beta chain
SA: Tubulin alpha chain
SB: Tubulin beta chain
SC: Tubulin alpha 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
T: Tubulin beta chain
TA: Tubulin alpha chain
TB: Tubulin beta chain
TC: Tubulin alpha 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
U: Tubulin beta chain
UA: Tubulin alpha chain
UB: Tubulin beta chain
UC: Tubulin alpha 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
V: Tubulin beta chain
VA: Tubulin alpha chain
VB: Tubulin beta chain
VC: Tubulin alpha 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 alpha chain
W: Tubulin beta chain
WA: Tubulin alpha chain
WB: Tubulin beta chain
WC: Tubulin alpha 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
WM: Tubulin alpha chain
X: CFAP20
XA: CFAP20
XB: CFAP20
XC: CFAP20
XD: CFAP20
XE: CFAP20
XF: CFAP20
XM: PACRGA
XN: PACRGB
XO: PACRGA
XP: PACRGB
XQ: PACRGA
XR: PACRGA
0A: CCDC81
0: CCDC81
0C: CFAP21
0D: CFAP21
0F: CFAP45
0G: CFAP45
0H: CFAP45
0I: CFAP45
0J: CFAP45
0L: CFAP52
0M: CFAP52
0N: CFAP52
0O: CFAP52
0R: CFAP53
0S: CFAP53
0U: CFAP67A
0W: CFAP67B
0Y: CFAP106A
0Z: CFAP106A
0a: CFAP106A
0c: CFAP106B
0d: CFAP106B
0f: CFAP107
0g: CFAP107
0l: CFAP115
0k: CFAP115
0m: CFAP127
0n: CFAP127
0o: CFAP127
0p: CFAP141
0r: CFAP143
0t: CFAP161
0u: CFAP161
0w: CFAP210
0x: CFAP210
0z: DMIP5
0v: CFAP210
1A: RIB43
1B: RIB43
1D: RIB43
1E: RIB43
1F: RIB43
1H: RIB72A
1I: RIB72A
1J: RIB72A
1K: RIB72A
1O: RIB72B
1Q: RIB72C
1S: RIB72D
1T: RIB72D
1U: DMIP1
1V: DMIP1
1X: DMIP1
1Y: DMIP1
1a: DMIP1
1b: DMIP1
1c: DMIP1
1d: DMIP1
1e: DMIP1
1g: DMIP1
1h: DMIP1
1j: DMIP2
1k: DMIP2
1l: DMIP2
1m: DMIP2
1o: DMIP3
1q: DMIP4
1r: DMIP4
1s: DMIP4
1t: DMIP4
1w: DMIP5
1x: DMIP5
1y: DMIP5
2B: DMIP6
2C: DMIP6
2F: DMIP7
2G: DMIP7
2H: DMIP7
2I: DMIP7
2L: DMIP8
2N: DMIP9
2O: DMIP9
2Q: DMIP10
2S: DMIP11
2U: DMIP12
2V: DMIP12
2X: DMIP13
2Z: DMIP14
2b: DMIP15
2c: DMIP15
2e: DMIP15
2f: DMIP15
2h: DMIP15
2i: DMIP15
2k: DMIP15
2l: DMIP15
2n: DMIP15
2o: DMIP15
2p: DMIP15
2r: DMIP16
2t: DMIP17
2v: DMIP18
2w: DMIP18
2y: DMIP19
2z: DMIP19
3B: DMIP20
3D: DMIP21
3I: DMIP22
3F: DMIP22
3G: DMIP22
3H: DMIP22
3M: DMIP22
3L: DMIP22
3P: DMIP23
3Q: DMIP23
3S: DMIP24
X1: DMIP24
3U: DMIP25
3X: DMIP26
3W: DMIP26
3Z: DMIP27
3a: DMIP27
4Y: DMIP27
3b: ArcMAP2
3d: ArcMAP1
3f: ArcMAP4
3g: ArcMAP4
3h: ArcMAP4
3i: ArcMAP4
3m: ArcMAP3
3o: CFAP96
3p: CFAP96
3r: CFAP97
3s: CFAP97
3t: CFAP97
3w: DMAP1
3x: DMAP1
4A: DMAP2
4B: DMAP2
4I: DMAP7
4O: CFAP96
4P: CFAP96
4V: DMIP1
4W: DMIP1
4a: CFAP96
4b: CFAP96
5B: distal DC1
5C: distal DC1
5D: distal DC1
5G: distal DC2
5H: distal DC2
5I: distal DC2
5K: distal DC4
5L: distal DC4
5O: DC5
5P: DC5
5S: DC6
5T: DC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,444,3411002
Polymers23,283,451491
Non-polymers160,889511
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 68 types, 491 molecules AABADAFAHAJALANBBBBDBFBHBJBLBNCACCCECGCICKCMDADCDEDGDIDKDM...

