[English] 日本語
Yorodumi
- PDB-8g3d: 48-nm doublet microtubule from Tetrahymena thermophila strain K40R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8g3d
Title48-nm doublet microtubule from Tetrahymena thermophila strain K40R
Components
  • (Cilia- and flagella-associated protein ...) x 3
  • (Parkin co-regulated protein ...) x 2
  • B2B3_fMIP
  • B5B6_fMIP
  • CFAM166A
  • CFAM166B
  • CFAM166C
  • CFAP107
  • CFAP112A
  • CFAP115
  • CFAP127
  • CFAP129
  • CFAP143
  • CFAP161A
  • CFAP182A
  • CFAP182B
  • CFAP20
  • CFAP210
  • CFAP21A
  • CFAP77A
  • DNA polymerase delta C4-type zinc-finger protein
  • Flagellar FliJ protein
  • Flagellar microtugule protofilament ribbon protein
  • IJ34
  • Nebulin
  • Nucleoside diphosphate kinaseNucleoside-diphosphate kinase
  • OJ2
  • OJ3
  • Protofilament ribbon protein
  • RIB22
  • RIB26
  • RIB27A
  • RIB27B
  • RIB35
  • RIB38
  • RIB43A protein
  • RIB57
  • RIB72B
  • SB1
  • STPG1A
  • STPG2
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / Cilia / Axoneme / Doublet Microtubule / Microtubule Inner Protein
Function / homology
Function and homology information


