6U42

Natively decorated ciliary doublet microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.cell.2019.09.030

  • 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 microtubu ...

    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 Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA.,Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA. Electronic address: zhangrui@wustl.edu.,Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. Electronic address: alan_brown@hms.harvard.edu.,Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, School of Medicine, St. Louis, MO, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta
1, 3, 5, 7, 9, A1, A3, A5, A7, A9, B1, B3, B5, B8, C0, C2, C4, C6, C8, D0, D2, D4, D6, D8, E0, E2, E4, E6, E8, F0, F2, F6, F8, G0, G2, G4, G6, G8, H2, H4, H6, H8, I0, I2, I4, I8, J0, J2, J4, J6, J8, K0, K4, K6, K8, L0, L2, L4, L6, M0, M2, M4, M6, M8, N0, N2, N6, N8, O0, O2, O4, O6, O8, P4, P6, P8, Q0, Q2, Q4, Q6, Q8, R0, R2, R4, R6, R8, S0, S2, S4, S6, S8, T0, T2, T4, T6, T8, U2, U4, U6, U8, V0, V2, V4, V6, V8, W0, W2, W4, W6, W8, X0, X2, X4, X6, X8, Y0, Y2, Y4, Y6, Y8, Z0, Z2, Z4, Z6, Z8, 0A, 0C, 0E, 0G, 0I, 0K, 0M, 0O, 0Q, 0S, 0U, 0W, 0Y, 1A, 1C, 1E, 1G, 1K, 1M, 1O, 1Q, 1S, 1U, 1W, 2A, 2C, 2E, 2G, 2I, 2K, 2M, 2Q, 2S, 2U, 2W, 2Y, 3A, 3C, 3G, 3I, 3K, 3M, 3O, 3Q, 3S
443Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: TUBB1, TUBB2
Find proteins for P04690 (Chlamydomonas reinhardtii)
Go to Gene View: TUBB1
Go to UniProtKB:  P04690
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha
2, 4, 6, 8, A0, A2, A4, A8, B0, B2, B4, B7, B9, C1, C5, C7, C9, D1, D3, D5, D7, E1, E3, E5, E7, E9, F1, F3, F5, F7, F9, G1, G3, G5, G7, G9, H1, H3, H5, H7, H9, I1, I3, I5, I7, I9, J1, J3, J5, J7, J9, K1, K3, K5, K7, K9, L1, L3, L5, L7, L9, M1, M3, M5, M7, M9, N1, N3, N5, N7, N9, O1, O3, O5, O7, O9, P3, P5, P7, P9, Q1, Q3, Q5, Q9, R1, R3, R5, R7, R9, S1, S5, S7, S9, T1, T3, T5, T7, U1, U3, U5, U7, U9, V1, V3, V7, V9, W1, W3, W5, W7, W9, X3, X5, X7, X9, Y1, Y3, Y5, Y9, Z1, Z3, Z5, Z7, Z9, 0B, 0F, 0H, 0J, 0L, 0N, 0P, 0R, 0V, 0X, 0Z, 1B, 1D, 1F, 1H, 1L, 1N, 1P, 1R, 1T, 1V, 1X, 1Z, 2B, 2D, 2F, 2H, 2J, 2L, 2N, 2P, 2R, 2T, 2V, 2X, 2Z, 3B, 3D, 3F, 3H, 3J, 3L, 3N, 3P, 3R, 3T
451Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: TUBA1
Find proteins for P09204 (Chlamydomonas reinhardtii)
Go to UniProtKB:  P09204
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PACRG
3V, 3X, 3Z, 4B, 4D, 4F, 4H, 4J
307Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PACRG
Find proteins for B1B601 (Chlamydomonas reinhardtii)
Go to Gene View: PACRG
Go to UniProtKB:  B1B601
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FAP20
3W, 3Y, 4A, 4C, 4E, 4G, 4I
190Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CFAP20 (BUG22, FAP20)
Find proteins for A8IU92 (Chlamydomonas reinhardtii)
Go to Gene View: CFAP20
Go to UniProtKB:  A8IU92
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
FAP53
4L, 4M
482Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CFAP53 (FAP53)
Find proteins for A8IRJ7 (Chlamydomonas reinhardtii)
Go to Gene View: CFAP53
Go to UniProtKB:  A8IRJ7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
FAP127
4N, 4O, 4P
505Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3CRG7 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3CRG7
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
RIB43a
4Q, 4R, 4S, 4T, 4U
367Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RIB43a
Find proteins for Q9M6B0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q9M6B0
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
FAP112
4V, 4W, 4X
475Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP112
Find proteins for A8J0X0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8J0X0
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
FAP210
4Y, 4Z
462Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3E0E3 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3E0E3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
FAP45
5A, 5B, 5C, 5D
501Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CFAP45 (FAP45)