#1: Protein ...
Tubulin beta chain


Mass: 49830.824 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KW82
#2: Protein ...
Tubulin alpha chain


Mass: 49811.133 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KB30
#3: Protein
CFAP20 / Cilia- and flagella-associated protein 20


Mass: 24686.338 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KF93
#4: Protein
PACRGA


Mass: 34208.086 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KPE2
#5: Protein PACRGB


Mass: 34656.672 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KTZ9
#6: Protein CCDC81 / CCDC81 HU domain-containing protein


Mass: 29507.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KV25
#7: Protein CFAP21 / Flagella associated protein


Mass: 44077.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KVL2
#8: Protein
CFAP45 / Cilia- and flagella-associated protein 45


Mass: 57008.625 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KAI7
#9: Protein
CFAP52 / Cilia- and flagella-associated protein 52


Mass: 68550.664 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KKL8
#10: Protein CFAP53 / Cilia- and flagella-associated protein 53


Mass: 59240.293 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KGJ4
#11: Protein CFAP67A / Nucleoside diphosphate kinase / putative


Mass: 37086.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KU72
#12: Protein CFAP67B / DM10 domain-containing protein


Mass: 37469.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KTK7
#13: Protein CFAP106A / Enkurin domain-containing protein


Mass: 30917.178 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KH30
#14: Protein CFAP106B / Enkurin domain-containing protein


Mass: 41609.734 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KEG0
#15: Protein CFAP107


Mass: 30415.637 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KR52
#16: Protein CFAP115 / EF-hand domain-containing protein


Mass: 105846.070 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KGR6
#17: Protein CFAP127 / Meiosis-specific nuclear structural protein 1


Mass: 53012.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KTX6
#18: Protein CFAP141 / Enkurin domain-containing protein


Mass: 34252.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K783
#19: Protein CFAP143 / Kinesin


Mass: 34200.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K7P9
#20: Protein CFAP161 / Calpain-like cysteine peptidase / putative


Mass: 32782.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KPK8
#21: Protein CFAP210 / Trichohyalin-plectin-homology domain-containing protein


Mass: 62177.062 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KCR0
#22: Protein
DMIP5


Mass: 31664.545 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KN81
#23: Protein
RIB43 / Flagellar protofilament ribbon protein-like protein


Mass: 47051.590 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KFR4
#24: Protein
RIB72A / EF-hand domain-containing family member C2


Mass: 85152.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KJJ1
#25: Protein RIB72B / EF-hand domain-containing family member C2


Mass: 88754.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KP69
#26: Protein RIB72C / Rib72 protein-like protein


Mass: 84034.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KWZ4
#27: Protein RIB72D / EF-hand domain-containing protein


Mass: 96057.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KA97
#28: Protein
DMIP1


Mass: 29929.906 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#29: Protein
DMIP2


Mass: 24484.893 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KRE6
#30: Protein DMIP3 / HMG box domain-containing protein


Mass: 25872.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KC27
#31: Protein
DMIP4


