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- PDB-7ung: 48-nm repeat of the human respiratory doublet microtubule -

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データベース: PDB / ID: 7ung
タイトル48-nm repeat of the human respiratory doublet microtubule
要素
  • (Cilia- and flagella-associated protein ...) x 5
  • (EF-hand domain-containing family member ...) x 2
  • (Uncharacterized protein ...) x 2
  • EF-hand domain-containing protein 1
  • Enkurin
  • Isoform 2 of Cilia- and flagella-associated protein 77
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase 7
  • Parkin coregulated gene protein
  • Protein CFAP107
  • Protein CFAP141
  • Protein CFAP210
  • Protein CFAP276
  • Protein CFAP95
  • Protein FAM166B
  • Protein FAM166C
  • Protein FAM183A
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome-associated protein 9
  • Sperm-associated antigen 8
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
  • UPF0686 protein C11orf1
  • UPF0691 protein C9orf116
キーワードSTRUCTURAL PROTEIN / cilia / microtubule / sperm / cell motility
機能・相同性
機能・相同性情報


axonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath ...axonemal microtubule doublet inner sheath / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry / regulation of brood size / establishment of left/right asymmetry / 9+0 motile cilium / sperm flagellum assembly / manchette assembly / axonemal B tubule inner sheath / axonemal A tubule inner sheath / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / regulation of microtubule nucleation / positive regulation of feeding behavior / cilium-dependent cell motility / 転移酵素; リンを含む基を移すもの / sperm principal piece / regulation of cilium beat frequency involved in ciliary motility / cerebrospinal fluid circulation / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / regulation of store-operated calcium entry / 9+2 motile cilium / intraciliary transport / acrosomal membrane / axoneme assembly / cilium movement / microtubule sliding / Post-chaperonin tubulin folding pathway / ciliary transition zone / left/right axis specification / calcium ion sensor activity / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / cilium organization / forebrain morphogenesis / gamma-tubulin ring complex / manchette / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / cerebellar cortex morphogenesis / dentate gyrus development / Formation of tubulin folding intermediates by CCT/TriC / glial cell differentiation / positive regulation of cilium assembly / neuron projection arborization / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / UTP biosynthetic process / CTP biosynthetic process / Kinesins / centrosome cycle / Assembly and cell surface presentation of NMDA receptors / determination of left/right symmetry / COPI-independent Golgi-to-ER retrograde traffic / response to L-glutamate / intermediate filament / pyramidal neuron differentiation / positive regulation of cell motility / COPI-dependent Golgi-to-ER retrograde traffic / motile cilium / GTP biosynthetic process / smoothened signaling pathway / natural killer cell mediated cytotoxicity / regulation of synapse organization / AMP binding / receptor clustering / ciliary base / regulation of neuron projection development / startle response / MHC class I protein binding / motor behavior / Recycling pathway of L1 / cerebral cortex cell migration / locomotory exploration behavior / microtubule organizing center / response to tumor necrosis factor / microtubule polymerization / regulation of cell division / mitotic cytokinesis / cellular response to UV-C / axoneme / cilium assembly / spermatid development / glial cell projection / cellular response to unfolded protein / alpha-tubulin binding / response to mechanical stimulus / beta-tubulin binding / RHO GTPases activate IQGAPs / single fertilization / sperm flagellum / microtubule-based process
類似検索 - 分子機能
Protein of unknown function DUF1143 / Cilia- and flagella-associated protein 68 / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / : / FAM183 family / FAM183A and FAM183B related / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain ...Protein of unknown function DUF1143 / Cilia- and flagella-associated protein 68 / Protein of unknown function DUF4541 / Cilia and flagella associated protein 90 / : / FAM183 family / FAM183A and FAM183B related / 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 / Sperm acrosome-associated protein 9 / : / Tektin family / Protein of unknown function (DUF3695) / Sperm acrosome-associated protein 9 / Uncharacterised protein FAM166/UPF0605 / Cilia- and flagella-associated protein 77 / Protein Flattop / Ciliary microtubule inner protein 2B-like / Cilia- and flagella-associated protein 77 / 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 / EFHB C-terminal EF-hand domain / : / Nucleoside diphosphate kinase 7 N-terminal PH 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 / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / 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 / 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 / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / 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
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 90 / Ciliary microtubule inner protein 2C / Cilia- and flagella-associated protein 144 / Ciliary microtubule inner protein 2B / Piercer of microtubule wall 2 protein / Tubulin beta-4B chain / Cilia- and flagella- associated protein 210 / Piercer of microtubule wall 1 protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Cilia- and flagella-associated protein 90 / Ciliary microtubule inner protein 2C / Cilia- and flagella-associated protein 144 / Ciliary microtubule inner protein 2B / Piercer of microtubule wall 2 protein / Tubulin beta-4B chain / Cilia- and flagella- associated protein 210 / Piercer of microtubule wall 1 protein / EF-hand domain-containing family member C2 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 276 / Protein Flattop / Cilia- and flagella-associated protein 95 / Cilia- and flagella-associated protein 141 / Cilia- and flagella-associated protein 161 / Cilia- and flagella-associated protein 77 / Tubulin alpha-1A chain / Cilia- and flagella-associated protein 107 / Cilia- and flagella-associated protein 52 / EF-hand domain-containing family member B / Meiosis-specific nuclear structural protein 1 / Enkurin / Tektin-4 / Tektin-1 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 53 / Parkin coregulated gene protein / Sperm-associated antigen 8 / Tektin-3 / RIB43A-like with coiled-coils protein 2 / Cilia- and flagella-associated protein 68 / Tektin-2 / Cilia- and flagella-associated protein 45 / Nucleoside diphosphate kinase homolog 7 / Cilia- and flagella-associated protein 20
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
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: 3.6 Å
データ登録者Gui, M. / Croft, J.T. / Zabeo, D. / Acharya, V. / Kollman, J.M. / Burgoyne, T. / Hoog, J.L. / Brown, A.
資金援助 米国, スウェーデン, 6件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141109 米国
Swedish Research Council2015-05427 スウェーデン
Swedish Research Council2019-04004 スウェーデン
Smith Family Foundation 米国
Pew Charitable Trusts 米国
Charles A. King TrustPostdoctoral Research Fellowship 米国
引用ジャーナル: Proc Natl Acad Sci U S A / 年: 2022
タイトル: SPACA9 is a lumenal protein of human ciliary singlet and doublet microtubules.
著者: Miao Gui / Jacob T Croft / Davide Zabeo / Vajradhar Acharya / Justin M Kollman / Thomas Burgoyne / Johanna L Höög / Alan Brown /
要旨: The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins ...The cilium-centrosome complex contains triplet, doublet, and singlet microtubules. The lumenal surfaces of each microtubule within this diverse array are decorated by microtubule inner proteins (MIPs). Here, we used single-particle cryo-electron microscopy methods to build atomic models of two types of human ciliary microtubule: the doublet microtubules of multiciliated respiratory cells and the distal singlet microtubules of monoflagellated human spermatozoa. We discover that SPACA9 is a polyspecific MIP capable of binding both microtubule types. SPACA9 forms intralumenal striations in the B tubule of respiratory doublet microtubules and noncontinuous spirals in sperm singlet microtubules. By acquiring new and reanalyzing previous cryo-electron tomography data, we show that SPACA9-like intralumenal striations are common features of different microtubule types in animal cilia. Our structures provide detailed references to help rationalize ciliopathy-causing mutations and position cryo-EM as a tool for the analysis of samples obtained directly from ciliopathy patients.
履歴
登録2022年4月11日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年10月5日Provider: repository / タイプ: Initial release
改定 1.12022年10月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
改定 1.22024年6月12日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond

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構造の表示

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 CFAP95
1: EF-hand domain-containing family member B
2: EF-hand domain-containing family member B
3: Cilia- and flagella-associated protein 53
4: Cilia- and flagella-associated protein 53
5: Nucleoside diphosphate kinase 7
6: Nucleoside diphosphate kinase 7
7: Protein CFAP95
8: Protein CFAP107
9: Protein CFAP107
A: Protein CFAP141
A0: Tektin-1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AA: Tubulin alpha-1A chain
AB: Tubulin beta-4B chain
AC: Tubulin alpha-1A chain
AD: Tubulin beta-4B chain
AE: Tubulin alpha-1A chain
AF: Tubulin beta-4B chain
AG: Tubulin alpha-1A chain
AH: Tubulin beta-4B chain
AI: Tubulin alpha-1A chain
AJ: Tubulin beta-4B chain
AK: Tubulin alpha-1A chain
AL: Tubulin beta-4B chain
AM: Tubulin alpha-1A 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-1A chain
BB: Tubulin beta-4B chain
BC: Tubulin alpha-1A chain
BD: Tubulin beta-4B chain
BE: Tubulin alpha-1A chain
BF: Tubulin beta-4B chain
BG: Tubulin alpha-1A chain
BH: Tubulin beta-4B chain
BI: Tubulin alpha-1A chain
BJ: Tubulin beta-4B chain
BK: Tubulin alpha-1A chain
BL: Tubulin beta-4B chain
BM: Tubulin alpha-1A chain
C: Meiosis-specific nuclear structural protein 1
C0: Tektin-3
C1: Tektin-3
C2: Tektin-3
C3: Tektin-3
C4: Tektin-3
CA: Tubulin alpha-1A chain
CB: Tubulin beta-4B chain
CC: Tubulin alpha-1A chain
CD: Tubulin beta-4B chain
CE: Tubulin alpha-1A chain
CF: Tubulin beta-4B chain
CG: Tubulin alpha-1A chain
CH: Tubulin beta-4B chain
CI: Tubulin alpha-1A chain
CJ: Tubulin beta-4B chain
CK: Tubulin alpha-1A chain
CL: Tubulin beta-4B chain
CM: Tubulin alpha-1A 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
DA: Tubulin alpha-1A chain
DB: Tubulin beta-4B chain
DC: Tubulin alpha-1A chain
DD: Tubulin beta-4B chain
DE: Tubulin alpha-1A chain
DF: Tubulin beta-4B chain
DG: Tubulin alpha-1A chain
DH: Tubulin beta-4B chain
DI: Tubulin alpha-1A chain
DJ: Tubulin beta-4B chain
DK: Tubulin alpha-1A chain
DL: Tubulin beta-4B chain
DM: Tubulin alpha-1A chain
E: Cilia- and flagella-associated protein 161
EB: Tubulin beta-4B chain
EC: Tubulin alpha-1A chain
ED: Tubulin beta-4B chain
EE: Tubulin alpha-1A chain
EF: Tubulin beta-4B chain
EG: Tubulin alpha-1A chain
EH: Tubulin beta-4B chain
EI: Tubulin alpha-1A chain
EJ: Tubulin beta-4B chain
EK: Tubulin alpha-1A chain
EL: Tubulin beta-4B chain
EM: Tubulin alpha-1A chain
EN: Tubulin beta-4B chain
F: Cilia- and flagella-associated protein 161
F0: Sperm acrosome-associated protein 9
F1: Sperm acrosome-associated protein 9
F2: Sperm acrosome-associated protein 9
F3: Sperm acrosome-associated protein 9
F4: Sperm acrosome-associated protein 9
F5: Sperm acrosome-associated protein 9
F6: Sperm acrosome-associated protein 9
F7: Sperm acrosome-associated protein 9
F8: Sperm acrosome-associated protein 9
FB: Tubulin beta-4B chain
FC: Tubulin alpha-1A chain
FD: Tubulin beta-4B chain
FE: Tubulin alpha-1A chain
FF: Tubulin beta-4B chain
FG: Tubulin alpha-1A chain
FH: Tubulin beta-4B chain
FI: Tubulin alpha-1A chain
FJ: Tubulin beta-4B chain
FK: Tubulin alpha-1A chain
FL: Tubulin beta-4B chain
FM: Tubulin alpha-1A chain
FN: Tubulin beta-4B chain
G: Uncharacterized protein C15orf65
G0: Sperm acrosome-associated protein 9
G1: Sperm acrosome-associated protein 9
G2: Sperm acrosome-associated protein 9
G3: Sperm acrosome-associated protein 9
G4: Sperm acrosome-associated protein 9
G5: Sperm acrosome-associated protein 9
G6: Sperm acrosome-associated protein 9
G7: Sperm acrosome-associated protein 9
G8: Sperm acrosome-associated protein 9
GB: Tubulin beta-4B chain
GC: Tubulin alpha-1A chain
GD: Tubulin beta-4B chain
GE: Tubulin alpha-1A chain
GF: Tubulin beta-4B chain
GG: Tubulin alpha-1A chain
GH: Tubulin beta-4B chain
GI: Tubulin alpha-1A chain
GJ: Tubulin beta-4B chain
GK: Tubulin alpha-1A chain
GL: Tubulin beta-4B chain
GM: Tubulin alpha-1A chain
GN: Tubulin beta-4B chain
H: Protein FAM166B
H0: Sperm acrosome-associated protein 9
H1: Sperm acrosome-associated protein 9
H2: Sperm acrosome-associated protein 9
HB: Tubulin beta-4B chain
HC: Tubulin alpha-1A chain
HD: Tubulin beta-4B chain
HE: Tubulin alpha-1A chain
HF: Tubulin beta-4B chain
HG: Tubulin alpha-1A chain
HH: Tubulin beta-4B chain
HI: Tubulin alpha-1A chain
HJ: Tubulin beta-4B chain
HK: Tubulin alpha-1A chain
HL: Tubulin beta-4B chain
HM: Tubulin alpha-1A chain
HN: Tubulin beta-4B chain
HO: Tubulin alpha-1A chain
I: Protein FAM166B
I1: UPF0686 protein C11orf1
IB: Tubulin beta-4B chain
IC: Tubulin alpha-1A chain
ID: Tubulin beta-4B chain
IE: Tubulin alpha-1A chain
IF: Tubulin beta-4B chain
IG: Tubulin alpha-1A chain
IH: Tubulin beta-4B chain
II: Tubulin alpha-1A chain
IJ: Tubulin beta-4B chain
IK: Tubulin alpha-1A chain
IL: Tubulin beta-4B chain
IM: Tubulin alpha-1A chain
IN: Tubulin beta-4B chain
IO: Tubulin alpha-1A chain
J: Protein FAM166B
J1: Isoform 2 of Cilia- and flagella-associated protein 77
J2: Isoform 2 of Cilia- and flagella-associated protein 77
J3: Isoform 2 of Cilia- and flagella-associated protein 77
J4: Isoform 2 of Cilia- and flagella-associated protein 77
J5: Isoform 2 of Cilia- and flagella-associated protein 77
JB: Tubulin beta-4B chain
JC: Tubulin alpha-1A chain
JD: Tubulin beta-4B chain
JE: Tubulin alpha-1A chain
JF: Tubulin beta-4B chain
JG: Tubulin alpha-1A chain
JH: Tubulin beta-4B chain
JI: Tubulin alpha-1A chain
JJ: Tubulin beta-4B chain
JK: Tubulin alpha-1A chain
JL: Tubulin beta-4B chain
JM: Tubulin alpha-1A chain
JN: Tubulin beta-4B chain
K: Protein FAM166B
K1: Protein FAM183A
KB: Tubulin beta-4B chain
KC: Tubulin alpha-1A chain
KD: Tubulin beta-4B chain
KE: Tubulin alpha-1A chain
KF: Tubulin beta-4B chain
KG: Tubulin alpha-1A chain
KH: Tubulin beta-4B chain
KI: Tubulin alpha-1A chain