Find proteins for A8I9E8 (Chlamydomonas reinhardtii)
Go to Gene View: CFAP45
Go to UniProtKB:  A8I9E8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RIB30
5E
274Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3E5X9 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3E5X9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
FAP363
5F, 5G, 7B
391Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A8IY81 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8IY81
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
FAP126
5H, 5I, 5J, 5K
137Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CFAP126 (FAP126, FLTP)
Find proteins for A8IVJ1 (Chlamydomonas reinhardtii)
Go to Gene View: CFAP126
Go to UniProtKB:  A8IVJ1
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
FAP52
5L, 5M, 5N
633Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3D260 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3D260
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
FAP67
5O, 5P
380Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP67
EC: 2.7.4.6
Find proteins for A8JGW5 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JGW5
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
FAP85
5Q
197Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP85
Find proteins for A8J250 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8J250
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
FAP106
5R, 5S, 5T, 5U, 5V
240Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP106
Find proteins for A8J098 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8J098
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
FAP115
5X, 5Y, 5Z, 6A, 6B, 6C, 6D
230Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP115
Find proteins for A8JDK1 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JDK1
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
FAP143
6E
268Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3E1X6 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3E1X6
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
FAP161
6F
403Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP161
Find proteins for A8HRH3 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8HRH3
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
FAP166
6G, 6H
214Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3DZF0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3DZF0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
FAP252
6I, 6J, 6K, 6L, 6M, 6N, 6O, 6P
352Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP252
Find proteins for A8I1S7 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8I1S7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
FAP276
6Q, 6R, 6S
87Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3DTN6 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3DTN6
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
RIB72
6T, 6U, 6V, 6W, 6X, 6Y, 6Z, 7A
635Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: RIB72
Find proteins for Q8LKK4 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q8LKK4
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
FAP141
7C
111Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP141
Find proteins for A8IMR3 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8IMR3
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
FAP222
7D, 7E, 7F
146Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP222
Find proteins for A8JF23 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JF23
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
FAP95
7G
235Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP95
Find proteins for A8HSW0 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8HSW0
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
FAP182
7H, 7X
471Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP182
Find proteins for A8JHR6 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JHR6
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
FAP129
7I, 7J
483Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3DZI2 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3DZI2
