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- PDB-7rro: Structure of the 48-nm repeat doublet microtubule from bovine tra... -

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基本情報

登録情報
データベース: PDB / ID: 7rro
タイトルStructure of the 48-nm repeat doublet microtubule from bovine tracheal cilia
要素
  • (Cilia and flagella associated protein ...) x 3
  • (Coiled-coil domain containing ...) x 2
  • (EF-hand domain ...) x 2
  • (Uncharacterized protein ...) x 2
  • Armadillo repeat containing 4
  • Chromosome 3 C1orf194 homolog
  • Cilia- and flagella-associated protein 20
  • EF-hand calcium-binding domain-containing protein 1
  • EFCAB6
  • EFHC2
  • Enkurin, TRPC channel interacting protein
  • Meiosis-specific nuclear structural protein 1
  • Methyl-CpG binding domain protein 1
  • Nucleoside diphosphate kinase 7
  • Outer dynein arm-docking complex subunit 3
  • PACRG protein
  • Pierce1
  • Pierce2
  • Protein C9orf135 homolog
  • Protein FAM166B
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm associated antigen 8
  • TEKTIP1
  • TTC25 protein
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tubulin alpha-1D chain
  • Tubulin beta-4B chain
キーワードSTRUCTURAL PROTEIN / cilia / microtubule / dynein / motility
機能・相同性
機能・相同性情報


