[English] 日本語
Yorodumi
- PDB-7rro: Structure of the 48-nm repeat doublet microtubule from bovine tra... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rro
TitleStructure of the 48-nm repeat doublet microtubule from bovine tracheal cilia
Components
  • (Cilia and flagella associated protein ...) x 3
  • (Coiled-coil domain containing ...) x 2
  • (EF-hand domain ...) x 2
  • (Uncharacterized protein ...) x 2
  • Armadillo repeat containing 4
  • Chromosome 3 C1orf194 homolog
  • Cilia- and flagella-associated protein 20
  • EF-hand calcium-binding domain-containing protein 1
  • EFCAB6
  • EFHC2
  • Enkurin, TRPC channel interacting protein
  • Meiosis-specific nuclear structural protein 1
  • Methyl-CpG binding domain protein 1
  • Nucleoside diphosphate kinase 7
  • Outer dynein arm-docking complex subunit 3
  • PACRG protein
  • Pierce1
  • Pierce2
  • Protein C9orf135 homolog
  • Protein FAM166B
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm associated antigen 8
  • TEKTIP1
  • TTC25 protein
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tubulin alpha-1D chain
  • Tubulin beta-4B chain
KeywordsSTRUCTURAL PROTEIN / cilia / microtubule / dynein / motility
Function / homology
Function and homology information


regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / protein localization to motile cilium / manchette assembly ...regulation of cilium beat frequency / mucociliary clearance / outer dynein arm docking complex / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / protein localization to motile cilium / manchette assembly / epithelial cilium movement involved in determination of left/right asymmetry / inner dynein arm assembly / protein polyglutamylation / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / sperm axoneme assembly / cerebrospinal fluid circulation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / outer dynein arm assembly / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / sperm principal piece / RHO GTPases Activate Formins / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / 9+2 motile cilium / Transferases; Transferring phosphorus-containing groups / acrosomal membrane / regulation of cilium assembly / MHC class II antigen presentation / ciliary transition zone / cilium movement / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / axoneme assembly / axonemal microtubule / Aggrephagy / left/right axis specification / cilium organization / gamma-tubulin ring complex / flagellated sperm motility / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / ventricular system development / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / positive regulation of cilium assembly / CTP biosynthetic process / UTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / Neutrophil degranulation / microtubule organizing center / intermediate filament / nucleoside diphosphate kinase activity / regulation of neuron projection development / ciliary base / beta-tubulin binding / AMP binding / regulation of cell division / cerebral cortex cell migration / axoneme / centriolar satellite / mitotic cytokinesis / spermatid development / alpha-tubulin binding / cilium assembly / single fertilization / sperm flagellum / cellular response to UV-C / sperm midpiece / Hsp70 protein binding / centriole / 3'-5' exonuclease activity / mitotic spindle organization / ciliary basal body / acrosomal vesicle / G protein-coupled receptor binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / lung development / protein localization
Similarity search - Function
Outer dynein arm-docking complex subunit 4 / Outer dynein arm-docking complex subunit 3 / MalT-like TPR region / MalT-like TPR region / Tektin bundle interacting protein 1 / Tektin bundle interacting protein 1 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 ...Outer dynein arm-docking complex subunit 4 / Outer dynein arm-docking complex subunit 3 / MalT-like TPR region / MalT-like TPR region / Tektin bundle interacting protein 1 / Tektin bundle interacting protein 1 / 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) / Uncharacterised protein FAM166/UPF0605 / Protein Flattop / Ciliary microtubule inner protein 2B-like / 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 / 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 / Recoverin family / : / Nucleoside diphosphate kinase (NDPK)-like domain profile. / EF hand / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Tubulin-beta mRNA autoregulation signal. / TPR repeat region circular profile. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / TPR repeat profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tetratricopeptide repeats / 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 / Tetratricopeptide repeat / 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 / Armadillo-like helical / EF-hand domain pair / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 / Piercer of microtubule wall 2 protein / EF-hand domain-containing family member C2 / TTC25 protein / Parkin coregulated gene protein / Tektin-3 / Outer dynein arm-docking complex subunit 3 / Enkurin / Armadillo repeat containing 4 ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Piercer of microtubule wall 2 protein / EF-hand domain-containing family member C2 / TTC25 protein / Parkin coregulated gene protein / Tektin-3 / Outer dynein arm-docking complex subunit 3 / Enkurin / Armadillo