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- PDB-7som: Ciliary C2 central pair apparatus isolated from Chlamydomonas rei... -

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Basic information

Entry
Database: PDB / ID: 7som
TitleCiliary C2 central pair apparatus isolated from Chlamydomonas reinhardtii
Components
  • (Unknown protein) x 3
  • Cilia- and flagella-associated protein 20
  • FAP147
  • FAP178
  • FAP196
  • FAP213
  • FAP225
  • FAP239
  • FAP388
  • FAP424
  • FAP65
  • FAP70
  • Flagellar WD repeat-containing protein Pf20
  • Flagellar associated protein
  • Tubulin alpha
  • Tubulin beta
KeywordsSTRUCTURAL PROTEIN / cilia / microtubule
Function / homology
Function and homology information


axonemal central pair / axonemal outer doublet / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / clathrin vesicle coat / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / motile cilium ...axonemal central pair / axonemal outer doublet / positive regulation of cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / clathrin vesicle coat / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / motile cilium / microtubule associated complex / regulation of cytoskeleton organization / clathrin binding / axoneme / cilium assembly / microtubule-based process / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / phospholipid binding / structural constituent of cytoskeleton / endocytosis / microtubule binding / microtubule / transcription coactivator activity / hydrolase activity / endosome / GTPase activity / calcium ion binding / GTP binding / regulation of DNA-templated transcription / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Associate of Myc 1 / CH-like domain in sperm protein / CH-like domain in sperm protein / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / EF-hand domain pair ...MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Associate of Myc 1 / CH-like domain in sperm protein / CH-like domain in sperm protein / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / EF-hand domain pair / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Quinoprotein alcohol dehydrogenase-like 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 / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / TPR_REGION domain-containing protein / ASH domain-containing protein / Flagellar associated protein / Uncharacterized protein / Calmodulin ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / WD_REPEATS_REGION domain-containing protein / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / TPR_REGION domain-containing protein / ASH domain-containing protein / Flagellar associated protein / Uncharacterized protein / Calmodulin / Predicted protein / Flagellar associated protein 174 / Cilia- and flagella-associated protein 20 / Flagellar associated protein / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Flagellar WD repeat-containing protein Pf20
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGui, M. / Wang, X. / Dutcher, S.K. / Brown, A. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Ciliary central apparatus structure reveals mechanisms of microtubule patterning.
Authors: Miao Gui / Xiangli Wang / Susan K Dutcher / Alan Brown / Rui Zhang /
Abstract: A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules ...A pair of extensively modified microtubules form the central apparatus (CA) of the axoneme of most motile cilia, where they regulate ciliary motility. The external surfaces of both CA microtubules are patterned asymmetrically with large protein complexes that repeat every 16 or 32 nm. The composition of these projections and the mechanisms that establish asymmetry and longitudinal periodicity are unknown. Here, by determining cryo-EM structures of the CA microtubules, we identify 48 different CA-associated proteins, which in turn reveal mechanisms for asymmetric and periodic protein binding to microtubules. We identify arc-MIPs, a novel class of microtubule inner protein, that bind laterally across protofilaments and remodel tubulin structure and lattice contacts. The binding mechanisms utilized by CA proteins may be generalizable to other microtubule-associated proteins. These structures establish a foundation to elucidate the contributions of individual CA proteins to ciliary motility and ciliopathies.
History
DepositionNov 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Tubulin beta
AB: Tubulin alpha
AC: Tubulin beta
AD: Tubulin alpha
AE: Tubulin beta
AF: Tubulin alpha
AG: Tubulin beta
AH: Tubulin alpha
AI: Tubulin beta
AJ: Tubulin alpha
AK: Tubulin beta
AL: Tubulin alpha
BA: Tubulin beta
BB: Tubulin alpha
BC: Tubulin beta
BD: Tubulin alpha
BE: Tubulin beta
BF: Tubulin alpha
BG: Tubulin beta
BH: Tubulin alpha
BI: Tubulin beta
BJ: Tubulin alpha
BK: Tubulin beta
BL: Tubulin alpha
CB: Tubulin alpha
CC: Tubulin beta
CD: Tubulin alpha
CE: Tubulin beta
CF: Tubulin alpha
CG: Tubulin beta
CH: Tubulin alpha
CI: Tubulin beta
CJ: Tubulin alpha
CK: Tubulin beta
DB: Tubulin alpha
DC: Tubulin beta
DD: Tubulin alpha
DE: Tubulin beta
DF: Tubulin alpha
DG: Tubulin beta
DH: Tubulin alpha
DI: Tubulin beta
DJ: Tubulin alpha
DK: Tubulin beta
DL: Tubulin alpha
EA: Tubulin beta
EB: Tubulin alpha
EC: Tubulin beta
ED: Tubulin alpha
EE: Tubulin beta
EF: Tubulin alpha
EG: Tubulin beta
EH: Tubulin alpha
EI: Tubulin beta
EJ: Tubulin alpha
EK: Tubulin beta
EL: Tubulin alpha
FA: Tubulin beta
FB: Tubulin alpha
FC: Tubulin beta
FD: Tubulin alpha
FE: Tubulin beta
FF: Tubulin alpha
FG: Tubulin beta
FH: Tubulin alpha
FI: Tubulin beta
FJ: Tubulin alpha
FK: Tubulin beta
FL: Tubulin alpha
GC: Tubulin beta
GD: Tubulin alpha
GE: Tubulin beta
GF: Tubulin alpha
GG: Tubulin beta
GH: Tubulin alpha
GI: Tubulin beta
GJ: Tubulin alpha
GK: Tubulin beta
GL: Tubulin alpha
GM: Tubulin beta
HC: Tubulin beta
HD: Tubulin alpha
HE: Tubulin beta
HF: Tubulin alpha
HG: Tubulin beta
HH: Tubulin alpha
HI: Tubulin beta
HJ: Tubulin alpha
HK: Tubulin beta
HL: Tubulin alpha
HM: Tubulin beta
IC: Tubulin beta
ID: Tubulin alpha
IE: Tubulin beta
IF: Tubulin alpha
IG: Tubulin beta
IH: Tubulin alpha
II: Tubulin beta
IJ: Tubulin alpha
IK: Tubulin beta
IL: Tubulin alpha
IM: Tubulin beta
JB: Tubulin alpha
JC: Tubulin beta
JD: Tubulin alpha
JE: Tubulin beta
JF: Tubulin alpha
JG: Tubulin beta
JH: Tubulin alpha
JI: Tubulin beta
JJ: Tubulin alpha
JK: Tubulin beta
JL: Tubulin alpha
JM: Tubulin beta
KB: Tubulin alpha
KC: Tubulin beta
KD: Tubulin alpha
KE: Tubulin beta
KF: Tubulin alpha
KG: Tubulin beta
KH: Tubulin alpha
KI: Tubulin beta
KJ: Tubulin alpha
KK: Tubulin beta
KL: Tubulin alpha
LB: Tubulin alpha
LC: Tubulin beta
LD: Tubulin alpha
LE: Tubulin beta
LF: Tubulin alpha
LG: Tubulin beta
LH: Tubulin alpha
LI: Tubulin beta
LJ: Tubulin alpha
LK: Tubulin beta
LL: Tubulin alpha
MB: Tubulin alpha
MC: Tubulin beta
MD: Tubulin alpha
ME: Tubulin beta
MF: Tubulin alpha
MG: Tubulin beta
MH: Tubulin alpha
MI: Tubulin beta
MJ: Tubulin alpha
MK: Tubulin beta
ML: Tubulin alpha
a: Cilia- and flagella-associated protein 20
b: Cilia- and flagella-associated protein 20
c: Cilia- and flagella-associated protein 20
d: Cilia- and flagella-associated protein 20
e: Unknown protein
f: Unknown protein
g: Unknown protein
h: Unknown protein
i: Unknown protein
j: Unknown protein
k: Unknown protein
l: Unknown protein
m: FAP65
n: FAP65
o: FAP65
p: FAP70
q: FAP70
r: FAP70
s: Unknown protein
A: FAP147
B: FAP147
C: FAP147
P: FAP178
Q: FAP178
R: FAP178
S: FAP178
T: Flagellar WD repeat-containing protein Pf20
U: Flagellar WD repeat-containing protein Pf20
V: Flagellar WD repeat-containing protein Pf20
W: Flagellar WD repeat-containing protein Pf20
aa: FAP178
bb: Flagellar associated protein
cc: FAP178
CA: Tubulin beta
F: FAP196
G: FAP196
H: FAP196
I: FAP196
D: Flagellar associated protein
E: Flagellar associated protein
J: FAP213
K: FAP213
O: FAP225
Y: FAP225
L: FAP225
M: FAP225
N: FAP225
X: FAP225
A1: FAP239
A2: FAP388
A3: FAP424
A4: FAP388
Z: FAP178
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,414,827422
Polymers10,341,516200
Non-polymers73,311222
Water0
1