membrane-bounded organelle / axoneme assembly / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process ...membrane-bounded organelle / axoneme assembly / axonemal microtubule / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / GTP biosynthetic process / nucleoside diphosphate kinase activity / microtubule-based process / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cilium / structural constituent of cytoskeleton / microtubule / hydrolase activity / phosphorylation / GTPase activity / calcium ion binding / GTP binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / Sperm-tail PG-rich repeat / Sperm-tail PG-rich repeat / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 77 / Uncharacterised protein FAM166/UPF0605 / Protein of unknown function (DUF2475) ...CCDC81, HU domain 1 / CCDC81, HU domain 2 / CCDC81 eukaryotic HU domain 1 / CCDC81 eukaryotic HU domain 2 / Sperm-tail PG-rich repeat / Sperm-tail PG-rich repeat / 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 / 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 / Dienelactone hydrolase / Dienelactone hydrolase family / 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 / EF-hand domain pair / Mir 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Alpha/Beta hydrolase fold / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Flagellar FliJ protein / Uncharacterized protein / RIB43A protein / EF hand protein / Uncharacterized protein / Meiosis-specific nuclear structural protein 1 / Flagellar microtugule protofilament ribbon protein / DNA polymerase delta C4-type zinc-finger protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Flagellar FliJ protein / Uncharacterized protein / RIB43A protein / EF hand protein / Uncharacterized protein / Meiosis-specific nuclear structural protein 1 / Flagellar microtugule protofilament ribbon protein / DNA polymerase delta C4-type zinc-finger protein / Sperm-tail PG-rich repeat protein / Parkin co-regulated protein / Ptype ATPase, putative / Uncharacterized protein / EF-hand protein / EF-hand pair protein / EF-hand pair protein / Uncharacterized protein / Parkin co-regulated protein / Uncharacterized protein / Tubulin alpha chain / Tubulin beta chain / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 20 / EF hand protein, putative / Sperm-tail PG-rich repeat protein / WD domain, G-beta repeat protein / Uncharacterized protein / Uncharacterized protein / Dienelactone hydrolase family protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Trichohyalin-plectin-homology domain-containing protein / STOP protein / EF hand protein / Tumor suppressor mitostatin protein / Protofilament ribbon protein / Uncharacterized protein / Sperm-tail PG-rich repeat protein / Cilia- and flagella-associated protein 45 / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBlack, C.S. / Kubo, S. / Yang, S.K. / Bui, K.H.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nat Commun / Year: 2023
Title: Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins.
Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente- ...Authors: Shintaroh Kubo / Corbin S Black / Ewa Joachimiak / Shun Kai Yang / Thibault Legal / Katya Peri / Ahmad Abdelzaher Zaki Khalifa / Avrin Ghanaeian / Caitlyn L McCafferty / Melissa Valente-Paterno / Chelsea De Bellis / Phuong M Huynh / Zhe Fan / Edward M Marcotte / Dorota Wloga / Khanh Huy Bui /
Abstract: Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine ...Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.
History
DepositionFeb 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0A: RIB27A
0B: RIB38
0C: CFAM166B
0D: CFAM166A
0E: RIB22
0F: CFAM166C
0G: CFAP107
0H: CFAP127
0N: CFAP161A
0Q: CFAP20
0S: Parkin co-regulated protein PACRGA
0T: IJ34
0U: Cilia- and flagella-associated protein 52
0V: DNA polymerase delta C4-type zinc-finger protein
0X: RIB43A protein
1A: RIB27A
1B: RIB57
1C: CFAM166B
1D: CFAM166A
1E: RIB22
1F: CFAP182A
1G: CFAP107
1H: CFAP127
1I: CFAP143
1J: CFAP21A
1K: Cilia- and flagella-associated protein 53
1L: CFAP115
1M: Nucleoside diphosphate kinase
1N: CFAP161A
1O: Cilia- and flagella-associated protein 45
1P: CFAP210
1Q: CFAP20
1R: RIB72B
1S: Parkin co-regulated protein PACRGA
1T: IJ34
1U: Cilia- and flagella-associated protein 52
1V: DNA polymerase delta C4-type zinc-finger protein
1W: Protofilament ribbon protein
1X: RIB43A protein
2A: RIB27A
2B: RIB57
2C: RIB35
2D: CFAM166A
2E: RIB22
2F: CFAP182B
2G: Flagellar FliJ protein
2H: RIB27B
2I: STPG2
2K: Cilia- and flagella-associated protein 53
2L: CFAP115
2M: Nucleoside diphosphate kinase
2N: CFAP161A
2O: Cilia- and flagella-associated protein 45
2P: CFAP210
2Q: CFAP20
2R: RIB72B
2S: Parkin co-regulated protein PACRGA
2T: IJ34
2U: Cilia- and flagella-associated protein 52
2V: DNA polymerase delta C4-type zinc-finger protein
2W: Protofilament ribbon protein
2X: RIB43A protein
3A: RIB27A
3B: RIB57
3C: RIB35
3D: RIB26
3E: RIB22
3H: RIB27B
3I: STPG2
3L: CFAP115
3O: Cilia- and flagella-associated protein 45
3Q: CFAP20
3R: RIB72B
3S: Parkin co-regulated protein PACRGA
3T: IJ34
3U: Cilia- and flagella-associated protein 52
3V: DNA polymerase delta C4-type zinc-finger protein
3X: RIB43A protein
4C: RIB35
4F: CFAP129
4H: RIB27B
4Q: CFAP20
4R: Flagellar microtugule protofilament ribbon protein
4S: Parkin co-regulated protein PACRGB
4X: RIB43A protein
5A: OJ2
5B: OJ2
5C: OJ2
5D: OJ2
5E: CFAP77A
5F: CFAP77A
5G: CFAP77A
5H: CFAP77A
5I: OJ3
5J: OJ3
5K: OJ3
5Q: CFAP20
5R: Flagellar microtugule protofilament ribbon protein
5S: Parkin co-regulated protein PACRGB
6F: SB1
6G: STPG1A
6H: Nebulin
6Q: CFAP20
6R: Flagellar microtugule protofilament ribbon protein
7R: Flagellar microtugule protofilament ribbon protein
8L: B5B6_fMIP
8N: B5B6_fMIP
8P: CFAP112A
8R: B2B3_fMIP
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
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
CA: Tubulin alpha chain
CB: Tubulin beta chain
CC: Tubulin alpha 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
CN: Tubulin beta chain
DA: Tubulin alpha chain
DB: Tubulin beta chain
DC: Tubulin alpha 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
DN: 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
EM: Tubulin alpha chain
EN: 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
FM: Tubulin alpha chain
FN: 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
GM: Tubulin alpha chain
GN: 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
HN: 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
IN: Tubulin beta chain
JA: Tubulin alpha chain
JB: Tubulin beta chain
JC: Tubulin alpha 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 alpha chain
JN: Tubulin beta chain
KA: Tubulin alpha chain
KB: Tubulin beta chain
KC: Tubulin alpha 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 alpha chain
KN: Tubulin beta chain
LA: Tubulin alpha chain
LB: Tubulin beta chain
LC: Tubulin alpha 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 alpha chain
LN: 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
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
NN: 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
ON: 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
PN: Tubulin beta chain
QA: Tubulin alpha chain
QB: Tubulin beta chain
QC: Tubulin alpha 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 beta chain
QM: Tubulin alpha chain
QN: Tubulin beta chain
RA: Tubulin alpha chain
RB: Tubulin beta chain
RC: Tubulin alpha 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 beta chain
RM: Tubulin alpha chain
RN: 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
SL: Tubulin beta chain
SM: Tubulin alpha chain
SN: 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
TM: Tubulin alpha chain
TN: 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
UM: Tubulin alpha chain
UN: 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
VN: 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
WN: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,362,468914
Polymers20,202,968431
Non-polymers159,500483
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

+
Protein , 41 types, 416 molecules 0A1A2A3A0B0C1C0D1D2D0E1E2E3E0F0G1G0H1H0N1N2N0Q1Q2Q3Q4Q5Q6Q0T...

#1: Protein
RIB27A


Mass: 27605.641 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LUL4
#2: Protein RIB38


Mass: 38175.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23JL9
#3: Protein CFAM166B


Mass: 17705.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q235M9
#4: Protein CFAM166A


Mass: 25779.852 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q238X3
#5: Protein
RIB22


Mass: 22401.135 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LT67
#6: Protein CFAM166C


Mass: 25069.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22B75
#7: Protein CFAP107


Mass: 21314.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q237T1
#8: Protein CFAP127


Mass: 55558.031 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7LV70
#9: Protein CFAP161A


Mass: 57489.621 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22WJ6
#10: Protein
CFAP20 / Transcription factor iib protein / putative


Mass: 22976.535 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22NU3
#12: Protein
IJ34


Mass: 34434.062 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M9T0
#14: Protein
DNA polymerase delta C4-type zinc-finger protein / CFAP106A


Mass: 31493.797 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M279
#15: Protein
RIB43A protein / RIB43A_S


Mass: 17321.414 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VDZ5
#16: Protein RIB57


Mass: 57580.914 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7ME23
#17: Protein CFAP182A


Mass: 20109.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24BV4
#18: Protein CFAP143


Mass: 30485.744 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VD56
#19: Protein CFAP21A


Mass: 48501.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLS4
#21: Protein CFAP115


Mass: 110656.180 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23KF9
#22: Protein Nucleoside diphosphate kinase / Nucleoside-diphosphate kinase / CFAP67A


Mass: 42642.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7XGD1
#24: Protein CFAP210


Mass: 61707.121 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23EX8
#25: Protein RIB72B


Mass: 60972.898 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MCU1
#26: Protein Protofilament ribbon protein / RIB43A_L


Mass: 34224.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q240R7
#27: Protein RIB35 / EF-hand pair protein


Mass: 34952.652 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7ME81
#28: Protein CFAP182B


Mass: 11702.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLW3
#29: Protein Flagellar FliJ protein / CFAP141


Mass: 12098.964 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: A4VCU8
#30: Protein RIB27B


Mass: 26270.043 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22CT6
#31: Protein STPG2 / Sperm-tail PG-rich repeat protein


Mass: 33647.141 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M2G0
#32: Protein RIB26


Mass: 26114.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q232I6
#33: Protein CFAP129


Mass: 31401.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M9I4
#34: Protein
Flagellar microtugule protofilament ribbon protein / RIB72A


Mass: 72643.695 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M0S7
#36: Protein
OJ2


Mass: 19931.387 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q236L2
#37: Protein
CFAP77A


Mass: 28989.633 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22WR6
#38: Protein OJ3


Mass: 14315.630 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#39: Protein SB1


Mass: 17793.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q231B2
#40: Protein STPG1A / Sperm-tail PG-rich repeat protein


Mass: 42132.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q24GM1
#41: Protein Nebulin /


Mass: 61040.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q231B6
#42: Protein B5B6_fMIP


Mass: 43166.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#43: Protein CFAP112A


Mass: 45038.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#44: Protein B2B3_fMIP


Mass: 31099.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
#45: Protein ...
Tubulin alpha chain / Alpha-tubulin


Mass: 49667.047 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote)
References: UniProt: P41351, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#46: Protein ...
Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41352

-
Parkin co-regulated protein ... , 2 types, 6 molecules 0S1S2S3S4S5S

#11: Protein
Parkin co-regulated protein PACRGA


Mass: 36304.816 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7MLV6
#35: Protein Parkin co-regulated protein PACRGB


Mass: 28413.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: I7M317

-
Cilia- and flagella-associated protein ... , 3 types, 9 molecules 0U1U2U3U1K2K1O2O3O

#13: Protein
Cilia- and flagella-associated protein 52 / CFAP52A


Mass: 73429.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q22ZH2
#20: Protein Cilia- and flagella-associated protein 53 / CFAP53


Mass: 60717.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: Q23YQ8
#23: Protein Cilia- and flagella-associated protein 45 / CFAP45


