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- PDB-6u42: Natively decorated ciliary doublet microtubule -

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Basic information

Entry
Database: PDB / ID: 6u42
TitleNatively decorated ciliary doublet microtubule
Components
  • DC1
  • DC2
  • DC3
  • FAP106
  • FAP107
  • FAP112
  • FAP115
  • FAP126
  • FAP127
  • FAP129
  • FAP141
  • FAP143
  • FAP161
  • FAP166
  • FAP182
  • FAP20
  • FAP21
  • FAP210
  • FAP222
  • FAP252
  • FAP273
  • FAP276
  • FAP363
  • FAP45
  • FAP52
  • FAP53
  • FAP67
  • FAP68
  • FAP85
  • FAP90
  • FAP95
  • PACRG
  • RIB21
  • RIB30
  • RIB43a
  • RIB72
  • Tubulin alpha
  • Tubulin beta
KeywordsPROTEIN FIBRIL / motile cilia / microtubule doublet / repetitive structure
Function / homology
Function and homology information


axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / outer dynein arm / outer dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / establishment of protein localization to organelle / cilium movement ...axonemal central pair / axonemal doublet microtubule / positive regulation of cilium-dependent cell motility / outer dynein arm / outer dynein arm assembly / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / establishment of protein localization to organelle / cilium movement / axoneme assembly / axonemal microtubule / negative regulation of microtubule depolymerization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / microtubule associated complex / motile cilium / nucleoside diphosphate kinase activity / GTP biosynthetic process / mitotic cytokinesis / axoneme / cilium assembly / alpha-tubulin binding / microtubule-based process / Hsp70 protein binding / mitotic spindle organization / meiotic cell cycle / Hsp90 protein binding / ATP-dependent protein folding chaperone / structural constituent of cytoskeleton / mitotic spindle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cytoskeleton / hydrolase activity / calmodulin binding / ciliary basal body / cilium / GTPase activity / calcium ion binding / GTP binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / WDR90, 4th beta-propeller / : / : / ODAD1 central coiled coil region / Protein Flattop / Flattop / Nucleoside diphosphate kinase 7 / Piercer of microtubule wall 1/2 / Piercer of microtubule wall 1/2 ...: / WDR90, 4th beta-propeller / : / : / ODAD1 central coiled coil region / Protein Flattop / Flattop / Nucleoside diphosphate kinase 7 / Piercer of microtubule wall 1/2 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 161-like domain / : / : / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 45 / NDPK7, second NDPk domain / Cilia- and flagella- associated protein 210 / CFAP53/TCHP / Trichohyalin-plectin-homology domain / Trichohyalin-plectin-homology domain / RIB43A / RIB43A / DM10 domain / EF-hand domain-containing protein EFHC1/EFHC2/EFHB / DM10 domain / DM10 domain profile. / Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. / Enkurin domain / : / Calmodulin-binding / Enkurin domain profile. / : / CFA20 domain / Cilia- and flagella-associated protein 20/CFAP20DC / CFA20 domain / : / Parkin co-regulated protein / Parkin co-regulated protein / EF-hand domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Heat shock protein 70kD, peptide-binding domain superfamily / Heat shock protein 70 family / Hsp70 protein / 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 / Nucleotide-diphospho-sugar transferases / 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 / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 52 / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Trichohyalin-plectin-homology domain-containing protein / Flagellar associated protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Meiosis-specific nuclear structural protein 1 / Cilia- and flagella-associated protein 52 / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Flagellar associated protein / Trichohyalin-plectin-homology domain-containing protein / Flagellar associated protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / EF-hand domain-containing protein / Cilia- and flagella-associated protein 45 / Uncharacterized protein / Flagellar associated protein / Uncharacterized protein / Cilia- and flagella-associated protein 53 / Cilia- and flagella-associated protein 20 / Protein Flattop homolog / Uncharacterized protein / Flagellar associated protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Outer dynein arm protein 1 / Nucleoside diphosphate kinase / Uncharacterized protein / Parkin-co-regulated gene product / Tubulin beta-1/beta-2 chain / Tubulin alpha-1 chain / Outer dynein arm-docking complex protein DC3 / RIB72 protein / Flagellar protofilament ribbon protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsMa, M. / Stoyanova, M. / Rademacher, G. / Dutcher, S.K. / Brown, A. / Zhang, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM032843 United States
CitationJournal: Cell / Year: 2019
Title: Structure of the Decorated Ciliary Doublet Microtubule.
Authors: Meisheng Ma / Mihaela Stoyanova / Griffin Rademacher / Susan K Dutcher / Alan Brown / Rui Zhang /
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 ...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.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
1: Tubulin beta
2: Tubulin alpha
3: Tubulin beta
4: Tubulin alpha
5: Tubulin beta
6: Tubulin alpha
7: Tubulin beta
8: Tubulin alpha
9: Tubulin beta
A0: Tubulin alpha
A1: Tubulin beta
A2: Tubulin alpha
A3: Tubulin beta
A4: Tubulin alpha
A5: Tubulin beta
A7: Tubulin beta
A8: Tubulin alpha
A9: Tubulin beta
B0: Tubulin alpha
B1: Tubulin beta
B2: Tubulin alpha
B3: Tubulin beta
B4: Tubulin alpha
B5: Tubulin beta
B7: Tubulin alpha
B8: Tubulin beta
B9: Tubulin alpha
C0: Tubulin beta
C1: Tubulin alpha
C2: Tubulin beta
C4: Tubulin beta
C5: Tubulin alpha
C6: Tubulin beta
C7: Tubulin alpha
C8: Tubulin beta
C9: Tubulin alpha
D0: Tubulin beta
D1: Tubulin alpha
D2: Tubulin beta
D3: Tubulin alpha
D4: Tubulin beta
D5: Tubulin alpha
D6: Tubulin beta
D7: Tubulin alpha
D8: Tubulin beta
E0: Tubulin beta
E1: Tubulin alpha
E2: Tubulin beta
E3: Tubulin alpha
E4: Tubulin beta
E5: Tubulin alpha
E6: Tubulin beta
E7: Tubulin alpha
E8: Tubulin beta
E9: Tubulin alpha
F0: Tubulin beta
F1: Tubulin alpha
F2: Tubulin beta
F3: Tubulin alpha
F5: Tubulin alpha
F6: Tubulin beta
F7: Tubulin alpha
F8: Tubulin beta
F9: Tubulin alpha
G0: Tubulin beta
G1: Tubulin alpha
G2: Tubulin beta
G3: Tubulin alpha
G4: Tubulin beta
G5: Tubulin alpha
G6: Tubulin beta
G7: Tubulin alpha
G8: Tubulin beta
G9: Tubulin alpha
H1: Tubulin alpha
H2: Tubulin beta
H3: Tubulin alpha
H4: Tubulin beta
H5: Tubulin alpha
H6: Tubulin beta
H7: Tubulin alpha
H8: Tubulin beta
H9: Tubulin alpha
I0: Tubulin beta
I1: Tubulin alpha
I2: Tubulin beta
I3: Tubulin alpha
I4: Tubulin beta
I5: Tubulin alpha
I7: Tubulin alpha
I8: Tubulin beta
I9: Tubulin alpha
J0: Tubulin beta
J1: Tubulin alpha
J2: Tubulin beta
J3: Tubulin alpha
J4: Tubulin beta
J5: Tubulin alpha
J6: Tubulin beta
J7: Tubulin alpha
J8: Tubulin beta
J9: Tubulin alpha
K0: Tubulin beta
K1: Tubulin alpha
K3: Tubulin alpha
K4: Tubulin beta
K5: Tubulin alpha
K6: Tubulin beta
K7: Tubulin alpha
K8: Tubulin beta
K9: Tubulin alpha
L0: Tubulin beta
L1: Tubulin alpha
L2: Tubulin beta
L3: Tubulin alpha
L4: Tubulin beta
L5: Tubulin alpha
L6: Tubulin beta
L7: Tubulin alpha
L9: Tubulin alpha
M0: Tubulin beta
M1: Tubulin alpha
M2: Tubulin beta
M3: Tubulin alpha
M4: Tubulin beta
M5: Tubulin alpha
M6: Tubulin beta
M7: Tubulin alpha
M8: Tubulin beta
M9: Tubulin alpha
N0: Tubulin beta
N1: Tubulin alpha
N2: Tubulin beta
N3: Tubulin alpha
N5: Tubulin alpha
N6: Tubulin beta
N7: Tubulin alpha
N8: Tubulin beta
N9: Tubulin alpha
O0: Tubulin beta
O1: Tubulin alpha
O2: Tubulin beta
O3: Tubulin alpha
O4: Tubulin beta
O5: Tubulin alpha
O6: Tubulin beta
O7: Tubulin alpha
O8: Tubulin beta
O9: Tubulin alpha
P3: Tubulin alpha
P4: Tubulin beta
P5: Tubulin alpha
P6: Tubulin beta
P7: Tubulin alpha
P8: Tubulin beta
P9: Tubulin alpha
Q0: Tubulin beta
Q1: Tubulin alpha
Q2: Tubulin beta
Q3: Tubulin alpha
Q4: Tubulin beta
Q5: Tubulin alpha
Q6: Tubulin beta
Q8: Tubulin beta
Q9: Tubulin alpha
R0: Tubulin beta
R1: Tubulin alpha
R2: Tubulin beta
R3: Tubulin alpha
R4: Tubulin beta
