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- PDB-7n61: structure of C2 projections and MIPs -

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Basic information

Entry
Database: PDB / ID: 7n61
Titlestructure of C2 projections and MIPs
Components
  • (Unassigned protein- ...) x 6
  • FAP147
  • FAP178
  • FAP196
  • FAP213
  • FAP225
  • FAP239
  • FAP65
  • FAP70
  • Flagellar WD repeat-containing protein Pf20
  • Kinesin-like protein
  • Tubulin alpha
  • Tubulin beta
KeywordsSTRUCTURAL PROTEIN / central pair apparatus / C2 projection / kinesin motor protein
Function / homology
Function and homology information


axonemal central apparatus / sperm axoneme assembly / cilium movement / axoneme assembly / motile cilium / microtubule motor activity / kinesin complex / microtubule-based movement / regulation of cytoskeleton organization / axoneme ...axonemal central apparatus / sperm axoneme assembly / cilium movement / axoneme assembly / motile cilium / microtubule motor activity / kinesin complex / microtubule-based movement / regulation of cytoskeleton organization / axoneme / cilium assembly / sperm flagellum / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / GTPase activity / calcium ion binding / GTP binding / ATP hydrolysis activity / extracellular exosome / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Flagellar-associated PapD-like / CH-like domain in sperm protein / CH-like domain in sperm protein / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain ...MYCBP-associated protein / Protein FAM228 / MYCBP-associated protein family / Flagellar-associated PapD-like / CH-like domain in sperm protein / CH-like domain in sperm protein / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Quinoprotein alcohol dehydrogenase-like superfamily / Kinesin motor 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 / Tetratricopeptide-like helical domain superfamily / G-protein beta WD-40 repeat / 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 / Immunoglobulin-like fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / Cilia- and flagella-associated protein 70 / Abnormal spindle-like microcephaly-associated protein ASH domain-containing protein / Flagellar associated protein / Flagellar associated protein / EF-hand domain-containing protein ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Calponin-homology (CH) domain-containing protein / Cilia- and flagella-associated protein 70 / Abnormal spindle-like microcephaly-associated protein ASH domain-containing protein / Flagellar associated protein / Flagellar associated protein / EF-hand domain-containing protein / Kinesin-like protein / 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: 3.5 Å
AuthorsHan, L. / Zhang, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Cryo-EM structure of an active central apparatus.
Authors: Long Han / Qinhui Rao / Renbin Yang / Yue Wang / Pengxin Chai / Yong Xiong / Kai Zhang /
Abstract: Accurately regulated ciliary beating in time and space is critical for diverse cellular activities, which impact the survival and development of nearly all eukaryotic species. An essential beating ...Accurately regulated ciliary beating in time and space is critical for diverse cellular activities, which impact the survival and development of nearly all eukaryotic species. An essential beating regulator is the conserved central apparatus (CA) of motile cilia, composed of a pair of microtubules (C1 and C2) associated with hundreds of protein subunits per repeating unit. It is largely unclear how the CA plays its regulatory roles in ciliary motility. Here, we present high-resolution structures of Chlamydomonas reinhardtii CA by cryo-electron microscopy (cryo-EM) and its dynamic conformational behavior at multiple scales. The structures show how functionally related projection proteins of CA are clustered onto a spring-shaped scaffold of armadillo-repeat proteins, facilitated by elongated rachis-like proteins. The two halves of the CA are brought together by elastic chain-like bridge proteins to achieve coordinated activities. We captured an array of kinesin-like protein (KLP1) in two different stepping states, which are actively correlated with beating wave propagation of cilia. These findings establish a structural framework for understanding the role of the CA in cilia.
History
DepositionJun 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0A: Flagellar WD repeat-containing protein Pf20
0B: Flagellar WD repeat-containing protein Pf20
0C: Flagellar WD repeat-containing protein Pf20
0D: Flagellar WD repeat-containing protein Pf20
0E: FAP178
0F: FAP178
0G: FAP178
0H: FAP178
0I: FAP147
0J: FAP147
0K: FAP239
0L: FAP239
0M: FAP225
0N: FAP225
0O: FAP213
0P: FAP213
0Q: FAP196
0S: FAP196
0T: Unassigned protein-1
0U: Unassigned protein-2
0V: Unassigned protein-3
0W: Unassigned protein-4
0X: Kinesin-like protein
0Y: Kinesin-like protein
0Z: Kinesin-like protein
1A: Kinesin-like protein
1B: FAP65
1C: FAP65
1D: FAP70
1E: FAP70
1F: FAP70
1G: FAP70
1H: Unassigned protein-5
1M: Unassigned protein-6
1a: Tubulin beta
1b: Tubulin alpha
1c: Tubulin beta
1d: Tubulin alpha
1e: Tubulin beta
1f: Tubulin alpha
1g: Tubulin beta
1h: Tubulin alpha
2a: Tubulin beta
2b: Tubulin alpha
2c: Tubulin beta
2d: Tubulin alpha
2e: Tubulin beta
2f: Tubulin alpha
2g: Tubulin beta
2h: Tubulin alpha
3a: Tubulin beta
3b: Tubulin alpha
3c: Tubulin beta
3d: Tubulin alpha
3e: Tubulin beta
3f: Tubulin alpha
3g: Tubulin beta
3h: Tubulin alpha
4a: Tubulin beta
4b: Tubulin alpha
4c: Tubulin beta
4d: Tubulin alpha
4e: Tubulin beta
4f: Tubulin alpha
4g: Tubulin beta
4h: Tubulin alpha
5a: Tubulin beta
5b: Tubulin alpha
5c: Tubulin beta
5d: Tubulin alpha
5e: Tubulin beta
5f: Tubulin alpha
5g: Tubulin beta
5h: Tubulin alpha
6a: Tubulin beta
6b: Tubulin alpha
6c: Tubulin beta
6d: Tubulin alpha
6e: Tubulin beta
6f: Tubulin alpha
6g: Tubulin beta
6h: Tubulin alpha
7a: Tubulin beta
7b: Tubulin alpha
7c: Tubulin beta
7d: Tubulin alpha
7e: Tubulin beta
7f: Tubulin alpha
7g: Tubulin beta
7h: Tubulin alpha
8a: Tubulin beta
8b: Tubulin alpha
8c: Tubulin beta
8d: Tubulin alpha
8e: Tubulin beta
8f: Tubulin alpha
8g: Tubulin beta
8h: Tubulin alpha
9a: Tubulin beta
9b: Tubulin alpha
9c: Tubulin beta
9d: Tubulin alpha
9e: Tubulin beta
9f: Tubulin alpha
9g: Tubulin beta
9h: Tubulin alpha
Aa: Tubulin beta
Ab: Tubulin alpha
Ac: Tubulin beta
Ad: Tubulin alpha
Ae: Tubulin beta
Af: Tubulin alpha
Ag: Tubulin beta
Ah: 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
Ca: Tubulin beta
Cb: Tubulin alpha
Cc: Tubulin beta
Cd: Tubulin alpha
Ce: Tubulin beta
Cf: Tubulin alpha
Cg: Tubulin beta
Ch: Tubulin alpha
Da: Tubulin beta
Db: Tubulin alpha
Dc: Tubulin beta
Dd: Tubulin alpha
De: Tubulin beta
Df: Tubulin alpha
Dg: Tubulin beta
Dh: Tubulin alpha
1L: Unassigned protein-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,556,780247
Polymers7,504,819139
Non-polymers51,961108
Water00
1


