6U42 | pdb_00006u42

Natively decorated ciliary doublet microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Decorated Ciliary Doublet Microtubule.

Ma, M.Stoyanova, M.Rademacher, G.Dutcher, S.K.Brown, A.Zhang, R.

(2019) Cell 179: 909-922.e12

  • DOI: https://doi.org/10.1016/j.cell.2019.09.030
  • Primary Citation of Related Structures:  
    6U42

  • PubMed Abstract: 

    The axoneme of motile cilia is the largest macromolecular machine of eukaryotic cells. In humans, impaired axoneme function causes a range of ciliopathies. Axoneme assembly, structure, and motility require a radially arranged set of doublet microtubules, each decorated in repeating patterns with non-tubulin components. We use single-particle cryo-electron microscopy to visualize and build an atomic model of the repeating structure of a native axonemal doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). The structure demonstrates how these proteins establish the unique architecture of doublet microtubules, maintain coherent periodicities along the axoneme, and stabilize the microtubules against the repeated mechanical stress induced by ciliary motility. Our work elucidates the architectural principles that underpin the assembly of this large, repetitive eukaryotic structure and provides a molecular basis for understanding the etiology of human ciliopathies.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta443Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha451Chlamydomonas reinhardtiiMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P09204 (Chlamydomonas reinhardtii)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PACRG307Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for B1B601 (Chlamydomonas reinhardtii)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
FAP20190Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IU92 (Chlamydomonas reinhardtii)
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UniProt GroupA8IU92
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
FAP53RM [auth 4L],
SM [auth 4M]
482Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IRJ7 (Chlamydomonas reinhardtii)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
FAP127TM [auth 4N],
UM [auth 4O],
VM [auth 4P]
505Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3CRG7 (Chlamydomonas reinhardtii)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43aAN [auth 4U],
WM [auth 4Q],
XM [auth 4R],
YM [auth 4S],
ZM [auth 4T]
367Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
FAP112BN [auth 4V],
CN [auth 4W],
DN [auth 4X]
475Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8J0X0 (Chlamydomonas reinhardtii)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
FAP210EN [auth 4Y],
FN [auth 4Z]
462Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E0E3 (Chlamydomonas reinhardtii)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
FAP45GN [auth 5A],
HN [auth 5B],
IN [auth 5C],
JN [auth 5D]
501Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8I9E8 (Chlamydomonas reinhardtii)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RIB30KN [auth 5E]274Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E5X9 (Chlamydomonas reinhardtii)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
FAP363GP [auth 7B],
LN [auth 5F],
MN [auth 5G]
391Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IY81 (Chlamydomonas reinhardtii)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
FAP126NN [auth 5H],
ON [auth 5I],
PN [auth 5J],
QN [auth 5K]
137Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
FAP52RN [auth 5L],
SN [auth 5M],
TN [auth 5N]
633Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3D260 (Chlamydomonas reinhardtii)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
FAP67UN [auth 5O],
VN [auth 5P]
380Chlamydomonas reinhardtiiMutation(s): 0 
EC: 2.7.4.6
UniProt
Find proteins for A8JGW5 (Chlamydomonas reinhardtii)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
FAP85WN [auth 5Q]197Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8J250 (Chlamydomonas reinhardtii)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
FAP106AO [auth 5U],
BO [auth 5V],
XN [auth 5R],
YN [auth 5S],
ZN [auth 5T]
240Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8J098 (Chlamydomonas reinhardtii)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
FAP115230Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JDK1 (Chlamydomonas reinhardtii)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
FAP143JO [auth 6E]268Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3E1X6 (Chlamydomonas reinhardtii)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
FAP161KO [auth 6F]403Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
FAP166LO [auth 6G],
MO [auth 6H]
214Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DZF0 (Chlamydomonas reinhardtii)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
FAP252352Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8I1S7 (Chlamydomonas reinhardtii)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
FAP276VO [auth 6Q],
WO [auth 6R],
XO [auth 6S]
87Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DTN6 (Chlamydomonas reinhardtii)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
RIB72635Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q8LKK4 (Chlamydomonas reinhardtii)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
FAP141HP [auth 7C]111Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
FAP222IP [auth 7D],
JP [auth 7E],
KP [auth 7F]
146Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JF23 (Chlamydomonas reinhardtii)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
FAP95LP [auth 7G]235Chlamydomonas reinhardtiiMutation(s): 0 
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Find proteins for A8HSW0 (Chlamydomonas reinhardtii)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
FAP182CQ [auth 7X],
MP [auth 7H]
471Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JHR6 (Chlamydomonas reinhardtii)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
FAP129NP [auth 7I],
OP [auth 7J]
483Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A0A2K3DZI2 (Chlamydomonas reinhardtii)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
FAP21PP [auth 7K],
QP [auth 7L]
458Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
FAP273RP [auth 7M],
SP [auth 7N]
139Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8IXN7 (Chlamydomonas reinhardtii)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
FAP107TP [auth 7O],
UP [auth 7P]
238Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for A8JC52 (Chlamydomonas reinhardtii)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RIB21VP [auth 7Q]189Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
DC1WP [auth 7R],
XP [auth 7S]
749Chlamydomonas reinhardtiiMutation(s): 0 
EC: 2.7.1
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Find proteins for A8IPZ5 (Chlamydomonas reinhardtii)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
DC2YP [auth 7T],
ZP [auth 7U]
552Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
DC3AQ [auth 7V],
BQ [auth 7W]
184Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
FAP68DQ [auth 7Y]312Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
FAP90EQ [auth 7Z],
FQ [auth 8A],
GQ [auth 8B],
HQ [auth 8C],
IQ [auth 8D]
242Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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AAA [auth R2]
AHA [auth 1T]
AIA [auth 2L]
AJA [auth 3D]
AZ [auth P4]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP
Query on GDP

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ABA [auth T0]
ADA [auth W8]
AEA [auth Y8]
AS [auth C2]
AT [auth E2]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
ACA [auth U9]
AFA [auth 0H]
AGA [auth 1A]
AR [auth A2]
BBA [auth T1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM032843

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary