ISDA

Entry Detail

PDB ID:

8G3D

EMDB ID:

EMD-29692

Keywords:

STRUCTURAL PROTEIN

Title:

48-nm doublet microtubule from Tetrahymena thermophila strain K40R

Biological Source:

Source Organism:

Tetrahymena thermophila

PDB Version:

Deposition Date:

2023-02-07

Release Date:

2023-06-14

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.70 Å

Aggregation State:

CELL

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB27A
Chain IDs:A (auth: 0A), P (auth: 1A), NA (auth: 2A), KB (auth: 3A)
Chain Length:236
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7LUL4

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB38
Chain IDs:B (auth: 0B)
Chain Length:329
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q23JL9

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAM166B
Chain IDs:C (auth: 0C), R (auth: 1C)
Chain Length:156
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:Q235M9 Pfam ID:PF10629

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAM166A
Chain IDs:D (auth: 0D), S (auth: 1D), QA (auth: 2D)
Chain Length:225
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:Q238X3 Pfam ID:PF10629

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB22
Chain IDs:E (auth: 0E), T (auth: 1E), RA (auth: 2E), OB (auth: 3E)
Chain Length:191
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7LT67 Pfam ID:PF13499

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAM166C
Chain IDs:F (auth: 0F)
Chain Length:219
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q22B75

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP107
Chain IDs:G (auth: 0G), V (auth: 1G)
Chain Length:183
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:Q237T1

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP127
Chain IDs:H (auth: 0H), W (auth: 1H)
Chain Length:447
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:I7LV70 Pfam ID:PF13868

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP161A
Chain IDs:I (auth: 0N), CA (auth: 1N), ZA (auth: 2N)
Chain Length:492
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:Q22WJ6

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP20
Chain IDs:J (auth: 0Q), FA (auth: 1Q), CB (auth: 2Q), TB (auth: 3Q), DC (auth: 4Q), SC (auth: 5Q), YC (auth: 6Q)
Chain Length:195
Number of Molecules:7
Biological Source:Tetrahymena thermophila

UniProt ID:Q22NU3 Pfam ID:PF05018

Protein Blast

Polymer Type:polypeptide(L)
Description:Parkin co-regulated protein PACRGA
Chain IDs:K (auth: 0S), HA (auth: 1S), EB (auth: 2S), VB (auth: 3S)
Chain Length:319
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7MLV6 Pfam ID:PF10274

Protein Blast

Polymer Type:polypeptide(L)
Description:IJ34
Chain IDs:L (auth: 0T), IA (auth: 1T), FB (auth: 2T), WB (auth: 3T)
Chain Length:298
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7M9T0 Pfam ID:PF14908, PF18289

Protein Blast

Polymer Type:polypeptide(L)
Description:Cilia- and flagella-associated protein 52
Chain IDs:M (auth: 0U), JA (auth: 1U), GB (auth: 2U), XB (auth: 3U)
Chain Length:656
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:Q22ZH2 Pfam ID:PF00400

Protein Blast

Polymer Type:polypeptide(L)
Description:DNA polymerase delta C4-type zinc-finger protein
Chain IDs:N (auth: 0V), KA (auth: 1V), HB (auth: 2V), YB (auth: 3V)
Chain Length:269
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7M279 Pfam ID:PF13864

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB43A protein
Chain IDs:O (auth: 0X), MA (auth: 1X), JB (auth: 2X), ZB (auth: 3X), GC (auth: 4X)
Chain Length:142
Number of Molecules:5
Biological Source:Tetrahymena thermophila

UniProt ID:A4VDZ5 Pfam ID:PF05914

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB57
Chain IDs:Q (auth: 1B), OA (auth: 2B), LB (auth: 3B)
Chain Length:498
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:I7ME23 Pfam ID:PF13499, PF13833

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP182A
Chain IDs:U (auth: 1F)
Chain Length:173
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q24BV4 Pfam ID:PF14892

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP143
Chain IDs:X (auth: 1I)
Chain Length:263
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:A4VD56

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP21A
Chain IDs:Y (auth: 1J)
Chain Length:422
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:I7MLS4

Protein Blast

Polymer Type:polypeptide(L)
Description:Cilia- and flagella-associated protein 53
Chain IDs:Z (auth: 1K), WA (auth: 2K)
Chain Length:489
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:Q23YQ8 Pfam ID:PF13868

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP115
Chain IDs:AA (auth: 1L), XA (auth: 2L), RB (auth: 3L)
Chain Length:940
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:Q23KF9

Protein Blast

Polymer Type:polypeptide(L)
Description:Nucleoside diphosphate kinase
Chain IDs:BA (auth: 1M), YA (auth: 2M)
Chain Length:372
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:W7XGD1 Pfam ID:PF00334