Mass: 59580.438 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: W7XCX2

-
Non-polymers , 3 types, 483 molecules

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


Mass: 523.180 Da / Num. of mol.: 161 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#48: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 161 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#49: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 161 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM

-
Details

Has ligand of interestY
Sequence detailsThe identities of those residues that could be observed in chains 5I, 5J, 5K, 8L, 8N and 8P could ...The identities of those residues that could be observed in chains 5I, 5J, 5K, 8L, 8N and 8P could not be determined, and so were modeled as unknown residues (UNK). The actual sequence of OJ3 (chains 5I, 5J, and 5K) is: MADKSSQVKTRDKSPVAEMITWSEVIKKEKSKQKIYEHFTINPRKLFLYSDKPCENALVEQKMQHSQTKNPFLDISKTSA LLDSLKSPELSQDILSKLTTINQTPGQKYKFPQTANQDIGWFNQHSRSLSPQRSSNQFNYPKKTCNETNYANEYYNMLRV SPFSNKFK. The actual sequence of B5B6_fMIP (chaind 8L and 8N) is: MMYPRKPPTKDEPKSRKNLTQFQREELKRAVAERLSKKYGINNTDLIFGEVANYMNEHQNITAEGLKNLEENIKAQTTNN KNAAPIRQDDEESVKSGISKMSGASNFDAVDKYTQKKSLTEINGDAKSEASKTKKLQGTQIKKPENDLGFLDEENEWAAI YKYNRFLYDKEEEMKKIKKLEQIKQIRRDLDAQVEEKKKIKDYDKKESEGYSKNMQIQMERYDEKEKEKEMQLQLIKDME KATRAKQIKDNKQRRRQEDKQQKQLDAYLMQKVKEELEAEQQYQTFKREHQAQVMKKLLQENEERKERLRKEAEQERQEN IQLMDAYCRLIAEQEQEREKNIKEREHKMKHYQKLALEQVAQENEDKLGQMERRRERYHQRHEKKLDQMELDQKKKIKDQ KHFMKDYLFKQMAEKDERKRKEKDQFNEQAVIWKKDNEEFIKFEEKKKIDKQGVMNTYASTLKEQMADNAVLKKTALQAM NENETLLNKRLLQELDDMRDQIKKKQQ. The actual sequence of CFAP112A (chain 8P) is: MSTIGKSQVSQSKTGNNPLVKQTISKAEAIQQREQLRQKVLSIFLKDYAKNSKSLQTAIEQEVDNFFKHEKVNESSLKDL KARVQALALGKAPSSVGAKSVNQNAHADDNKSVRSQVSQKSHVSGVSQKNQQQNHNQYQQQHDNVSHRDEDGLSVTSSKA PQSVYYLEGDEDDEWAAIVKFDTELFKKEQELEKQRNAEFKKKMRNELDKQLAEKGSRKQHERVENDAYVDLQNHQLNVY DEREKQKEQEKQAKIMNEKRQRDKQVQDENLRRKLEKKREKELDAMLVAKIKEEKEIEEREILNKKLKEKERLAQMMKEN EDYRIKSEKEARDEKANDIRLQQEYTRLTEEMEANREREKKNREDKIKKIMSAFADTVVKDQKAIIREEDEKMMRHIIDQ EEKDRQEEQRRQENLRKQKQDMRNFLNKQIDEKNDRKVQEDQINKKQAEIWAKDRENYMEHEQTKQTYIKSVNKKHQDIL KQQMDEKHNPKKGKMNVNELLQNKQLFEEIAQKNDRIQLKKADPSAIKR.

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 48-nm repeat unit of microtubule doublet from Tetrahymena thermophila strain CU428
Type: ORGANELLE OR CELLULAR COMPONENT
Details: Single Particle Analysis of the 48-nm repeating unit of the axoneme from intact cilia purified from Tetrahymena strain CU428
Entity ID: #1-#46 / Source: NATURAL
Molecular weightValue: 7.6 MDa / Experimental value: YES
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Strain: CU428 / Organelle: Cilia
Buffer solutionpH: 7.4
SpecimenConc.: 2.2 mg/ml / Embedding 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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.2_4158+SVNrefinement
PHENIX1.19.2_4158+SVNrefinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182355 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 32 / Num. of volumes extracted: 2608
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 114.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00431352419
ELECTRON MICROSCOPYf_angle_d0.68911832507
ELECTRON MICROSCOPYf_chiral_restr0.0474200132
ELECTRON MICROSCOPYf_plane_restr0.0053238808
ELECTRON MICROSCOPYf_dihedral_angle_d9.0447185729

+
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://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