repeat containing 4 / Cilia- and flagella-associated protein 276 / Cilia- and flagella- associated protein 210 / Cilia- and flagella-associated protein 52 / EF-hand domain-containing protein 1 / Sperm-associated antigen 8 / Meiosis-specific nuclear structural protein 1 / EF-hand domain-containing family member B / Coiled-coil domain containing 114 / Cilia- and flagella-associated protein 53 / Cilia- and flagella-associated protein 161 / Tubulin alpha-1D chain / Uncharacterized protein C19orf71 homolog / Tektin-2 / Cilia- and flagella-associated protein 107 / Tektin-4 / Protein FAM166B / Tektin-1 / EF-hand calcium-binding domain-containing protein 1 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 95 / RIB43A-like with coiled-coils protein 2 / Cilia- and flagella-associated protein 45 / Piercer of microtubule wall 1 protein / Tubulin beta-4B chain / Protein Flattop / Nucleoside diphosphate kinase homolog 7 / Cilia- and flagella-associated protein 20
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGui, M. / Anderson, J.R. / Botsch, J.J. / Meleppattu, S. / Singh, S.K. / Zhang, Q. / Brown, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell / Year: 2021
Title: De novo identification of mammalian ciliary motility proteins using cryo-EM.
Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James ...Authors: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James Thompson / Jane S Lucas / Colin D Bingle / Dominic P Norris / Sudipto Roy / Alan Brown /
Abstract: Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner ...Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility.
History
DepositionAug 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 24, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-24664
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: Protein C9orf135 homolog
1: EF-hand domain family member B
2: EF-hand domain family member B
3: Methyl-CpG binding domain protein 1
4: Methyl-CpG binding domain protein 1
5: Nucleoside diphosphate kinase 7
6: Nucleoside diphosphate kinase 7
7: Protein C9orf135 homolog
8: Uncharacterized protein C1orf158 homolog
9: Uncharacterized protein C1orf158 homolog
A: Meiosis-specific nuclear structural protein 1
A0: Tektin-1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AA: Tubulin alpha-1D chain
AB: Tubulin beta-4B chain
AC: Tubulin alpha-1D chain
AD: Tubulin beta-4B chain
AE: Tubulin alpha-1D chain
AF: Tubulin beta-4B chain
AG: Tubulin alpha-1D chain
AH: Tubulin beta-4B chain
AI: Tubulin alpha-1D chain
AJ: Tubulin beta-4B chain
AK: Tubulin alpha-1D chain
AL: Tubulin beta-4B chain
AM: Tubulin alpha-1D 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-1D chain
BB: Tubulin beta-4B chain
BC: Tubulin alpha-1D chain
BD: Tubulin beta-4B chain
BE: Tubulin alpha-1D chain
BF: Tubulin beta-4B chain
BG: Tubulin alpha-1D chain
BH: Tubulin beta-4B chain
BI: Tubulin alpha-1D chain
BJ: Tubulin beta-4B chain
BK: Tubulin alpha-1D chain
BL: Tubulin beta-4B chain
BM: Tubulin alpha-1D chain
C: Uncharacterized protein C1orf189 homolog
C0: Tektin-3
C1: Tektin-3
C2: Tektin-3
C3: Tektin-3
C4: Tektin-3
C5: Tektin-3
C6: Tektin-3
C7: Tektin-3
C8: Tektin-3
C9: Tektin-3
CA: Tubulin alpha-1D chain
CB: Tubulin beta-4B chain
CC: Tubulin alpha-1D chain
CD: Tubulin beta-4B chain
CE: Tubulin alpha-1D chain
CF: Tubulin beta-4B chain
CG: Tubulin alpha-1D chain
CH: Tubulin beta-4B chain
CI: Tubulin alpha-1D chain
CJ: Tubulin beta-4B chain
CK: Tubulin alpha-1D chain
CL: Tubulin beta-4B chain
CM: Tubulin alpha-1D 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
D9: Tektin-4
DA: Tubulin alpha-1D chain
DB: Tubulin beta-4B chain
DC: Tubulin alpha-1D chain
DD: Tubulin beta-4B chain
DE: Tubulin alpha-1D chain
DF: Tubulin beta-4B chain
DG: Tubulin alpha-1D chain
DH: Tubulin beta-4B chain
DI: Tubulin alpha-1D chain
DJ: Tubulin beta-4B chain
DK: Tubulin alpha-1D chain
DL: Tubulin beta-4B chain
DM: Tubulin alpha-1D chain
DN: Tubulin beta-4B chain
E: Cilia and flagella associated protein 161
E0: TEKTIP1
E1: TEKTIP1
E2: TEKTIP1
E3: TEKTIP1
EB: Tubulin beta-4B chain
EC: Tubulin alpha-1D chain
ED: Tubulin beta-4B chain
EE: Tubulin alpha-1D chain
EF: Tubulin beta-4B chain