Protein Blast

Polymer Type:polypeptide(L)
Description:Cilia- and flagella-associated protein 45
Chain IDs:DA (auth: 1O), AB (auth: 2O), SB (auth: 3O)
Chain Length:494
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:W7XCX2 Pfam ID:PF13868

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP210
Chain IDs:EA (auth: 1P), BB (auth: 2P)
Chain Length:507
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:Q23EX8 Pfam ID:PF13868

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB72B
Chain IDs:GA (auth: 1R), DB (auth: 2R), UB (auth: 3R)
Chain Length:516
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:I7MCU1 Pfam ID:PF06565

Protein Blast

Polymer Type:polypeptide(L)
Description:Protofilament ribbon protein
Chain IDs:LA (auth: 1W), IB (auth: 2W)
Chain Length:280
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:Q240R7 Pfam ID:PF05914

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB35
Chain IDs:PA (auth: 2C), MB (auth: 3C), AC (auth: 4C)
Chain Length:300
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:I7ME81 Pfam ID:PF13499

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP182B
Chain IDs:SA (auth: 2F)
Chain Length:96
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:I7MLW3 Pfam ID:PF14892

Protein Blast

Polymer Type:polypeptide(L)
Description:Flagellar FliJ protein
Chain IDs:TA (auth: 2G)
Chain Length:99
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:A4VCU8 Pfam ID:PF15104

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB27B
Chain IDs:UA (auth: 2H), PB (auth: 3H), CC (auth: 4H)
Chain Length:229
Number of Molecules:3
Biological Source:Tetrahymena thermophila

UniProt ID:Q22CT6

Protein Blast

Polymer Type:polypeptide(L)
Description:STPG2
Chain IDs:VA (auth: 2I), QB (auth: 3I)
Chain Length:293
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:I7M2G0 Pfam ID:PF07004

Protein Blast

Polymer Type:polypeptide(L)
Description:RIB26
Chain IDs:NB (auth: 3D)
Chain Length:237
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q232I6 Pfam ID:PF01738

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP129
Chain IDs:BC (auth: 4F)
Chain Length:276
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:I7M9I4

Protein Blast

Polymer Type:polypeptide(L)
Description:Flagellar microtugule protofilament ribbon protein
Chain IDs:EC (auth: 4R), TC (auth: 5R), ZC (auth: 6R), AD (auth: 7R)
Chain Length:613
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:I7M0S7 Pfam ID:PF06565

Protein Blast

Polymer Type:polypeptide(L)
Description:Parkin co-regulated protein PACRGB
Chain IDs:FC (auth: 4S), UC (auth: 5S)
Chain Length:249
Number of Molecules:2
Biological Source:Tetrahymena thermophila

UniProt ID:I7M317 Pfam ID:PF10274

Protein Blast

Polymer Type:polypeptide(L)
Description:OJ2
Chain IDs:HC (auth: 5A), IC (auth: 5B), JC (auth: 5C), KC (auth: 5D)
Chain Length:175
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:Q236L2

Protein Blast

Polymer Type:polypeptide(L)
Description:CFAP77A
Chain IDs:LC (auth: 5E), MC (auth: 5F), NC (auth: 5G), OC (auth: 5H)
Chain Length:247
Number of Molecules:4
Biological Source:Tetrahymena thermophila

UniProt ID:Q22WR6 Pfam ID:PF14825

Polymer Type:polypeptide(L)
Description:OJ3
Chain IDs:PC (auth: 5I), QC (auth: 5J), RC (auth: 5K)
Chain Length:168
Number of Molecules:3
Biological Source:Tetrahymena thermophila

Protein Blast

Polymer Type:polypeptide(L)
Description:SB1
Chain IDs:VC (auth: 6F)
Chain Length:145
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q231B2

Protein Blast

Polymer Type:polypeptide(L)
Description:STPG1A
Chain IDs:WC (auth: 6G)
Chain Length:364
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q24GM1 Pfam ID:PF07004

Protein Blast

Polymer Type:polypeptide(L)
Description:Nebulin
Chain IDs:XC (auth: 6H)
Chain Length:518
Number of Molecules:1
Biological Source:Tetrahymena thermophila

UniProt ID:Q231B6

Polymer Type:polypeptide(L)
Description:B5B6_fMIP
Chain IDs:BD (auth: 8L), CD (auth: 8N)
Chain Length:507
Number of Molecules:2
Biological Source:Tetrahymena thermophila

Polymer Type:polypeptide(L)
Description:CFAP112A
Chain IDs:DD (auth: 8P)
Chain Length:529
Number of Molecules:1
Biological Source:Tetrahymena thermophila

Polymer Type:polypeptide(L)
Description:B2B3_fMIP
Chain IDs:ED (auth: 8R)
Chain Length:361
Number of Molecules:1
Biological Source:Tetrahymena thermophila