KJ: Tubulin beta-4B chain
KK: Tubulin alpha-1A chain
KL: Tubulin beta-4B chain
KM: Tubulin alpha-1A chain
KN: Tubulin beta-4B chain
KO: Tubulin alpha-1A chain
L: Protein FAM166B
L1: Uncharacterized protein C5orf49
L2: Uncharacterized protein C5orf49
LB: Tubulin beta-4B chain
LC: Tubulin alpha-1A chain
LD: Tubulin beta-4B chain
LE: Tubulin alpha-1A chain
LF: Tubulin beta-4B chain
LG: Tubulin alpha-1A chain
LH: Tubulin beta-4B chain
LI: Tubulin alpha-1A chain
LJ: Tubulin beta-4B chain
LK: Tubulin alpha-1A chain
LL: Tubulin beta-4B chain
LM: Tubulin alpha-1A chain
LN: Tubulin beta-4B chain
M: Protein FAM166B
M1: Protein FAM166C
M2: Protein FAM166C
M3: Protein FAM166C
M4: Protein FAM166C
MB: Tubulin beta-4B chain
MC: Tubulin alpha-1A chain
MD: Tubulin beta-4B chain
ME: Tubulin alpha-1A chain
MF: Tubulin beta-4B chain
MG: Tubulin alpha-1A chain
MH: Tubulin beta-4B chain
MI: Tubulin alpha-1A chain
MJ: Tubulin beta-4B chain
MK: Tubulin alpha-1A chain
ML: Tubulin beta-4B chain
MM: Tubulin alpha-1A chain
MN: Tubulin beta-4B chain
N: Protein FAM166B
NB: Tubulin beta-4B chain
NC: Tubulin alpha-1A chain
ND: Tubulin beta-4B chain
NE: Tubulin alpha-1A chain
NF: Tubulin beta-4B chain
NG: Tubulin alpha-1A chain
NH: Tubulin beta-4B chain
NI: Tubulin alpha-1A chain
NJ: Tubulin beta-4B chain
NK: Tubulin alpha-1A chain
NL: Tubulin beta-4B chain
NM: Tubulin alpha-1A chain
NN: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
OB: Tubulin beta-4B chain
OC: Tubulin alpha-1A chain
OD: Tubulin beta-4B chain
OE: Tubulin alpha-1A chain
OF: Tubulin beta-4B chain
OG: Tubulin alpha-1A chain
OH: Tubulin beta-4B chain
OI: Tubulin alpha-1A chain
OJ: Tubulin beta-4B chain
OK: Tubulin alpha-1A chain
OL: Tubulin beta-4B chain
OM: Tubulin alpha-1A chain
ON: Tubulin beta-4B chain
OO: Tubulin alpha-1A chain
P: RIB43A-like with coiled-coils protein 2
PC: Tubulin alpha-1A chain
PD: Tubulin beta-4B chain
PE: Tubulin alpha-1A chain
PF: Tubulin beta-4B chain
PG: Tubulin alpha-1A chain
PH: Tubulin beta-4B chain
PI: Tubulin alpha-1A chain
PJ: Tubulin beta-4B chain
PK: Tubulin alpha-1A chain
PL: Tubulin beta-4B chain
PM: Tubulin alpha-1A chain
PN: Tubulin beta-4B chain
PO: Tubulin alpha-1A chain
Q: RIB43A-like with coiled-coils protein 2
QC: Tubulin alpha-1A chain
QD: Tubulin beta-4B chain
QE: Tubulin alpha-1A chain
QF: Tubulin beta-4B chain
QG: Tubulin alpha-1A chain
QH: Tubulin beta-4B chain
QI: Tubulin alpha-1A chain
QJ: Tubulin beta-4B chain
QK: Tubulin alpha-1A chain
QL: Tubulin beta-4B chain
QM: Tubulin alpha-1A chain
QN: Tubulin beta-4B chain
QO: Tubulin alpha-1A chain
R: RIB43A-like with coiled-coils protein 2
RC: Tubulin alpha-1A chain
RD: Tubulin beta-4B chain
RE: Tubulin alpha-1A chain
RF: Tubulin beta-4B chain
RG: Tubulin alpha-1A chain
RH: Tubulin beta-4B chain
RI: Tubulin alpha-1A chain
RJ: Tubulin beta-4B chain
RK: Tubulin alpha-1A chain
RL: Tubulin beta-4B chain
RM: Tubulin alpha-1A chain
RN: Tubulin beta-4B chain
RO: Tubulin alpha-1A chain
S: RIB43A-like with coiled-coils protein 2
SD: Tubulin beta-4B chain
SE: Tubulin alpha-1A chain
SF: Tubulin beta-4B chain
SG: Tubulin alpha-1A chain
SH: Tubulin beta-4B chain
SI: Tubulin alpha-1A chain
SJ: Tubulin beta-4B chain
SK: Tubulin alpha-1A chain
SL: Tubulin beta-4B chain
SM: Tubulin alpha-1A chain
SN: Tubulin beta-4B chain
SO: Tubulin alpha-1A chain
T: EF-hand domain-containing protein 1
TD: Tubulin beta-4B chain
TE: Tubulin alpha-1A chain
TF: Tubulin beta-4B chain
TG: Tubulin alpha-1A chain
TH: Tubulin beta-4B chain
TI: Tubulin alpha-1A chain
TJ: Tubulin beta-4B chain
TK: Tubulin alpha-1A chain
TL: Tubulin beta-4B chain
TM: Tubulin alpha-1A chain
TN: Tubulin beta-4B chain
TO: Tubulin alpha-1A chain
TP: Tubulin beta-4B chain
U: EF-hand domain-containing protein 1
UD: Tubulin beta-4B chain
UE: Tubulin alpha-1A chain
UF: Tubulin beta-4B chain
UG: Tubulin alpha-1A chain
UH: Tubulin beta-4B chain
UI: Tubulin alpha-1A chain
UJ: Tubulin beta-4B chain
UK: Tubulin alpha-1A chain
UL: Tubulin beta-4B chain
UM: Tubulin alpha-1A chain
UN: Tubulin beta-4B chain
UO: Tubulin alpha-1A chain
UP: Tubulin beta-4B chain
V: EF-hand domain-containing protein 1
VD: Tubulin beta-4B chain
VE: Tubulin alpha-1A chain
VF: Tubulin beta-4B chain
VG: Tubulin alpha-1A chain
VH: Tubulin beta-4B chain
VI: Tubulin alpha-1A chain
VJ: Tubulin beta-4B chain
VK: Tubulin alpha-1A chain
VL: Tubulin beta-4B chain
VM: Tubulin alpha-1A chain
VN: Tubulin beta-4B chain
VO: Tubulin alpha-1A chain
VP: Tubulin beta-4B chain
W: EF-hand domain-containing family member C2
WD: Tubulin beta-4B chain
WE: Tubulin alpha-1A chain
WF: Tubulin beta-4B chain
WG: Tubulin alpha-1A chain
WH: Tubulin beta-4B chain
WI: Tubulin alpha-1A chain
WJ: Tubulin beta-4B chain
WK: Tubulin alpha-1A chain
WL: Tubulin beta-4B chain
WM: Tubulin alpha-1A chain
WN: Tubulin beta-4B chain
WO: Tubulin alpha-1A chain
WP: Tubulin beta-4B chain
X: EF-hand domain-containing family member C2
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: EF-hand domain-containing family member C2
YB: Parkin coregulated gene protein
YC: Parkin coregulated gene protein
YD: Parkin coregulated gene protein
YE: Parkin coregulated gene protein
YF: Parkin coregulated gene protein
YG: Parkin coregulated gene protein
Z: EF-hand domain-containing family member C2
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
i: Enkurin
j: Enkurin
k: Enkurin
l: Protein Flattop
m: Protein Flattop
n: Protein Flattop
o: Protein CFAP210
o1: Protein CFAP210
p: Protein CFAP210
q: Protein CFAP276
r: Protein CFAP276
s: Protein CFAP276
y: UPF0691 protein C9orf116
z: UPF0691 protein C9orf116
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)20,589,726886
ポリマ－20,440,341435
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 , 26種, 408分子 075689AA0A1A2A3A4AAACAEAGAIAKAMBABCBEBGBIBKBMCACCCECG...

#1: タンパク質 Protein CFAP95 / Cilia- and flagella-associated protein 95


分子量: 26483.875 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5VTT2
#4: タンパク質 Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7 / nm23-H7


分子量: 42545.707 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y5B8, nucleoside-diphosphate kinase
#5: タンパク質 Protein CFAP107 / Cilia- and flagella-associated protein 107


分子量: 23105.348 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8N1D5
#6: タンパク質 Protein CFAP141 / Cilia- and flagella-associated protein 141


分子量: 12151.156 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5VU69
#7: タンパク質
Tektin-1


分子量: 48360.113 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q969V4
#8: タンパク質 ...
Tubulin alpha-1A chain / Alpha-tubulin 3 / Tubulin B-alpha-1 / Tubulin alpha-3 chain


分子量: 50188.441 Da / 分子数: 149 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q71U36
#9: タンパク質 ...
Tubulin beta-4B chain / Tubulin beta-2 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) Homo sapiens (ヒト) / 参照: UniProt: P68371
#10: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 60687.531 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8NEH6
#11: タンパク質
Tektin-2 / Tektin-t / Testicular tektin / Testicular tektin B1-like protein / TEKTB1 / Tektin-B1


分子量: 49743.176 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UIF3
#12: タンパク質
Tektin-3


分子量: 56717.902 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9BXF9
#13: タンパク質 Sperm-associated antigen 8 / HSD-1 / Sperm membrane protein 1 / SMP-1 / Sperm membrane protein BS-84


分子量: 51187.598 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q99932
#14: タンパク質
Tektin-4


分子量: 50725.926 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8WW24
#16: タンパク質 ...
Sperm acrosome-associated protein 9


分子量: 25208.977 Da / 分子数: 21 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96E40
#18: タンパク質
Protein FAM166B


分子量: 30610.637 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: A8MTA8
#19: タンパク質 UPF0686 protein C11orf1


分子量: 17806.924 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9H5F2
#20: タンパク質
Isoform 2 of Cilia- and flagella-associated protein 77


分子量: 33037.211 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q6ZQR2
#21: タンパク質 Protein FAM183A


分子量: 16028.189 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: A6NL82
#23: タンパク質
Protein FAM166C / Family with sequence similarity 166 member C


分子量: 23457.842 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: A6NJV1
#24: タンパク質
RIB43A-like with coiled-coils protein 2


分子量: 45510.234 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9H4K1
#25: タンパク質 EF-hand domain-containing protein 1 / Myoclonin-1


分子量: 74084.102 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5JVL4
#28: タンパク質
Parkin coregulated gene protein / Molecular chaperone/chaperonin-binding protein / PARK2 coregulated gene protein


分子量: 29352.184 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96M98
#31: タンパク質
Enkurin


分子量: 29510.348 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8TC29
#32: タンパク質 Protein Flattop / Cilia- and flagella-associated protein 126


分子量: 19320.871 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5VTH2
#33: タンパク質 Protein CFAP210 / Cilia- and flagella- associated protein 210 / Coiled-coil domain-containing protein 173


分子量: 66544.008 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q0VFZ6
#34: タンパク質 Protein CFAP276 / Cilia- and flagella-associated protein 276


分子量: 19376.688 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5T5A4
#35: タンパク質 UPF0691 protein C9orf116 / p53-induced expression in RB-null cells protein 1 / Pierce1


分子量: 15278.101 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5BN46

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EF-hand domain-containing family member ... , 2種, 6分子 12WXYZ

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


分子量: 93940.008 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8N7U6
#26: タンパク質
EF-hand domain-containing family member C2


分子量: 87516.828 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q5JST6

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Cilia- and flagella-associated protein ... , 5種, 18分子 34EFXAXBXCXDXEXFXGabcdefg

#3: タンパク質 Cilia- and flagella-associated protein 53 / Coiled-coil domain-containing protein 11


分子量: 61960.844 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q96M91
#15: タンパク質 Cilia- and flagella-associated protein 161


分子量: 34339.973 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q6P656
#27: タンパク質
Cilia- and flagella-associated protein 20 / Basal body up-regulated protein 22 / Transcription factor IIB


分子量: 22807.469 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9Y6A4
#29: タンパク質
Cilia- and flagella-associated protein 45 / Coiled-coil domain-containing protein 19 / Nasopharyngeal epithelium-specific protein 1


分子量: 65858.109 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q9UL16
#30: タンパク質 Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16 / WD40-repeat protein up-regulated in HCC


分子量: 68379.062 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q8N1V2

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Uncharacterized protein ... , 2種, 3分子 GL1L2

#17: タンパク質 Uncharacterized protein C15orf65


分子量: 13778.468 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: H3BRN8
#22: タンパク質 Uncharacterized protein C5orf49


分子量: 17019.980 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: A4QMS7

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非ポリマー , 3種, 451分子

#36: 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
#37: 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
#38: 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 and associated proteins / タイプ: COMPLEX / Entity ID: #1-#35 / 由来: NATURAL
分子量実験値: NO
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 7.3
試料包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドのタイプ: Quantifoil R2/1
急速凍結凍結剤: ETHANE / 湿度: 100 %

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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 / 倍率（公称値）: 64000 X / 最大 デフォーカス（公称値）: 2000 nm / 最小 デフォーカス（公称値）: 800 nm / 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
13PHENIX1.19モデル精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 208558 / 対称性のタイプ: POINT

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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