R5: Tubulin alpha
R6: Tubulin beta
R7: Tubulin alpha
R8: Tubulin beta
R9: Tubulin alpha
S0: Tubulin beta
S1: Tubulin alpha
S2: Tubulin beta
S4: Tubulin beta
S5: Tubulin alpha
S6: Tubulin beta
S7: Tubulin alpha
S8: Tubulin beta
S9: Tubulin alpha
T0: Tubulin beta
T1: Tubulin alpha
T2: Tubulin beta
T3: Tubulin alpha
T4: Tubulin beta
T5: Tubulin alpha
T6: Tubulin beta
T7: Tubulin alpha
T8: Tubulin beta
U1: Tubulin alpha
U2: Tubulin beta
U3: Tubulin alpha
U4: Tubulin beta
U5: Tubulin alpha
U6: Tubulin beta
U7: Tubulin alpha
U8: Tubulin beta
U9: Tubulin alpha
V0: Tubulin beta
V1: Tubulin alpha
V2: Tubulin beta
V3: Tubulin alpha
V4: Tubulin beta
V6: Tubulin beta
V7: Tubulin alpha
V8: Tubulin beta
V9: Tubulin alpha
W0: Tubulin beta
W1: Tubulin alpha
W2: Tubulin beta
W3: Tubulin alpha
W4: Tubulin beta
W5: Tubulin alpha
W6: Tubulin beta
W7: Tubulin alpha
W8: Tubulin beta
W9: Tubulin alpha
X0: Tubulin beta
X2: Tubulin beta
X3: Tubulin alpha
X4: Tubulin beta
X5: Tubulin alpha
X6: Tubulin beta
X7: Tubulin alpha
X8: Tubulin beta
X9: Tubulin alpha
Y0: Tubulin beta
Y1: Tubulin alpha
Y2: Tubulin beta
Y3: Tubulin alpha
Y4: Tubulin beta
Y5: Tubulin alpha
Y6: Tubulin beta
Y8: Tubulin beta
Y9: Tubulin alpha
Z0: Tubulin beta
Z1: Tubulin alpha
Z2: Tubulin beta
Z3: Tubulin alpha
Z4: Tubulin beta
Z5: Tubulin alpha
Z6: Tubulin beta
Z7: Tubulin alpha
Z8: Tubulin beta
Z9: Tubulin alpha
0A: Tubulin beta
0B: Tubulin alpha
0C: Tubulin beta
0E: Tubulin beta
0F: Tubulin alpha
0G: Tubulin beta
0H: Tubulin alpha
0I: Tubulin beta
0J: Tubulin alpha
0K: Tubulin beta
0L: Tubulin alpha
0M: Tubulin beta
0N: Tubulin alpha
0O: Tubulin beta
0P: Tubulin alpha
0Q: Tubulin beta
0R: Tubulin alpha
0S: Tubulin beta
0U: Tubulin beta
0V: Tubulin alpha
0W: Tubulin beta
0X: Tubulin alpha
0Y: Tubulin beta
0Z: Tubulin alpha
1A: Tubulin beta
1B: Tubulin alpha
1C: Tubulin beta
1D: Tubulin alpha
1E: Tubulin beta
1F: Tubulin alpha
1G: Tubulin beta
1H: Tubulin alpha
1K: Tubulin beta
1L: Tubulin alpha
1M: Tubulin beta
1N: Tubulin alpha
1O: Tubulin beta
1P: Tubulin alpha
1Q: Tubulin beta
1R: Tubulin alpha
1S: Tubulin beta
1T: Tubulin alpha
1U: Tubulin beta
1V: Tubulin alpha
1W: Tubulin beta
1X: Tubulin alpha
1Z: 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
2I: Tubulin beta
2J: Tubulin alpha
2K: Tubulin beta
2L: Tubulin alpha
2M: Tubulin beta
2N: Tubulin alpha
2P: Tubulin alpha
2Q: Tubulin beta
2R: Tubulin alpha
2S: Tubulin beta
2T: Tubulin alpha
2U: Tubulin beta
2V: Tubulin alpha
2W: Tubulin beta
2X: Tubulin alpha
2Y: Tubulin beta
2Z: Tubulin alpha
3A: Tubulin beta
3B: Tubulin alpha
3C: Tubulin beta
3D: Tubulin alpha
3F: Tubulin alpha
3G: Tubulin beta
3H: Tubulin alpha
3I: Tubulin beta
3J: Tubulin alpha
3K: Tubulin beta
3L: Tubulin alpha
3M: Tubulin beta
3N: Tubulin alpha
3O: Tubulin beta
3P: Tubulin alpha
3Q: Tubulin beta
3R: Tubulin alpha
3S: Tubulin beta
3T: Tubulin alpha
3V: PACRG
3W: FAP20
3X: PACRG
3Y: FAP20
3Z: PACRG
4A: FAP20
4B: PACRG
4C: FAP20
4D: PACRG
4E: FAP20
4F: PACRG
4G: FAP20
4H: PACRG
4I: FAP20
4J: PACRG
4L: FAP53
4M: FAP53
4N: FAP127
4O: FAP127
4P: FAP127
4Q: RIB43a
4R: RIB43a
4S: RIB43a
4T: RIB43a
4U: RIB43a
4V: FAP112
4W: FAP112
4X: FAP112
4Y: FAP210
4Z: FAP210
5A: FAP45
5B: FAP45
5C: FAP45
5D: FAP45
5E: RIB30
5F: FAP363
5G: FAP363
5H: FAP126
5I: FAP126
5J: FAP126
5K: FAP126
5L: FAP52
5M: FAP52
5N: FAP52
5O: FAP67
5P: FAP67
5Q: FAP85
5R: FAP106
5S: FAP106
5T: FAP106
5U: FAP106
5V: FAP106
5X: FAP115
5Y: FAP115
5Z: FAP115
6A: FAP115
6B: FAP115
6C: FAP115
6D: FAP115
6E: FAP143
6F: FAP161
6G: FAP166
6H: FAP166
6I: FAP252
6J: FAP252
6K: FAP252
6L: FAP252
6M: FAP252
6N: FAP252
6O: FAP252
6P: FAP252
6Q: FAP276
6R: FAP276
6S: FAP276
6T: RIB72
6U: RIB72
6V: RIB72
6W: RIB72
6X: RIB72
6Y: RIB72
6Z: RIB72
7A: RIB72
7B: FAP363
7C: FAP141
7D: FAP222
7E: FAP222
7F: FAP222
7G: FAP95
7H: FAP182
7I: FAP129
7J: FAP129
7K: FAP21
7L: FAP21
7M: FAP273
7N: FAP273
7O: FAP107
7P: FAP107
7Q: RIB21
7R: DC1
7S: DC1
7T: DC2
7U: DC2
7V: DC3
7W: DC3
7X: FAP182
7Y: FAP68
7Z: FAP90
8A: FAP90
8B: FAP90
8C: FAP90
8D: FAP90
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,385,503961
Polymers21,217,086451
Non-polymers168,417510
Water00
1