EG: Tubulin alpha-1D chain
EH: Tubulin beta-4B chain
EI: Tubulin alpha-1D chain
EJ: Tubulin beta-4B chain
EK: Tubulin alpha-1D chain
EL: Tubulin beta-4B chain
EM: Tubulin alpha-1D chain
EN: Tubulin beta-4B chain
F: Cilia and flagella associated protein 161
F0: Tektin-3
F1: Tektin-3
F2: Tektin-3
F3: Tektin-3
F4: Tektin-3
FB: Tubulin beta-4B chain
FC: Tubulin alpha-1D chain
FD: Tubulin beta-4B chain
FE: Tubulin alpha-1D chain
FF: Tubulin beta-4B chain
FG: Tubulin alpha-1D chain
FH: Tubulin beta-4B chain
FI: Tubulin alpha-1D chain
FJ: Tubulin beta-4B chain
FK: Tubulin alpha-1D chain
FL: Tubulin beta-4B chain
FM: Tubulin alpha-1D chain
FN: Tubulin beta-4B chain
G: Pierce2
GB: Tubulin beta-4B chain
GC: Tubulin alpha-1D chain
GD: Tubulin beta-4B chain
GE: Tubulin alpha-1D chain
GF: Tubulin beta-4B chain
GG: Tubulin alpha-1D chain
GH: Tubulin beta-4B chain
GI: Tubulin alpha-1D chain
GJ: Tubulin beta-4B chain
GK: Tubulin alpha-1D chain
GL: Tubulin beta-4B chain
GM: Tubulin alpha-1D chain
GN: Tubulin beta-4B chain
H: Protein FAM166B
H1: Coiled-coil domain containing 114
H2: Coiled-coil domain containing 114
H3: Coiled-coil domain containing 114
H4: Outer dynein arm-docking complex subunit 3
H5: Outer dynein arm-docking complex subunit 3
H6: Outer dynein arm-docking complex subunit 3
H7: Armadillo repeat containing 4
H8: Armadillo repeat containing 4
H9: Armadillo repeat containing 4
HB: Tubulin beta-4B chain
HC: Tubulin alpha-1D chain
HD: Tubulin beta-4B chain
HE: Tubulin alpha-1D chain
HF: Tubulin beta-4B chain
HG: Tubulin alpha-1D chain
HH: Tubulin beta-4B chain
HI: Tubulin alpha-1D chain
HJ: Tubulin beta-4B chain
HK: Tubulin alpha-1D chain
HL: Tubulin beta-4B chain
HM: Tubulin alpha-1D chain
HN: Tubulin beta-4B chain
HO: Tubulin alpha-1D chain
I: Protein FAM166B
I1: TTC25 protein
I2: TTC25 protein
I3: EF-hand calcium-binding domain-containing protein 1
I4: EF-hand calcium-binding domain-containing protein 1
IB: Tubulin beta-4B chain
IC: Tubulin alpha-1D chain
ID: Tubulin beta-4B chain
IE: Tubulin alpha-1D chain
IF: Tubulin beta-4B chain
IG: Tubulin alpha-1D chain
IH: Tubulin beta-4B chain
II: Tubulin alpha-1D chain
IJ: Tubulin beta-4B chain
IK: Tubulin alpha-1D chain
IL: Tubulin beta-4B chain
IM: Tubulin alpha-1D chain
IN: Tubulin beta-4B chain
IO: Tubulin alpha-1D chain
J: Protein FAM166B
JB: Tubulin beta-4B chain
JC: Tubulin alpha-1D chain
JD: Tubulin beta-4B chain
JE: Tubulin alpha-1D chain
JF: Tubulin beta-4B chain
JG: Tubulin alpha-1D chain
JH: Tubulin beta-4B chain
JI: Tubulin alpha-1D chain
JJ: Tubulin beta-4B chain
JK: Tubulin alpha-1D chain
JL: Tubulin beta-4B chain
JM: Tubulin alpha-1D chain
JN: Tubulin beta-4B chain
K: Protein FAM166B
KB: Tubulin beta-4B chain
KC: Tubulin alpha-1D chain
KD: Tubulin beta-4B chain
KE: Tubulin alpha-1D chain
KF: Tubulin beta-4B chain
KG: Tubulin alpha-1D chain
KH: Tubulin beta-4B chain
KI: Tubulin alpha-1D chain
KJ: Tubulin beta-4B chain
KK: Tubulin alpha-1D chain
KL: Tubulin beta-4B chain
KM: Tubulin alpha-1D chain
KN: Tubulin beta-4B chain
KO: Tubulin alpha-1D chain
L: Protein FAM166B
LB: Tubulin beta-4B chain
LC: Tubulin alpha-1D chain
LD: Tubulin beta-4B chain
LE: Tubulin alpha-1D chain
LF: Tubulin beta-4B chain
LG: Tubulin alpha-1D chain
LH: Tubulin beta-4B chain
LI: Tubulin alpha-1D chain
LJ: Tubulin beta-4B chain
LK: Tubulin alpha-1D chain
LL: Tubulin beta-4B chain
LM: Tubulin alpha-1D chain
LN: Tubulin beta-4B chain
M: Protein FAM166B
MB: Tubulin beta-4B chain
MC: Tubulin alpha-1D chain
MD: Tubulin beta-4B chain
ME: Tubulin alpha-1D chain
MF: Tubulin beta-4B chain
MG: Tubulin alpha-1D chain
MH: Tubulin beta-4B chain
MI: Tubulin alpha-1D chain
MJ: Tubulin beta-4B chain
MK: Tubulin alpha-1D chain
ML: Tubulin beta-4B chain
MM: Tubulin alpha-1D chain
MN: Tubulin beta-4B chain
N: Protein FAM166B
N0: Tubulin beta-4B chain
NA: Tubulin alpha-1D chain
NB: Tubulin beta-4B chain
NC: Tubulin alpha-1D chain
ND: Tubulin beta-4B chain
NE: Tubulin alpha-1D chain
NF: Tubulin beta-4B chain
NG: Tubulin alpha-1D chain
NH: Tubulin beta-4B chain
NI: Tubulin alpha-1D chain
NJ: Tubulin beta-4B chain
NK: Tubulin alpha-1D chain
NL: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
O0: Tubulin beta-4B chain
OA: Tubulin alpha-1D chain
OB: Tubulin beta-4B chain
OC: Tubulin alpha-1D chain
OD: Tubulin beta-4B chain
OE: Tubulin alpha-1D chain
OF: Tubulin beta-4B chain
OG: Tubulin alpha-1D chain
OH: Tubulin beta-4B chain
OI: Tubulin alpha-1D chain
OJ: Tubulin beta-4B chain
OK: Tubulin alpha-1D chain
OL: Tubulin beta-4B chain
P: RIB43A-like with coiled-coils protein 2
PA: Tubulin alpha-1D chain
PB: Tubulin beta-4B chain
PC: Tubulin alpha-1D chain
PD: Tubulin beta-4B chain
PE: Tubulin alpha-1D chain
PF: Tubulin beta-4B chain
PG: Tubulin alpha-1D chain
PH: Tubulin beta-4B chain
PI: Tubulin alpha-1D chain
PJ: Tubulin beta-4B chain
PK: Tubulin alpha-1D chain
PL: Tubulin beta-4B chain
PM: Tubulin alpha-1D chain
Q: RIB43A-like with coiled-coils protein 2
QA: Tubulin alpha-1D chain
QB: Tubulin beta-4B chain
QC: Tubulin alpha-1D chain
QD: Tubulin beta-4B chain
QE: Tubulin alpha-1D chain
QF: Tubulin beta-4B chain
QG: Tubulin alpha-1D chain
QH: Tubulin beta-4B chain
QI: Tubulin alpha-1D chain
QJ: Tubulin beta-4B chain
QK: Tubulin alpha-1D chain
QL: Tubulin beta-4B chain
QM: Tubulin alpha-1D chain
R: RIB43A-like with coiled-coils protein 2
RA: Tubulin alpha-1D chain
RB: Tubulin beta-4B chain
RC: Tubulin alpha-1D chain
RD: Tubulin beta-4B chain
RE: Tubulin alpha-1D chain
RF: Tubulin beta-4B chain
RG: Tubulin alpha-1D chain
RH: Tubulin beta-4B chain
RI: Tubulin alpha-1D chain
RJ: Tubulin beta-4B chain
RK: Tubulin alpha-1D chain
RL: Tubulin beta-4B chain
RM: Tubulin alpha-1D chain
S: RIB43A-like with coiled-coils protein 2
SA: Tubulin alpha-1D chain
SB: Tubulin beta-4B chain
SC: Tubulin alpha-1D chain
SD: Tubulin beta-4B chain
SE: Tubulin alpha-1D chain
SF: Tubulin beta-4B chain
SG: Tubulin alpha-1D chain
SH: Tubulin beta-4B chain
SI: Tubulin alpha-1D chain
SJ: Tubulin beta-4B chain
SK: Tubulin alpha-1D chain
SL: Tubulin beta-4B chain
SM: Tubulin alpha-1D chain
T: EF-hand domain containing 1
TB: Tubulin beta-4B chain
TC: Tubulin alpha-1D chain
TD: Tubulin beta-4B chain
TE: Tubulin alpha-1D chain
TF: Tubulin beta-4B chain
TG: Tubulin alpha-1D chain
TH: Tubulin beta-4B chain
TI: Tubulin alpha-1D chain
TJ: Tubulin beta-4B chain
TK: Tubulin alpha-1D chain
TL: Tubulin beta-4B chain
TM: Tubulin alpha-1D chain
U: EF-hand domain containing 1
UB: Tubulin beta-4B chain
UC: Tubulin alpha-1D chain
UD: Tubulin beta-4B chain
UE: Tubulin alpha-1D chain
UF: Tubulin beta-4B chain
UG: Tubulin alpha-1D chain
UH: Tubulin beta-4B chain
UI: Tubulin alpha-1D chain
UJ: Tubulin beta-4B chain
UK: Tubulin alpha-1D chain
UL: Tubulin beta-4B chain
UM: Tubulin alpha-1D chain
UN: Tubulin beta-4B chain
V: EF-hand domain containing 1
VB: Tubulin beta-4B chain
VC: Tubulin alpha-1D chain
VD: Tubulin beta-4B chain
VE: Tubulin alpha-1D chain
VF: Tubulin beta-4B chain
VG: Tubulin alpha-1D chain
VH: Tubulin beta-4B chain
VI: Tubulin alpha-1D chain
VJ: Tubulin beta-4B chain
VK: Tubulin alpha-1D chain
VL: Tubulin beta-4B chain
VM: Tubulin alpha-1D chain
VN: Tubulin beta-4B chain
W: EFHC2
WB: Tubulin beta-4B chain
WC: Tubulin alpha-1D chain
WD: Tubulin beta-4B chain
WE: Tubulin alpha-1D chain
WF: Tubulin beta-4B chain
WG: Tubulin alpha-1D chain
WH: Tubulin beta-4B chain
WI: Tubulin alpha-1D chain
WJ: Tubulin beta-4B chain
WK: Tubulin alpha-1D chain
WL: Tubulin beta-4B chain
WM: Tubulin alpha-1D chain
WN: Tubulin beta-4B chain
X: EFHC2
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: EFHC2
YB: PACRG protein
YC: PACRG protein
YD: PACRG protein
YE: PACRG protein
YF: PACRG protein
YG: PACRG protein
Z: EFHC2
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, TRPC channel interacting protein
i: Enkurin, TRPC channel interacting protein
j: Enkurin, TRPC channel interacting protein
k: Enkurin, TRPC channel interacting protein
l: Protein Flattop
m: Protein Flattop
n: Protein Flattop
o: Coiled-coil domain containing 173
p: Coiled-coil domain containing 173
q: Chromosome 3 C1orf194 homolog
r: Chromosome 3 C1orf194 homolog
s: Chromosome 3 C1orf194 homolog
t: EFCAB6
y: Pierce1
z: Pierce1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,608,302880
Polymers21,458,917429
Non-polymers149,385451
Water00
1


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

-
Components

+
Protein , 27 types, 407 molecules 073456ABA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCE...

#1: Protein Protein C9orf135 homolog


Mass: 26661.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32L77
#3: Protein Methyl-CpG binding domain protein 1


Mass: 62138.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1N7G5
#4: Protein Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7


Mass: 42650.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q5E9Y9, nucleoside-diphosphate kinase
#6: Protein Meiosis-specific nuclear structural protein 1


Mass: 60572.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MH18
#7: Protein
Tektin-1


Mass: 48798.375 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32KZ9
#8: Protein ...
Tubulin alpha-1D chain


Mass: 50335.594 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2HJ86
#9: Protein ...
Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3MHM5
#10: Protein
Tektin-2


Mass: 49962.656 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2T9Q6
#12: Protein
Tektin-3


Mass: 56760.910 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A6H782
#13: Protein Sperm associated antigen 8


Mass: 51604.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BNS6
#14: Protein
Tektin-4


Mass: 52025.488 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA38
#16: Protein
TEKTIP1


Mass: 24533.445 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2M2T2
#17: Protein Pierce2


Mass: 13784.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1LFK7
#18: Protein
Protein FAM166B


Mass: 30551.627 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TBR5
#20: Protein Outer dynein arm-docking complex subunit 3 / Coiled-coil domain-containing protein 151


Mass: 72163.984 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A7MBH5
#21: Protein Armadillo repeat containing 4


Mass: 116017.070 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1B8W3
#22: Protein TTC25 protein / Tetratricopeptide repeat domain 25


Mass: 78492.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A5PK42
#23: Protein EF-hand calcium-binding domain-containing protein 1 / Calaxin


Mass: 24667.131 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32L26
#24: Protein
RIB43A-like with coiled-coils protein 2


Mass: 44773.418 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32LJ7
#26: Protein
EFHC2


Mass: 85566.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A0A3Q1N1R0
#27: Protein
Cilia- and flagella-associated protein 20


Mass: 22781.389 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B857
#28: Protein
PACRG protein / Parkin coregulated


Mass: 29323.059 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: A5PK71
#31: Protein
Enkurin, TRPC channel interacting protein


Mass: 30215.129 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1B836
#32: Protein Protein Flattop / Cilia- and flagella-associated protein 126


Mass: 21214.035 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3SZT6
#34: Protein Chromosome 3 C1orf194 homolog


Mass: 19387.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1B9I5
#35: Protein EFCAB6


Mass: 172993.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle)
#36: Protein Pierce1


Mass: 15673.458 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32P67

-
EF-hand domain ... , 2 types, 5 molecules 12TUV

#2: Protein EF-hand domain family member B


Mass: 97960.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1MMV1
#25: Protein EF-hand domain containing 1


Mass: 74125.344 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BKH1

-
Uncharacterized protein ... , 2 types, 3 molecules 89C

#5: Protein Uncharacterized protein C1orf158 homolog


Mass: 23271.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2TA11
#11: Protein Uncharacterized protein C1orf189 homolog


Mass: 12361.437 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32L75

-
Cilia and flagella associated protein ... , 3 types, 9 molecules EFabcdefg

#15: Protein Cilia and flagella associated protein 161 / CFAP161


Mass: 36519.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F6RJC2
#29: Protein
Cilia and flagella associated protein 45 / Coiled-coil domain containing 19


Mass: 65800.328 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32LN4
#30: Protein Cilia and flagella associated protein 52


Mass: 68719.602 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BKF9

-
Coiled-coil domain containing ... , 2 types, 5 molecules H1H2H3op

#19: Protein Coiled-coil domain containing 114


Mass: 77675.969 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F1N2N9
#33: Protein Coiled-coil domain containing 173


Mass: 65437.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: E1BJL9

-
Non-polymers , 3 types, 451 molecules

#37: 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
#38: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 149 / Source method: obtained synthetically / Formula: Mg
#39: 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 / Type: COMPLEX / Entity ID: #1-#36 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
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 FIELD / 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
4CTFFIND4CTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
13PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1267170
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80503 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more