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

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Components

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Protein , 12 types, 132 molecules 0A0B0C0D0E0F0G0H0I0J0K0L0M0N0O0P0Q0S0X0Y0Z1A1B1C1D1E1F1G1a1c...

#1: Protein
Flagellar WD repeat-containing protein Pf20


Mass: 65929.133 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P93107
#2: Protein
FAP178 / Calponin-homology (CH) domain-containing protein


Mass: 23511.406 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D8Z6
#3: Protein FAP147


Mass: 102141.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DUG8
#4: Protein FAP239


Mass: 57734.598 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DV98
#5: Protein FAP225 / Flagellar associated protein


Mass: 81430.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HNF2
#6: Protein FAP213 / Flagellar associated protein


Mass: 22262.674 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JB78
#7: Protein FAP196 / WD_REPEATS_REGION domain-containing protein


Mass: 64880.324 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CQT7
#12: Protein
Kinesin-like protein


Mass: 83108.039 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I9T2
#13: Protein FAP65


Mass: 233221.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DLJ2
#14: Protein
FAP70


Mass: 111116.258 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DKW3
#17: Protein ...
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#18: Protein ...
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204

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Unassigned protein- ... , 6 types, 7 molecules 0T0U0V0W1H1M1L

#8: Protein Unassigned protein-1


Mass: 14400.733 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124
#9: Protein Unassigned protein-2


Mass: 14485.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124
#10: Protein Unassigned protein-3


Mass: 13634.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124
#11: Protein/peptide Unassigned protein-4


Mass: 3337.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124
#15: Protein Unassigned protein-5


Mass: 7507.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124
#16: Protein Unassigned protein-6


Mass: 14826.253 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / Strain: CC124

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Non-polymers , 3 types, 108 molecules

#19: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#20: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#21: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 52 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestY

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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: Structure of C2 projections and MIPs / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC124
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 38.6 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192253 / Symmetry type: POINT

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