9NTM | pdb_00009ntm

SPEF1 bound to 14-pf microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1.

Legal, T.Joachimiak, E.Parra, M.Peng, W.Tam, A.Black, C.Guha, M.Nguyen, C.A.Ghanaeian, A.Valente-Paterno, M.Brouhard, G.Gaertig, J.Wloga, D.Bui, K.H.

(2025) Curr Biol 35: 3404

  • DOI: https://doi.org/10.1016/j.cub.2025.06.020
  • Primary Citation of Related Structures:  
    9NTM, 9NW3, 9OT2

  • PubMed Abstract: 

    Motile cilia are unique organelles with the ability to move autonomously. The force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet microtubules and a central pair (CP) with a distinct structure at the tip. In this study, we present a high-resolution structure of the CP in the ciliary tip of the ciliate Tetrahymena thermophila and identify several tip proteins that bind and form unique patterns on both microtubules of the tip CP. Two of those proteins that contain tubulin polymerization-promoting protein (TPPP)-like domains, TLP1 and TLP2, bind to high curvature regions of the microtubule. TLP2, which contains two TPPP-like domains, is an unusually long protein that wraps laterally around half a microtubule and forms the bridge between the two microtubules. Moreover, we found that the conserved protein SPEF1 binds to both microtubule seams and crosslinked the two microtubules. In vitro, human SPEF1 binds to the microtubule seam as visualized by cryoelectron tomography and subtomogram averaging. Single-molecule microtubule dynamics assays indicate that SPEF1 stabilizes microtubules in vitro. Together, these data show that the proteins in the tip CP maintain stable microtubule structures and play important roles in maintaining the integrity of the axoneme.


  • Organizational Affiliation
    • Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montreal, QC H3A 0C7, Canada.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sperm flagellar protein 1,G protein/GFP fusion proteinA [auth 1A],
B [auth 1B],
C [auth 1C],
D [auth 1D],
E [auth 1E]
393Homo sapiensRecombinant vesicular stomatitis Indiana virus rVSV-G/GFP
This entity is chimeric
Mutation(s): 0 
Gene Names: SPEF1C20orf28GGFP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4P9 (Homo sapiens)
Explore Q9Y4P9 
Go to UniProtKB:  Q9Y4P9
PHAROS:  Q9Y4P9
GTEx:  ENSG00000101222 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4P9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain445Bos taurusMutation(s): 0 
UniProt
Find proteins for A0A4W2DT89 (Bos indicus x Bos taurus)
Explore A0A4W2DT89 
Go to UniProtKB:  A0A4W2DT89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4W2DT89
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
AD [auth BB]
AF [auth FD]
AH [auth JF]
CE [auth DD]
CG [auth HF]
AD [auth BB],
AF [auth FD],
AH [auth JF],
CE [auth DD],
CG [auth HF],
CI [auth MB],
ED [auth BD],
EF [auth FF],
EH [auth KB],
GE [auth DF],
GG [auth IB],
GI [auth MD],
ID [auth BF],
IF [auth GB],
IH [auth KD],
KE [auth EB],
KG [auth ID],
KI [auth MF],
MD [auth CB],
MF [auth GD],
MH [auth KF],
OC [auth AB],
OE [auth ED],
OG [auth IF],
OI [auth NB],
QD [auth CD],
QF [auth GF],
QH [auth LB],
SC [auth AD],
SE [auth EF],
SG [auth JB],
SI [auth ND],
UD [auth CF],
UF [auth HB],
UH [auth LD],
WC [auth AF],
WE [auth FB],
WG [auth JD],
WI [auth NF],
YD [auth DB],
YF [auth HD],
YH [auth LF]
TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
BD [auth BC]
BF [auth FE]
BH [auth KA]
DE
DG [auth IA]
BD [auth BC],
BF [auth FE],
BH [auth KA],
DE,
DG [auth IA],
DI [auth MC],
FD [auth BE],
FF [auth GA],
FH [auth KC],
HE [auth EA],
HG [auth IC],
HI [auth ME],
JD [auth CA],
JF [auth GC],
JH [auth KE],
LC [auth AA],
LE [auth EC],
LG [auth IE],
LI [auth NA],
ND [auth CC],
NF [auth GE],
NH [auth LA],
PC [auth AC],
PE [auth EE],
PG [auth JA],
PI [auth NC],
RD [auth CE],
RF [auth HA],
RH [auth LC],
TC [auth AE],
TE [auth FA],
TG [auth JC],
TI [auth NE],
VD [auth DA],
VF [auth HC],
VH [auth LE],
XC [auth BA],
XE [auth FC],
XG [auth JE],
ZD [auth DC],
ZF [auth HE],
ZH [auth MA]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
BE [auth DD]
BG [auth HF]
BI [auth MB]
DD [auth BD]
DF [auth FF]
BE [auth DD],
BG [auth HF],
BI [auth MB],
DD [auth BD],
DF [auth FF],
DH [auth KB],
FE [auth DF],
FG [auth IB],
FI [auth MD],
HD [auth BF],
HF [auth GB],
HH [auth KD],
JE [auth EB],
JG [auth ID],
JI [auth MF],
LD [auth CB],
LF [auth GD],
LH [auth KF],
NC [auth AB],
NE [auth ED],
NG [auth IF],
NI [auth NB],
PD [auth CD],
PF [auth GF],
PH [auth LB],
RC [auth AD],
RE [auth EF],
RG [auth JB],
RI [auth ND],
TD [auth CF],
TF [auth HB],
TH [auth LD],
VC [auth AF],
VE [auth FB],
VG [auth JD],
VI [auth NF],
XD [auth DB],
XF [auth HD],
XH [auth LF],
ZC [auth BB],
ZE [auth FD],
ZG [auth JF]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth DC]
AG [auth HE]
AI [auth MA]
CD [auth BC]
CF [auth FE]
AE [auth DC],
AG [auth HE],
AI [auth MA],
CD [auth BC],
CF [auth FE],
CH [auth KA],
EE [auth DE],
EG [auth IA],
EI [auth MC],
GD [auth BE],
GF [auth GA],
GH [auth KC],
IE [auth EA],
IG [auth IC],
II [auth ME],
KD [auth CA],
KF [auth GC],
KH [auth KE],
MC [auth AA],
ME [auth EC],
MG [auth IE],
MI [auth NA],
OD [auth CC],
OF [auth GE],
OH [auth LA],
QC [auth AC],
QE [auth EE],
QG [auth JA],
QI [auth NC],
SD [auth CE],
SF [auth HA],
SH [auth LC],
UC [auth AE],
UE [auth FA],
UG [auth JC],
UI [auth NE],
WD [auth DA],
WF [auth HC],
WH [auth LE],
YC [auth BA],
YE [auth FC],
YG [auth JE]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.10 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaPJT-156354
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2022-04774

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-08-06
    Changes: Data collection, Database references