Mass: 30468.156 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KUF4
#32: Protein DMIP6


Mass: 32116.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KN39
#33: Protein
DMIP7


Mass: 34757.172 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K9D8
#34: Protein DMIP8


Mass: 35479.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KRG7
#35: Protein DMIP9


Mass: 35540.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KD70
#36: Protein DMIP10 / EF-hand domain-containing protein


Mass: 37695.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640L0J2
#37: Protein DMIP11 / Cyclophilin / putative


Mass: 38623.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KD25
#38: Protein DMIP12


Mass: 39016.898 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KW55
#39: Protein DMIP13


Mass: 39095.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KNM8
#40: Protein DMIP14 / EF-hand domain-containing protein


Mass: 40517.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KC99
#41: Protein
DMIP15 / Flagellar protofilament ribbon protein-like protein


Mass: 42884.211 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KWI5
#42: Protein DMIP16


Mass: 44827.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KNX7
#43: Protein DMIP17 / EF-hand domain-containing protein


Mass: 38751.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640K8K7
#44: Protein DMIP18 / Calcium-binding protein / putative


Mass: 46871.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KTC5
#45: Protein DMIP19


Mass: 48416.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KK97
#46: Protein DMIP20 / Calcium-binding protein / putative


Mass: 49477.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KSW5
#47: Protein DMIP21 / Calcyphosin


Mass: 50008.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KE04
#48: Protein
DMIP22


Mass: 52058.332 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KQI0
#49: Protein DMIP23 / EF-hand domain-containing protein


Mass: 64778.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KUS5
#50: Protein DMIP24


Mass: 19253.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KNU0
#51: Protein DMIP24


Mass: 32014.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KNU0
#52: Protein DMIP25


Mass: 43062.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#53: Protein DMIP26


Mass: 42725.043 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KUX5
#54: Protein DMIP27


Mass: 47948.129 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KC26
#55: Protein ArcMAP2


Mass: 20891.818 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KST0
#56: Protein ArcMAP1


Mass: 30210.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KW15
#57: Protein
ArcMAP4


Mass: 23592.498 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KM13
#58: Protein ArcMAP3


Mass: 23019.268 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KVN0
#59: Protein
CFAP96 / Cilia-and flagella-associated protein 96


Mass: 33732.098 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KFJ0
#60: Protein CFAP97


Mass: 18835.117 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KU76
#61: Protein DMAP1


Mass: 32976.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KRL4
#62: Protein DMAP2


Mass: 52924.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KMR0
#63: Protein DMAP7 / Sperm-tail PG-rich repeat


Mass: 63279.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KT50
#64: Protein distal DC1 / Axonemal dynein intermediate chain protein


Mass: 75528.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KDI0
#65: Protein distal DC2


Mass: 70576.641 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#66: Protein distal DC4


Mass: 56663.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote)
#67: Protein DC5 / peptidylprolyl isomerase


Mass: 11938.780 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KHE0, peptidylprolyl isomerase
#68: Protein DC6


Mass: 19663.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Leishmania tarentolae (eukaryote) / References: UniProt: A0A640KCT8

-
Non-polymers , 6 types, 511 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 161 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#70: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 158 / Source method: obtained synthetically / Formula: Mg
#71: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 158 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#72: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Zn
#73: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#74: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 48-nm structure of the Leishmania tarentolae doublet microtubule
Type: COMPLEX / Entity ID: #1-#49, #52-#68 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Strain: P10 / Organelle: Flagella
Buffer solutionpH: 7.2
SpecimenConc.: 6.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: This sample consisted of freshly splayed Leishmania tarentolae axonemes.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 62.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 / Num. of real images: 37665

-
Processing

EM software
IDNameCategory
1crYOLOparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 533420 / Symmetry type: POINT
Atomic model buildingDetails: The initial model consisted of rigid body fit AlphaFold models and models build with ModelAngelo.
Source name: Other / Type: integrative model

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