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
FAP21
7K, 7L
458N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
FAP273
7M, 7N
139Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP273
Find proteins for A8IXN7 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8IXN7
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
FAP107
7O, 7P
238Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP107
Find proteins for A8JC52 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JC52
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
RIB21
7Q
189Chlamydomonas reinhardtiiMutation(s): 0 
Find proteins for A0A2K3D7C7 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A0A2K3D7C7
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
DC1
7R, 7S
749Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ODA3
EC: 2.7.1.-
Find proteins for A8IPZ5 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8IPZ5
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
DC2
7T, 7U
552Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ODA1 (DCC2)
Find proteins for A8JF70 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8JF70
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
DC3
7V, 7W
184Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: ODA14
Find proteins for Q7Y0H2 (Chlamydomonas reinhardtii)
Go to UniProtKB:  Q7Y0H2
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
FAP68
7Y
312Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP68
Find proteins for A8HPK6 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8HPK6
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
FAP90
7Z, 8A, 8B, 8C, 8D
242Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: FAP90
Find proteins for A8ICC1 (Chlamydomonas reinhardtii)
Go to UniProtKB:  A8ICC1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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Download CCD File 
0A, 0C, 0E, 0G, 0I, 0K, 0M, 0O, 0Q, 0S, 0U, 0W, 0Y, 1A, 1C, 1E, 1G, 1K, 1M, 1O, 1Q, 1S, 1U, 1W, 2, 2A, 2C, 2E, 2G, 2I, 2K, 2M, 2Q, 2S, 2U, 2W, 2Y, 3, 3A, 3C, 3G, 3I, 3K, 3M, 3O, 3Q, 3S, 5, 7, 9, A1, A3, A5, A7, A9, B1, B3, B5, B8, C0, C2, C4, C6, C8, D0, D2, D4, D6, D8, E0, E2, E4, E6, E8, F0, F2, F6, F8, G0, G2, G4, G6, G8, H2, H4, H6, H8, I0, I2, I4, I8, J0, J2, J4, J6, J8, K0, K4, K6, K8, L0, L2, L4, L6, M0, M2, M4, M6, M8, N0, N2, N6, N8, O0, O2, O4, O6, O8, P4, P6, P8, Q0, Q2, Q4, Q6, Q8, R0, R2, R4, R6, R8, S0, S2, S4, S6, S8, T0, T2, T4, T6, T8, U2, U4, U6, U8, V0, V2, V4, V6, V8, W0, W2, W4, W6, W8, X0, X2, X4, X6, X8, Y0, Y2, Y4, Y6, Y8, Z0, Z2, Z4, Z6, Z8
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
0A, 0C, 0F, 0I, 0K, 0M, 0O, 0Q, 0S, 0V, 0Y, 1A, 1C, 1D, 1G, 1H, 1L, 1N, 1Q, 1S, 1T, 1W, 1X, 2A, 2C, 2E, 2G, 2I, 2K, 2L, 2N, 2Q, 2S, 2U, 2W, 2Y, 3, 3A, 3C, 3D, 3G, 3I, 3K, 3M, 3O, 3P, 3S, 3T, 4, 7, 8, A1, A2, A4, A9, B0, B2, B5, B7, C0, C1, C5, C8, C9, D1, D3, D5, D7, E1, E4, E6, E8, F0, F1, F3, F5, F8, G0, G1, G4, G5, G7, G9, H2, H3, H6, H8, I0, I1, I4, I5, I8, J0, J2, J4, J6, J8, K0, K1, K4, K6, K7, K9, L2, L4, L6, L7, M0, M2, M4, M6, M7, N0, N1, N3, N6, N8, O0, O2, O4, O6, O8, O9, P4, P6, P8, P9, Q2, Q4, Q6, R0, R2, R4, R6, R8, S0, S2, S5, S8, S9, T2, T4, T6, T8, U2, U4, U6, U7, U9, V2, V3, V8, W0, W2, W4, W5, W8, X0, X4, X6, X7, Y0, Y1, Y4, Y6, Z0, Z2, Z3, Z6, Z7
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
0A, 0B, 0F, 0H, 0J, 0L, 0N, 0P, 0R, 0W, 0X, 1A, 1B, 1D, 1F, 1H, 1L, 1N, 1P, 1R, 1T, 1V, 1X, 1Z, 2, 2B, 2D, 2F, 2H, 2J, 2L, 2N, 2P, 2R, 2T, 2V, 2X, 2Z, 3B, 3D, 3F, 3H, 3K, 3L, 3N, 3P, 3R, 3T, 4, 6, 8, A0, A2, A4, A8, B0, B2, B4, B7, B9, C1, C5, C7, C9, D1, D3, D5, D7, E1, E3, E5, E7, E9, F1, F3, F5, F7, F9, G1, G3, G5, G7, G9, H2, H3, H5, H8, H9, I1, I3, I5, I7, I9, J1, J4, J5, J7, J9, K1, K3, K5, K7, K9, L1, L3, L5, L7, L9, M1, M3, M5, M7, M9, N1, N3, N6, N7, O0, O1, O3, O5, O8, O9, P4, P6, P7, P9, Q1, Q3, Q5, Q9, R1, R3, R6, R7, R9, S1, S5, S7, S9, T1, T3, T5, T7, U1, U3, U5, U7, U9, V2, V3, V7, V9, W2, W3, W5, W8, W9, X3, X5, X7, X9, Y1, Y3, Y5, Y9, Z2, Z3, Z5, Z7
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2020-01-08
    Type: Author supporting evidence