Protein Blast

Polymer Type:polypeptide(L)
Description:Tubulin alpha chain
Chain IDs:FD (auth: AA), HD (auth: AC), JD (auth: AE), LD (auth: AG), ND (auth: AI), PD (auth: AK), RD (auth: AM), TD (auth: BA), VD (auth: BC), XD (auth: BE), ZD (auth: BG), BE (auth: BI), DE (auth: BK), FE (auth: BM), HE (auth: CA), JE (auth: CC), LE (auth: CE), NE (auth: CG), PE (auth: CI), RE (auth: CK), TE (auth: CM), VE (auth: DA), XE (auth: DC), ZE (auth: DE), BF (auth: DG), DF (auth: DI), FF (auth: DK), HF (auth: DM), JF (auth: EA), LF (auth: EC), NF (auth: EE), PF (auth: EG), RF (auth: EI), TF (auth: EK), VF (auth: EM), XF (auth: FA), ZF (auth: FC), BG (auth: FE), DG (auth: FG), FG (auth: FI), HG (auth: FK), JG (auth: FM), LG (auth: GA), NG (auth: GC), PG (auth: GE), RG (auth: GG), TG (auth: GI), VG (auth: GK), XG (auth: GM), ZG (auth: HA), BH (auth: HC), DH (auth: HE), FH (auth: HG), HH (auth: HI), JH (auth: HK), LH (auth: HM), NH (auth: IA), PH (auth: IC), RH (auth: IE), TH (auth: IG), VH (auth: II), XH (auth: IK), ZH (auth: IM), BI (auth: JA), DI (auth: JC), FI (auth: JE), HI (auth: JG), JI, LI (auth: JK), NI (auth: JM), PI (auth: KA), RI (auth: KC), TI (auth: KE), VI (auth: KG), XI (auth: KI), ZI (auth: KK), BJ (auth: KM), DJ (auth: LA), FJ (auth: LC), HJ (auth: LE), JJ (auth: LG), LJ (auth: LI), NJ (auth: LK), PJ (auth: LM), RJ (auth: MA), TJ (auth: MC), VJ (auth: ME), XJ (auth: MG), ZJ (auth: MI), BK (auth: MK), DK (auth: MM), FK (auth: NA), HK (auth: NC), JK (auth: NE), LK (auth: NG), NK (auth: NI), PK (auth: NK), RK (auth: NM), TK (auth: OA), VK (auth: OC), XK (auth: OE), ZK (auth: OG), BL (auth: OI), DL (auth: OK), FL (auth: OM), HL (auth: PA), JL (auth: PC), LL (auth: PE), NL (auth: PG), PL (auth: PI), RL (auth: PK), TL (auth: PM), VL (auth: QA), XL (auth: QC), ZL (auth: QE), BM (auth: QG), DM (auth: QI), FM (auth: QK), HM (auth: QM), JM (auth: RA), LM (auth: RC), NM (auth: RE), PM (auth: RG), RM (auth: RI), TM (auth: RK), VM (auth: RM), XM (auth: SA), ZM (auth: SC), BN (auth: SE), DN (auth: SG), FN (auth: SI), HN (auth: SK), JN (auth: SM), LN (auth: TA), NN (auth: TC), PN (auth: TE), RN (auth: TG), TN (auth: TI), VN (auth: TK), XN (auth: TM), ZN (auth: UA), BO (auth: UC), DO (auth: UE), FO (auth: UG), HO (auth: UI), JO (auth: UK), LO (auth: UM), NO (auth: VA), PO (auth: VC), RO (auth: VE), TO (auth: VG), VO (auth: VI), XO (auth: VK), ZO (auth: VM), BP (auth: WA), DP (auth: WC), FP (auth: WE), HP (auth: WG), JP (auth: WI), LP (auth: WK), NP (auth: WM)
Chain Length:449
Number of Molecules:161
Biological Source:Tetrahymena thermophila