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

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Components

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Protein , 16 types, 198 molecules AAACAEAGAIAKBABCBEBGBIBKCCCECGCICKDCDEDGDIDKEAECEEEGEIEKFAFC...

#1: Protein ...
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#2: Protein ...
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204
#3: Protein
Cilia- and flagella-associated protein 20 / Basal body up-regulated protein 22 / Bug22p / Flagellar-associated protein 20


Mass: 64880.324 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IU92
#4: Protein Unknown protein


Mass: 22262.674 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#5: Protein Unknown protein


Mass: 81430.711 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#6: Protein Unknown protein


Mass: 57734.598 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#7: Protein FAP65


Mass: 46261.570 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DLJ2
#8: Protein FAP70


Mass: 10089.324 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DKW3
#9: Protein FAP147


Mass: 22193.566 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DUG8
#10: Protein
FAP178 / Calponin-homology (CH) domain-containing protein


Mass: 65929.133 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D8Z6
#11: Protein
Flagellar WD repeat-containing protein Pf20


Mass: 10336.616 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P93107
#12: Protein Flagellar associated protein / Flagellar associated protein 174


Mass: 233221.547 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I439
#13: Protein
FAP196 / WD_REPEATS_REGION domain-containing protein


Mass: 111116.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CQT7
#14: Protein FAP213 / Flagellar associated protein


Mass: 102141.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JB78
#15: Protein
FAP225 / Flagellar associated protein


Mass: 23511.406 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNF2
#17: Protein FAP388


Mass: 6571.091 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CXB9

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Protein/peptide , 2 types, 2 molecules A1A3

#16: Protein/peptide FAP239


Mass: 4103.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DV98
#18: Protein/peptide FAP424


Mass: 4017.944 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HZB8

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Non-polymers , 3 types, 222 molecules

#19: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#20: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#21: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 74 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: C2 central pair apparatus complex / Type: COMPLEX / Entity ID: #1-#2, #13-#18, #3, #11-#12, #7-#10, #4-#6 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 39.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
7Coot0.9.5model fitting
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104806 / Symmetry type: POINT

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