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- PDB-7n32: protofilaments of microtubule doublets bound to outer-arm dynein -

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Basic information

Entry
Database: PDB / ID: 7n32
Titleprotofilaments of microtubule doublets bound to outer-arm dynein
Components
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / protofilament of microtubule doublet
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha chain / Tubulin beta chain
Similarity search - Component
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRao, Q. / Zhang, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Structures of outer-arm dynein array on microtubule doublet reveal a motor coordination mechanism.
Authors: Qinhui Rao / Long Han / Yue Wang / Pengxin Chai / Yin-Wei Kuo / Renbin Yang / Fangheng Hu / Yuchen Yang / Jonathon Howard / Kai Zhang /
Abstract: Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule ...Thousands of outer-arm dyneins (OADs) are arrayed in the axoneme to drive a rhythmic ciliary beat. Coordination among multiple OADs is essential for generating mechanical forces to bend microtubule doublets (MTDs). Using electron microscopy, we determined high-resolution structures of Tetrahymena thermophila OAD arrays bound to MTDs in two different states. OAD preferentially binds to MTD protofilaments with a pattern resembling the native tracks for its distinct microtubule-binding domains. Upon MTD binding, free OADs are induced to adopt a stable parallel conformation, primed for array formation. Extensive tail-to-head (TTH) interactions between OADs are observed, which need to be broken for ATP turnover by the dynein motor. We propose that OADs in an array sequentially hydrolyze ATP to slide the MTDs. ATP hydrolysis in turn relaxes the TTH interfaces to effect free nucleotide cycles of downstream OADs. These findings lead to a model explaining how conformational changes in the axoneme produce coordinated action of dyneins.
History
DepositionMay 31, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
w: Tubulin alpha chain
x: Tubulin beta chain
u: Tubulin alpha chain
v: Tubulin beta chain
s: Tubulin alpha chain
t: Tubulin beta chain
q: Tubulin alpha chain
r: Tubulin beta chain
o: Tubulin alpha chain
p: Tubulin beta chain
m: Tubulin alpha chain
n: Tubulin beta chain
k: Tubulin alpha chain
l: Tubulin beta chain
g: Tubulin alpha chain
h: Tubulin beta chain
e: Tubulin alpha chain
f: Tubulin beta chain
c: Tubulin alpha chain
a: Tubulin alpha chain
b: Tubulin beta chain
d: Tubulin beta chain
i: Tubulin alpha chain
j: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,202,52659
Polymers1,191,08124
Non-polymers11,44535
Water00
1


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

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Components

#1: Protein
Tubulin alpha chain / Alpha-tubulin


Mass: 49639.035 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41351
#2: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49617.676 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Tetrahymena thermophila (eukaryote) / References: UniProt: P41352
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
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: protofilaments of microtubule doublets / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
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
Image recordingElectron dose: 53.3 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0257 / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191776 / Symmetry type: POINT
RefinementResolution: 4.5→287.93 Å / Cor.coef. Fo:Fc: 0.904 / SU B: 49.122 / SU ML: 0.561 / ESU R: 1.578
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.38001 --
obs0.38001 424457 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 198.355 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å21.47 Å2-3.53 Å2
2--1.59 Å2-1.21 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Total: 82021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01383786
ELECTRON MICROSCOPYr_bond_other_d0.0020.01775489
ELECTRON MICROSCOPYr_angle_refined_deg1.3551.649113666
ELECTRON MICROSCOPYr_angle_other_deg1.1051.573175282
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.586510434
ELECTRON MICROSCOPYr_dihedral_angle_2_deg27.81822.594428
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.0841513832
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.00215516
ELECTRON MICROSCOPYr_chiral_restr0.050.210944
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.0294549
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0217663
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it11.43320.45941814
ELECTRON MICROSCOPYr_mcbond_other11.43420.45941813
ELECTRON MICROSCOPYr_mcangle_it19.68930.68152222
ELECTRON MICROSCOPYr_mcangle_other19.68930.68252223
ELECTRON MICROSCOPYr_scbond_it10.31622.1141972
ELECTRON MICROSCOPYr_scbond_other10.31522.11141964
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other19.66232.52261432
ELECTRON MICROSCOPYr_long_range_B_refined31.73391244
ELECTRON MICROSCOPYr_long_range_B_other31.73291242
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 4.5→4.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.435 31392 -
obs--100 %

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