mucociliary clearance / outer dynein arm docking complex / regulation of cilium movement / epithelial cilium movement involved in determination of left/right asymmetry / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / outer acrosomal membrane / regulation of brood size / protein localization to motile cilium ...mucociliary clearance / outer dynein arm docking complex / regulation of cilium movement / epithelial cilium movement involved in determination of left/right asymmetry / sperm flagellum assembly / establishment of left/right asymmetry / 9+0 motile cilium / outer acrosomal membrane / regulation of brood size / protein localization to motile cilium / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / regulation of flagellated sperm motility / protein polyglutamylation / positive regulation of feeding behavior / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / cerebrospinal fluid circulation / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / outer dynein arm assembly / cilium-dependent cell motility / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / cilium movement involved in cell motility / regulation of cilium beat frequency involved in ciliary motility / 9+2 motile cilium / 転移酵素; リンを含む基を移すもの / acrosomal membrane / MHC class II antigen presentation / ciliary transition zone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cilium movement / regulation of cilium assembly / axoneme assembly / axonemal microtubule / Aggrephagy / cilium organization / flagellated sperm motility / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / gamma-tubulin ring complex / ciliary tip / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / manchette / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / GTP biosynthetic process / microtubule organizing center / Neutrophil degranulation / ciliary rootlet / nucleoside diphosphate kinase activity / regulation of neuron projection development / beta-tubulin binding / axoneme / mitotic cytokinesis / centriolar satellite / spermatid development / cilium assembly / cellular response to UV-C / single fertilization / alpha-tubulin binding / sperm flagellum / sperm midpiece / 3'-5' exonuclease activity / Hsp70 protein binding / centriole / mitotic spindle organization / acrosomal vesicle / ciliary basal body / meiotic cell cycle / G protein-coupled receptor binding / lung development / brain development / Hsp90 protein binding / cilium / structural constituent of cytoskeleton / mitotic spindle / SH3 domain binding / microtubule cytoskeleton organization / spindle pole
類似検索 - 分子機能
Outer dynein arm-docking complex subunit 4 / Outer dynein arm-docking complex subunit 3 / Tektin bundle interacting protein 1 / Tektin bundle interacting protein 1 / : / : / ODAD1 central coiled coil region / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain ...Outer dynein arm-docking complex subunit 4 / Outer dynein arm-docking complex subunit 3 / Tektin bundle interacting protein 1 / Tektin bundle interacting protein 1 / : / : / ODAD1 central coiled coil region / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / Protein CFAP95 / Cilia- and flagella-associated protein 143 / Cilia and flagella associated protein 107 / Tektin / Cilia- and flagella-associated protein 276 / : / Tektin family / Protein of unknown function (DUF3695) / Uncharacterised protein FAM166/UPF0605 / Protein Flattop / Ciliary microtubule inner protein 2B-like / Flattop / Nucleoside diphosphate kinase 7 / Meiosis-specific nuclear structural protein 1 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / 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 / Piercer of microtubule wall 1/2 / Cilia- and flagella-associated protein 141 / 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 / Recoverin family / EF hand / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Tetratricopeptide repeat / TPR repeat region circular profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / TPR repeat profile. / 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 / Tetratricopeptide repeats / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Tetratricopeptide repeat / 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 / Armadillo-like helical / EF-hand domain pair / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile.
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Piercer of microtubule wall 2 protein / EF-hand domain-containing family member C2 / Outer dynein arm-docking complex subunit 4 / Parkin coregulated gene protein / Tektin-3 / Outer dynein arm-docking complex subunit 3 / Enkurin / Outer dynein arm-docking complex subunit 2 ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Piercer of microtubule wall 2 protein / EF-hand domain-containing family member C2 / Outer dynein arm-docking complex subunit 4 / Parkin coregulated gene protein / Tektin-3 / Outer dynein arm-docking complex subunit 3 / Enkurin / Outer dynein arm-docking complex subunit 2 / Cilia- and flagella-associated protein 276 / Cilia- and flagella- associated protein 210 / Cilia- and flagella-associated protein 52 / EF-hand domain-containing protein 1 / Sperm-associated antigen 8 / Meiosis-specific nuclear structural protein 1 / EF-hand domain-containing family member B / Outer dynein arm-docking complex subunit 1 / Cilia- and flagella-associated protein 53 / Cilia- and flagella-associated protein 161 / Tubulin alpha-1D chain / Tektin bundle-interacting protein 1 / Tektin-2 / Cilia- and flagella-associated protein 107 / Tektin-4 / Ciliary microtubule inner protein 2B / Tektin-1 / Calaxin / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 95 / RIB43A-like with coiled-coils protein 2 / Cilia- and flagella-associated protein 45 / Piercer of microtubule wall 1 protein / Tubulin beta-4B chain / Protein Flattop / Nucleoside diphosphate kinase homolog 7 / Cilia- and flagella-associated protein 20
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.4 Å
データ登録者Gui, M. / Anderson, J.R. / Botsch, J.J. / Meleppattu, S. / Singh, S.K. / Zhang, Q. / Brown, A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) 米国
引用ジャーナル: Cell / 年: 2021
タイトル: De novo identification of mammalian ciliary motility proteins using cryo-EM.
著者: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James ...著者: Miao Gui / Hannah Farley / Priyanka Anujan / Jacob R Anderson / Dale W Maxwell / Jonathan B Whitchurch / J Josephine Botsch / Tao Qiu / Shimi Meleppattu / Sandeep K Singh / Qi Zhang / James Thompson / Jane S Lucas / Colin D Bingle / Dominic P Norris / Sudipto Roy / Alan Brown /
要旨: Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner ...Dynein-decorated doublet microtubules (DMTs) are critical components of the oscillatory molecular machine of cilia, the axoneme, and have luminal surfaces patterned periodically by microtubule inner proteins (MIPs). Here we present an atomic model of the 48-nm repeat of a mammalian DMT, derived from a cryoelectron microscopy (cryo-EM) map of the complex isolated from bovine respiratory cilia. The structure uncovers principles of doublet microtubule organization and features specific to vertebrate cilia, including previously unknown MIPs, a luminal bundle of tektin filaments, and a pentameric dynein-docking complex. We identify a mechanism for bridging 48- to 24-nm periodicity across the microtubule wall and show that loss of the proteins involved causes defective ciliary motility and laterality abnormalities in zebrafish and mice. Our structure identifies candidate genes for diagnosis of ciliopathies and provides a framework to understand their functions in driving ciliary motility.
履歴
登録2021年8月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年10月27日Provider: repository / タイプ: Initial release
改定 1.12021年11月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22021年11月24日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first
改定 1.32024年6月5日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-24664
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
0: Protein C9orf135 homolog
1: EF-hand domain family member B
2: EF-hand domain family member B
3: Methyl-CpG binding domain protein 1
4: Methyl-CpG binding domain protein 1
5: Nucleoside diphosphate kinase 7
6: Nucleoside diphosphate kinase 7
7: Protein C9orf135 homolog
8: Uncharacterized protein C1orf158 homolog
9: Uncharacterized protein C1orf158 homolog
A: Meiosis-specific nuclear structural protein 1
A0: Tektin-1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AA: Tubulin alpha-1D chain
AB: Tubulin beta-4B chain
AC: Tubulin alpha-1D chain
AD: Tubulin beta-4B chain
AE: Tubulin alpha-1D chain
AF: Tubulin beta-4B chain
AG: Tubulin alpha-1D chain
AH: Tubulin beta-4B chain
AI: Tubulin alpha-1D chain
AJ: Tubulin beta-4B chain
AK: Tubulin alpha-1D chain
AL: Tubulin beta-4B chain
AM: Tubulin alpha-1D chain
B: Meiosis-specific nuclear structural protein 1
B0: Tektin-2
B1: Tektin-2
B2: Tektin-2
B3: Tektin-2
B4: Tektin-2
B5: Tektin-2
B6: Tektin-2
B7: Tektin-2
B8: Tektin-2
B9: Tektin-2
BA: Tubulin alpha-1D chain
BB: Tubulin beta-4B chain
BC: Tubulin alpha-1D chain
BD: Tubulin beta-4B chain
BE: Tubulin alpha-1D chain
BF: Tubulin beta-4B chain
BG: Tubulin alpha-1D chain
BH: Tubulin beta-4B chain
BI: Tubulin alpha-1D chain
BJ: Tubulin beta-4B chain
BK: Tubulin alpha-1D chain
BL: Tubulin beta-4B chain
BM: Tubulin alpha-1D chain
C: Uncharacterized protein C1orf189 homolog
C0: Tektin-3
C1: Tektin-3
C2: Tektin-3
C3: Tektin-3
C4: Tektin-3
C5: Tektin-3
C6: Tektin-3
C7: Tektin-3
C8: Tektin-3
C9: Tektin-3
CA: Tubulin alpha-1D chain
CB: Tubulin beta-4B chain
CC: Tubulin alpha-1D chain
CD: Tubulin beta-4B chain
CE: Tubulin alpha-1D chain
CF: Tubulin beta-4B chain
CG: Tubulin alpha-1D chain
CH: Tubulin beta-4B chain
CI: Tubulin alpha-1D chain
CJ: Tubulin beta-4B chain
CK: Tubulin alpha-1D chain
CL: Tubulin beta-4B chain
CM: Tubulin alpha-1D chain
D: Sperm associated antigen 8
D0: Tektin-4
D1: Tektin-4
D2: Tektin-4
D3: Tektin-4
D5: Tektin-4
D6: Tektin-4
D7: Tektin-4
D8: Tektin-4
D9: Tektin-4
DA: Tubulin alpha-1D chain
DB: Tubulin beta-4B chain
DC: Tubulin alpha-1D chain
DD: Tubulin beta-4B chain
DE: Tubulin alpha-1D chain
DF: Tubulin beta-4B chain
DG: Tubulin alpha-1D chain
DH: Tubulin beta-4B chain
DI: Tubulin alpha-1D chain
DJ: Tubulin beta-4B chain
DK: Tubulin alpha-1D chain
DL: Tubulin beta-4B chain
DM: Tubulin alpha-1D chain
DN: Tubulin beta-4B chain
E: Cilia and flagella associated protein 161
E0: TEKTIP1
E1: TEKTIP1
E2: TEKTIP1
E3: TEKTIP1
EB: Tubulin beta-4B chain
EC: Tubulin alpha-1D chain
ED: Tubulin beta-4B chain
EE: Tubulin alpha-1D chain
EF: Tubulin beta-4B chain
EG: Tubulin alpha-1D chain
EH: Tubulin beta-4B chain
EI: Tubulin alpha-1D chain
EJ: Tubulin beta-4B chain
EK: Tubulin alpha-1D chain
EL: Tubulin beta-4B chain
EM: Tubulin alpha-1D chain
EN: Tubulin beta-4B chain
F: Cilia and flagella associated protein 161
F0: Tektin-3
F1: Tektin-3
F2: Tektin-3
F3: Tektin-3
F4: Tektin-3
FB: Tubulin beta-4B chain
FC: Tubulin alpha-1D chain
FD: Tubulin beta-4B chain
FE: Tubulin alpha-1D chain
FF: Tubulin beta-4B chain
FG: Tubulin alpha-1D chain
FH: Tubulin beta-4B chain
FI: Tubulin alpha-1D chain
FJ: Tubulin beta-4B chain
FK: Tubulin alpha-1D chain
FL: Tubulin beta-4B chain
FM: Tubulin alpha-1D chain
FN: Tubulin beta-4B chain
G: Pierce2
GB: Tubulin beta-4B chain
GC: Tubulin alpha-1D chain
GD: Tubulin beta-4B chain
GE: Tubulin alpha-1D chain
GF: Tubulin beta-4B chain
GG: Tubulin alpha-1D chain
GH: Tubulin beta-4B chain
GI: Tubulin alpha-1D chain
GJ: Tubulin beta-4B chain
GK: Tubulin alpha-1D chain
GL: Tubulin beta-4B chain
GM: Tubulin alpha-1D chain
GN: Tubulin beta-4B chain
H: Protein FAM166B
H1: Coiled-coil domain containing 114
H2: Coiled-coil domain containing 114
H3: Coiled-coil domain containing 114
H4: Outer dynein arm-docking complex subunit 3
H5: Outer dynein arm-docking complex subunit 3
H6: Outer dynein arm-docking complex subunit 3
H7: Armadillo repeat containing 4
H8: Armadillo repeat containing 4
H9: Armadillo repeat containing 4
HB: Tubulin beta-4B chain
HC: Tubulin alpha-1D chain
HD: Tubulin beta-4B chain
HE: Tubulin alpha-1D chain
HF: Tubulin beta-4B chain
HG: Tubulin alpha-1D chain
HH: Tubulin beta-4B chain
HI: Tubulin alpha-1D chain
HJ: Tubulin beta-4B chain
HK: Tubulin alpha-1D chain
HL: Tubulin beta-4B chain
HM: Tubulin alpha-1D chain
HN: Tubulin beta-4B chain
HO: Tubulin alpha-1D chain
I: Protein FAM166B
I1: TTC25 protein
I2: TTC25 protein
I3: EF-hand calcium-binding domain-containing protein 1
I4: EF-hand calcium-binding domain-containing protein 1
IB: Tubulin beta-4B chain
IC: Tubulin alpha-1D chain
ID: Tubulin beta-4B chain
IE: Tubulin alpha-1D chain
IF: Tubulin beta-4B chain
IG: Tubulin alpha-1D chain
IH: Tubulin beta-4B chain
II: Tubulin alpha-1D chain
IJ: Tubulin beta-4B chain
IK: Tubulin alpha-1D chain
IL: Tubulin beta-4B chain
IM: Tubulin alpha-1D chain
IN: Tubulin beta-4B chain
IO: Tubulin alpha-1D chain
J: Protein FAM166B
JB: Tubulin beta-4B chain
JC: Tubulin alpha-1D chain
JD: Tubulin beta-4B chain
JE: Tubulin alpha-1D chain
JF: Tubulin beta-4B chain
JG: Tubulin alpha-1D chain
JH: Tubulin beta-4B chain
JI: Tubulin alpha-1D chain
JJ: Tubulin beta-4B chain
JK: Tubulin alpha-1D chain
JL: Tubulin beta-4B chain
JM: Tubulin alpha-1D chain
JN: Tubulin beta-4B chain
K: Protein FAM166B
KB: Tubulin beta-4B chain
KC: Tubulin alpha-1D chain
KD: Tubulin beta-4B chain
KE: Tubulin alpha-1D chain
KF: Tubulin beta-4B chain
KG: Tubulin alpha-1D chain
KH: Tubulin beta-4B chain
KI: Tubulin alpha-1D chain
KJ: Tubulin beta-4B chain
KK: Tubulin alpha-1D chain
KL: Tubulin beta-4B chain
KM: Tubulin alpha-1D chain
KN: Tubulin beta-4B chain
KO: Tubulin alpha-1D chain
L: Protein FAM166B
LB: Tubulin beta-4B chain
LC: Tubulin alpha-1D chain
LD: Tubulin beta-4B chain
LE: Tubulin alpha-1D chain
LF: Tubulin beta-4B chain
LG: Tubulin alpha-1D chain
LH: Tubulin beta-4B chain
LI: Tubulin alpha-1D chain
LJ: Tubulin beta-4B chain
LK: Tubulin alpha-1D chain
LL: Tubulin beta-4B chain
LM: Tubulin alpha-1D chain
LN: Tubulin beta-4B chain
M: Protein FAM166B
MB: Tubulin beta-4B chain
MC: Tubulin alpha-1D chain
MD: Tubulin beta-4B chain
ME: Tubulin alpha-1D chain
MF: Tubulin beta-4B chain
MG: Tubulin alpha-1D chain
MH: Tubulin beta-4B chain
MI: Tubulin alpha-1D chain
MJ: Tubulin beta-4B chain
MK: Tubulin alpha-1D chain
ML: Tubulin beta-4B chain
MM: Tubulin alpha-1D chain
MN: Tubulin beta-4B chain
N: Protein FAM166B
N0: Tubulin beta-4B chain
NA: Tubulin alpha-1D chain
NB: Tubulin beta-4B chain
NC: Tubulin alpha-1D chain
ND: Tubulin beta-4B chain
NE: Tubulin alpha-1D chain
NF: Tubulin beta-4B chain
NG: Tubulin alpha-1D chain
NH: Tubulin beta-4B chain
NI: Tubulin alpha-1D chain
NJ: Tubulin beta-4B chain
NK: Tubulin alpha-1D chain
NL: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
O0: Tubulin beta-4B chain
OA: Tubulin alpha-1D chain
OB: Tubulin beta-4B chain
OC: Tubulin alpha-1D chain
OD: Tubulin beta-4B chain
OE: Tubulin alpha-1D chain
OF: Tubulin beta-4B chain
OG: Tubulin alpha-1D chain
OH: Tubulin beta-4B chain
OI: Tubulin alpha-1D chain
OJ: Tubulin beta-4B chain
OK: Tubulin alpha-1D chain
OL: Tubulin beta-4B chain
P: RIB43A-like with coiled-coils protein 2
PA: Tubulin alpha-1D chain
PB: Tubulin beta-4B chain
PC: Tubulin alpha-1D chain
PD: Tubulin beta-4B chain
PE: Tubulin alpha-1D chain
PF: Tubulin beta-4B chain
PG: Tubulin alpha-1D chain
PH: Tubulin beta-4B chain
PI: Tubulin alpha-1D chain
PJ: Tubulin beta-4B chain
PK: Tubulin alpha-1D chain
PL: Tubulin beta-4B chain
PM: Tubulin alpha-1D chain
Q: RIB43A-like with coiled-coils protein 2
QA: Tubulin alpha-1D chain
QB: Tubulin beta-4B chain
QC: Tubulin alpha-1D chain
QD: Tubulin beta-4B chain
QE: Tubulin alpha-1D chain
QF: Tubulin beta-4B chain
QG: Tubulin alpha-1D chain
QH: Tubulin beta-4B chain
QI: Tubulin alpha-1D chain
QJ: Tubulin beta-4B chain
QK: Tubulin alpha-1D chain
QL: Tubulin beta-4B chain
QM: Tubulin alpha-1D chain
R: RIB43A-like with coiled-coils protein 2
RA: Tubulin alpha-1D chain
RB: Tubulin beta-4B chain
RC: Tubulin alpha-1D chain
RD: Tubulin beta-4B chain
RE: Tubulin alpha-1D chain
RF: Tubulin beta-4B chain
RG: Tubulin alpha-1D chain
RH: Tubulin beta-4B chain
RI: Tubulin alpha-1D chain
RJ: Tubulin beta-4B chain
RK: Tubulin alpha-1D chain
RL: Tubulin beta-4B chain
RM: Tubulin alpha-1D chain
S: RIB43A-like with coiled-coils protein 2
SA: Tubulin alpha-1D chain
SB: Tubulin beta-4B chain
SC: Tubulin alpha-1D chain
SD: Tubulin beta-4B chain
SE: Tubulin alpha-1D chain
SF: Tubulin beta-4B chain
SG: Tubulin alpha-1D chain
SH: Tubulin beta-4B chain
SI: Tubulin alpha-1D chain
SJ: Tubulin beta-4B chain
SK: Tubulin alpha-1D chain
SL: Tubulin beta-4B chain
SM: Tubulin alpha-1D chain
T: EF-hand domain containing 1
TB: Tubulin beta-4B chain
TC: Tubulin alpha-1D chain
TD: Tubulin beta-4B chain
TE: Tubulin alpha-1D chain
TF: Tubulin beta-4B chain
TG: Tubulin alpha-1D chain
TH: Tubulin beta-4B chain
TI: Tubulin alpha-1D chain
TJ: Tubulin beta-4B chain
TK: Tubulin alpha-1D chain
TL: Tubulin beta-4B chain
TM: Tubulin alpha-1D chain
U: EF-hand domain containing 1
UB: Tubulin beta-4B chain
UC: Tubulin alpha-1D chain
UD: Tubulin beta-4B chain
UE: Tubulin alpha-1D chain
UF: Tubulin beta-4B chain
UG: Tubulin alpha-1D chain
UH: Tubulin beta-4B chain
UI: Tubulin alpha-1D chain
UJ: Tubulin beta-4B chain
UK: Tubulin alpha-1D chain
UL: Tubulin beta-4B chain
UM: Tubulin alpha-1D chain
UN: Tubulin beta-4B chain
V: EF-hand domain containing 1
VB: Tubulin beta-4B chain
VC: Tubulin alpha-1D chain
VD: Tubulin beta-4B chain
VE: Tubulin alpha-1D chain
VF: Tubulin beta-4B chain
VG: Tubulin alpha-1D chain
VH: Tubulin beta-4B chain
VI: Tubulin alpha-1D chain
VJ: Tubulin beta-4B chain
VK: Tubulin alpha-1D chain
VL: Tubulin beta-4B chain
VM: Tubulin alpha-1D chain
VN: Tubulin beta-4B chain
W: EFHC2
WB: Tubulin beta-4B chain
WC: Tubulin alpha-1D chain
WD: Tubulin beta-4B chain
WE: Tubulin alpha-1D chain
WF: Tubulin beta-4B chain
WG: Tubulin alpha-1D chain
WH: Tubulin beta-4B chain
WI: Tubulin alpha-1D chain
WJ: Tubulin beta-4B chain
WK: Tubulin alpha-1D chain
WL: Tubulin beta-4B chain
WM: Tubulin alpha-1D chain
WN: Tubulin beta-4B chain
X: EFHC2
XA: Cilia- and flagella-associated protein 20
XB: Cilia- and flagella-associated protein 20
XC: Cilia- and flagella-associated protein 20
XD: Cilia- and flagella-associated protein 20
XE: Cilia- and flagella-associated protein 20
XF: Cilia- and flagella-associated protein 20
XG: Cilia- and flagella-associated protein 20
Y: EFHC2
YB: PACRG protein
YC: PACRG protein
YD: PACRG protein
YE: PACRG protein
YF: PACRG protein
YG: PACRG protein
Z: EFHC2
a: Cilia and flagella associated protein 45
b: Cilia and flagella associated protein 45
c: Cilia and flagella associated protein 45
d: Cilia and flagella associated protein 45
e: Cilia and flagella associated protein 52
f: Cilia and flagella associated protein 52
g: Cilia and flagella associated protein 52
h: Enkurin, TRPC channel interacting protein
i: Enkurin, TRPC channel interacting protein
j: Enkurin, TRPC channel interacting protein
k: Enkurin, TRPC channel interacting protein
l: Protein Flattop
m: Protein Flattop
n: Protein Flattop
o: Coiled-coil domain containing 173
p: Coiled-coil domain containing 173
q: Chromosome 3 C1orf194 homolog
r: Chromosome 3 C1orf194 homolog
s: Chromosome 3 C1orf194 homolog
t: EFCAB6
y: Pierce1
z: Pierce1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,608,302880
ポリマ－21,458,917429
非ポリマー149,385451
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法
タイプ名称対称操作数
identity operation1_5551

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要素

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タンパク質 , 27種, 407分子 073456ABA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCE...

#1: タンパク質 Protein C9orf135 homolog


分子量: 26661.025 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L77
#3: タンパク質 Methyl-CpG binding domain protein 1


分子量: 62138.992 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1N7G5
#4: タンパク質 Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7


分子量: 42650.895 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q5E9Y9, nucleoside-diphosphate kinase
#6: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 60572.148 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1MH18
#7: タンパク質
Tektin-1


分子量: 48798.375 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32KZ9
#8: タンパク質 ...
Tubulin alpha-1D chain


分子量: 50335.594 Da / 分子数: 149 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2HJ86
#9: タンパク質 ...
Tubulin beta-4B chain / Tubulin beta-2C chain


分子量: 49877.824 Da / 分子数: 153 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q3MHM5
#10: タンパク質
Tektin-2


分子量: 49962.656 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2T9Q6
#12: タンパク質
Tektin-3


分子量: 56760.910 Da / 分子数: 15 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A6H782
#13: タンパク質 Sperm associated antigen 8


分子量: 51604.398 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BNS6
#14: タンパク質
Tektin-4


分子量: 52025.488 Da / 分子数: 9 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TA38
#16: タンパク質
TEKTIP1


分子量: 24533.445 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2M2T2
#17: タンパク質 Pierce2


分子量: 13784.531 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1LFK7
#18: タンパク質
Protein FAM166B


分子量: 30551.627 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TBR5
#20: タンパク質 Outer dynein arm-docking complex subunit 3 / Coiled-coil domain-containing protein 151


分子量: 72163.984 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A7MBH5
#21: タンパク質 Armadillo repeat containing 4


分子量: 116017.070 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B8W3
#22: タンパク質 TTC25 protein / Tetratricopeptide repeat domain 25


分子量: 78492.633 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A5PK42
#23: タンパク質 EF-hand calcium-binding domain-containing protein 1 / Calaxin


分子量: 24667.131 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L26
#24: タンパク質
RIB43A-like with coiled-coils protein 2


分子量: 44773.418 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32LJ7
#26: タンパク質
EFHC2


分子量: 85566.766 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A0A3Q1N1R0
#27: タンパク質
Cilia- and flagella-associated protein 20


分子量: 22781.389 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q6B857
#28: タンパク質
PACRG protein / Parkin coregulated


分子量: 29323.059 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: A5PK71
#31: タンパク質
Enkurin, TRPC channel interacting protein


分子量: 30215.129 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B836
#32: タンパク質 Protein Flattop / Cilia- and flagella-associated protein 126


分子量: 21214.035 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q3SZT6
#34: タンパク質 Chromosome 3 C1orf194 homolog


分子量: 19387.805 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1B9I5
#35: タンパク質 EFCAB6


分子量: 172993.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ)
#36: タンパク質 Pierce1


分子量: 15673.458 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32P67

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EF-hand domain ... , 2種, 5分子 12TUV

#2: タンパク質 EF-hand domain family member B


分子量: 97960.547 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1MMV1
#25: タンパク質 EF-hand domain containing 1


分子量: 74125.344 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BKH1

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Uncharacterized protein ... , 2種, 3分子 89C

#5: タンパク質 Uncharacterized protein C1orf158 homolog


分子量: 23271.453 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q2TA11
#11: タンパク質 Uncharacterized protein C1orf189 homolog


分子量: 12361.437 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32L75

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Cilia and flagella associated protein ... , 3種, 9分子 EFabcdefg

#15: タンパク質 Cilia and flagella associated protein 161 / CFAP161


分子量: 36519.594 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F6RJC2
#29: タンパク質
Cilia and flagella associated protein 45 / Coiled-coil domain containing 19


分子量: 65800.328 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: Q32LN4
#30: タンパク質 Cilia and flagella associated protein 52


分子量: 68719.602 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BKF9

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Coiled-coil domain containing ... , 2種, 5分子 H1H2H3op

#19: タンパク質 Coiled-coil domain containing 114


分子量: 77675.969 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: F1N2N9
#33: タンパク質 Coiled-coil domain containing 173


分子量: 65437.598 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: E1BJL9

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非ポリマー , 3種, 451分子

#37: 化合物...
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP


分子量: 523.180 Da / 分子数: 149 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, エネルギー貯蔵分子*YM
#38: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 149 / 由来タイプ: 合成 / 式: Mg
#39: 化合物...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 153 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / コメント: GDP, エネルギー貯蔵分子*YM

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詳細

研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: FILAMENT / ３次元再構成法: 単粒子再構成法

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試料調製

構成要素名称: Doublet microtubule / タイプ: COMPLEX / Entity ID: #1-#36 / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Bos taurus (ウシ)
緩衝液pH: 7.4
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持詳細: unspecified
急速凍結凍結剤: ETHANE

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影電子線照射量: 60 e/Å2
フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k)

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解析

EMソフトウェア
ID名称バージョンカテゴリ
2SerialEM3.7画像取得
4CTFFIND4CTF補正
9RELION3.1初期オイラー角割当
10RELION3.1最終オイラー角割当
12RELION3.1３次元再構成
13PHENIX1.18モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
粒子像の選択選択した粒子像数: 1267170
3次元再構成解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 80503 / 対称性のタイプ: POINT
原子モデル構築プロトコル: AB INITIO MODEL

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る