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

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Components

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Protein , 38 types, 451 molecules 13579A1A3A5A7A9B1B3B5B8C0C2C4C6C8D0D2D4D6D8E0E2E4E6E8F0...

#1: Protein ...
Tubulin beta / Tubulin beta-1/beta-2 chain / Beta-tubulin


Mass: 49665.809 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P04690
#2: Protein ...
Tubulin alpha / Tubulin alpha-1 chain


Mass: 49638.008 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P09204
#3: Protein
PACRG / Parkin-co-regulated gene product


Mass: 34215.148 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: B1B601
#4: Protein
FAP20 / Cilia- and flagella-associated protein 20 / Basal body up-regulated protein 22 / Bug22p / Flagellar- ...Cilia- and flagella-associated protein 20 / Basal body up-regulated protein 22 / Bug22p / Flagellar-associated protein 20


Mass: 22193.566 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IU92
#5: Protein FAP53 / Cilia- and flagella-associated protein 53


Mass: 56655.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IRJ7
#6: Protein FAP127


Mass: 60027.434 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3CRG7
#7: Protein
RIB43a / Coiled-coil protein associated with protofilament ribbons / Flagellar protofilament ribbon protein


Mass: 42712.711 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q9M6B0
#8: Protein FAP112 / Flagellar associated protein


Mass: 53126.352 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J0X0
#9: Protein FAP210


Mass: 53637.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E0E3
#10: Protein
FAP45 / Cilia- and flagella-associated protein 45 / Flagellum-associated protein 45


Mass: 59041.469 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I9E8
#11: Protein RIB30


Mass: 29859.654 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E5X9
#12: Protein FAP363


Mass: 43879.367 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IY81
#13: Protein
FAP126 / Cilia- and flagella-associated protein 126 / Flagellum-associated protein 126


Mass: 15435.397 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IVJ1
#14: Protein FAP52


Mass: 68546.508 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D260
#15: Protein FAP67


Mass: 41994.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JGW5, nucleoside-diphosphate kinase
#16: Protein FAP85 / Flagellar associated protein 85


Mass: 22228.705 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J250
#17: Protein
FAP106 / Flagellar associated protein 106


Mass: 27019.803 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8J098
#18: Protein
FAP115 / Flagellar associated protein 115


Mass: 26647.648 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JDK1
#19: Protein FAP143


Mass: 29216.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3E1X6
#20: Protein FAP161 / Flagellar associated protein 161


Mass: 42849.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HRH3
#21: Protein FAP166


Mass: 23303.205 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DZF0
#22: Protein
FAP252 / Flagellar associated protein 252


Mass: 39507.379 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I1S7
#23: Protein FAP276


Mass: 10073.385 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DTN6
#24: Protein
RIB72 / Protofilament ribbon protein of flagellar microtubules / RIB72 protein / p72


Mass: 72082.609 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q8LKK4
#25: Protein FAP141 / Flagellar associated protein 141


Mass: 12740.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IMR3
#26: Protein FAP222 / Flagellar associated protein 222


Mass: 15920.962 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF23
#27: Protein FAP95 / Flagellar associated protein 95


Mass: 25576.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HSW0
#28: Protein FAP182 / Flagellar associated protein 182


Mass: 48843.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JHR6
#29: Protein FAP129


Mass: 51330.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3DZI2
#30: Protein FAP21


Mass: 49657.867 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
#31: Protein FAP273 / Flagellar associated protein 273


Mass: 15469.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8IXN7
#32: Protein FAP107 / Flagellar associated protein 107


Mass: 25937.781 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JC52
#33: Protein RIB21


Mass: 20949.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A0A2K3D7C7
#34: Protein DC1 / Outer dynein arm-docking complex subunit 1


Mass: 83518.180 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant)
References: UniProt: A8IPZ5, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#35: Protein DC2 / Docking complex component 2


Mass: 62292.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8JF70
#36: Protein DC3 / Outer dynein arm-docking complex protein DC3 / Outer dynein arm-docking complex subunit 3


Mass: 21371.311 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q7Y0H2
#37: Protein FAP68 / Flagellar associated protein 68


Mass: 35568.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8HPK6
#38: Protein
FAP90 / Flagellar associated protein 90


Mass: 27760.064 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8ICC1

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Non-polymers , 3 types, 510 molecules

#39: Chemical...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 170 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#40: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 170 / Source method: obtained synthetically / Formula: Mg
#41: Chemical...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 170 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Compound detailsThe authors state that there are eight copies of the RIB72 protein, each connected by a flexible ...The authors state that there are eight copies of the RIB72 protein, each connected by a flexible linker to an N-terminus. They are not sure which N-terminus belongs to which protein. The N-terminus that has been assigned to chain 6U could, therefore, belong to another molecule or even to one not in their reconstruction.
Has ligand of interestN
Has protein modificationY

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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: Doublet microtubule from wild-type Chlamydomonas reinhardtii
Type: COMPLEX / Entity ID: #1-#38 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-125
Buffer solutionpH: 7.4
Details: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 0.5 mM EGTA, 25 mM KCl, PH 7.4
Buffer componentName: HMDEKP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K / Details: blot for 4 seconds before plunging

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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 magnification: 81000 X / Calibrated magnification: 81000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3100 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9 sec. / Electron dose: 38.9 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 6 / Num. of real images: 8314
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Microscope is equipped with a Cs corrector
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameCategory
2EPUimage acquisition
4RELIONCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11EMANinitial Euler assignment
12RELIONfinal Euler assignment
13RELIONclassification
14RELION3D reconstruction
Image processingDetails: The movies were drift-corrected using UCSF MotionCorr2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: doublet microtubules were manually selected
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143765 / Symmetry type: POINT
Atomic model buildingB value: 50 / Protocol: AB INITIO MODEL / Space: REAL

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