UniProt ID:P41351 Pfam ID:PF00091, PF03953

Protein Blast

Polymer Type:polypeptide(L)
Description:Tubulin beta chain
Chain IDs:GD (auth: AB), ID (auth: AD), KD (auth: AF), MD (auth: AH), OD (auth: AJ), QD (auth: AL), SD (auth: AN), UD (auth: BB), WD (auth: BD), YD (auth: BF), AE (auth: BH), CE (auth: BJ), EE (auth: BL), GE (auth: BN), IE (auth: CB), KE (auth: CD), ME (auth: CF), OE (auth: CH), QE (auth: CJ), SE (auth: CL), UE (auth: CN), WE (auth: DB), YE (auth: DD), AF (auth: DF), CF (auth: DH), EF (auth: DJ), GF (auth: DL), IF (auth: DN), KF (auth: EB), MF (auth: ED), OF (auth: EF), QF (auth: EH), SF (auth: EJ), UF (auth: EL), WF (auth: EN), YF (auth: FB), AG (auth: FD), CG (auth: FF), EG (auth: FH), GG (auth: FJ), IG (auth: FL), KG (auth: FN), MG (auth: GB), OG (auth: GD), QG (auth: GF), SG (auth: GH), UG (auth: GJ), WG (auth: GL), YG (auth: GN), AH (auth: HB), CH (auth: HD), EH (auth: HF), GH (auth: HH), IH (auth: HJ), KH (auth: HL), MH (auth: HN), OH (auth: IB), QH (auth: ID), SH (auth: IF), UH (auth: IH), WH (auth: IJ), YH (auth: IL), AI (auth: IN), CI (auth: JB), EI (auth: JD), GI (auth: JF), II (auth: JH), KI (auth: JJ), MI (auth: JL), OI (auth: JN), QI (auth: KB), SI (auth: KD), UI (auth: KF), WI (auth: KH), YI (auth: KJ), AJ (auth: KL), CJ (auth: KN), EJ (auth: LB), GJ (auth: LD), IJ (auth: LF), KJ (auth: LH), MJ (auth: LJ), OJ (auth: LL), QJ (auth: LN), SJ (auth: MB), UJ (auth: MD), WJ (auth: MF), YJ (auth: MH), AK (auth: MJ), CK (auth: ML), EK (auth: MN), GK (auth: NB), IK (auth: ND), KK (auth: NF), MK (auth: NH), OK (auth: NJ), QK (auth: NL), SK (auth: NN), UK (auth: OB), WK (auth: OD), YK (auth: OF), AL (auth: OH), CL (auth: OJ), EL (auth: OL), GL (auth: ON), IL (auth: PB), KL (auth: PD), ML (auth: PF), OL (auth: PH), QL (auth: PJ), SL (auth: PL), UL (auth: PN), WL (auth: QB), YL (auth: QD), AM (auth: QF), CM (auth: QH), EM (auth: QJ), GM (auth: QL), IM (auth: QN), KM (auth: RB), MM (auth: RD), OM (auth: RF), QM (auth: RH), SM (auth: RJ), UM (auth: RL), WM (auth: RN), YM (auth: SB), AN (auth: SD), CN (auth: SF), EN (auth: SH), GN (auth: SJ), IN (auth: SL), KN (auth: SN), MN (auth: TB), ON (auth: TD), QN (auth: TF), SN (auth: TH), UN (auth: TJ), WN (auth: TL), YN (auth: TN), AO (auth: UB), CO (auth: UD), EO (auth: UF), GO (auth: UH), IO (auth: UJ), KO (auth: UL), MO (auth: UN), OO (auth: VB), QO (auth: VD), SO (auth: VF), UO (auth: VH), WO (auth: VJ), YO (auth: VL), AP (auth: VN), CP (auth: WB), EP (auth: WD), GP (auth: WF), IP (auth: WH), KP (auth: WJ), MP (auth: WL), OP (auth: WN)
Chain Length:443
Number of Molecules:161
Biological Source:Tetrahymena thermophila

UniProt ID:P41352 Pfam ID:PF00091, PF03953

Ligand Molecules

GDP

GTP

Primary Citation

Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins.

Kubo, S, Black, C.S, Joachimiak, E, Yang, S.K, Legal, T, Peri, K, Khalifa, A.A.Z, Ghanaeian, A, McCafferty, C.L, Valente-Paterno, M, De Bellis, C, Huynh, P.M, Fan, Z, Marcotte, E.M, Wloga, D, Bui, K.H.Show

Nat Commun 14 2168 2168 (2023)

PMID: 37061538 DOI: 10.1038/s41467-023-37868-0

Abstact

Cilia are ubiquitous eukaryotic organelles responsible for cellular motility and sensory functions. The ciliary axoneme is a microtubule-based cytoskeleton consisting of two central singlets and nine outer doublet microtubules. Cryo-electron microscopy-based studies have revealed a complex network inside the lumen of both tubules composed of microtubule-inner proteins (MIPs). However, the functions of most MIPs remain unknown. Here, we present single-particle cryo-EM-based analyses of the Tetrahymena thermophila native doublet microtubule and identify 42 MIPs. These data shed light on the evolutionarily conserved and diversified roles of MIPs. In addition, we identified MIPs potentially responsible for the assembly and stability of the doublet outer junction. Knockout of the evolutionarily conserved outer junction component CFAP77 moderately diminishes Tetrahymena swimming speed and beat frequency, indicating the important role of CFAP77 and outer junction stability in cilia beating generation and/or regulation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures