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- PDB-8to0: 48-nm repeating structure of doublets from mouse sperm flagella -

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基本情報

登録情報
データベース: PDB / ID: 8to0
タイトル48-nm repeating structure of doublets from mouse sperm flagella
要素
  • (Cilia- and flagella-associated protein ...) x 9
  • (EF-hand domain-containing family member ...) x 2
  • (Piercer of microtubule wall ...) x 2
  • Cilia- and flagella- associated protein 210
  • Coiled-coil domain-containing protein 105
  • Detyrosinated tubulin alpha-1A chain
  • Dual specificity protein phosphatase 3
  • EF-hand calcium-binding domain-containing protein 6
  • EF-hand domain-containing protein 1
  • Enkurin
  • Meiosis-specific nuclear structural protein 1
  • Nucleoside diphosphate kinase 7
  • Parkin coregulated gene protein homolog
  • Protein FAM166B
  • Protein Flattop
  • RIB43A-like with coiled-coils protein 2
  • Sperm acrosome-associated protein 9
  • Sperm-associated antigen 8
  • Tektin bundle-interacting protein 1
  • Tektin-1
  • Tektin-2
  • Tektin-3
  • Tektin-4
  • Tektin-5
  • Tubulin beta-4B chain
キーワードSTRUCTURAL PROTEIN / Mammalian sperm / axoneme / microtubule-based structure / microtubule inner protein / non-motor proteins / cellular motility / fertility
機能・相同性
機能・相同性情報


ERKs are inactivated / receptor signaling protein tyrosine kinase inhibitor activity / protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / outer acrosomal membrane / epithelial cilium movement involved in determination of left/right asymmetry ...ERKs are inactivated / receptor signaling protein tyrosine kinase inhibitor activity / protein localization to motile cilium / left/right pattern formation / axonemal microtubule doublet inner sheath / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / 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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / sperm axoneme assembly / inner dynein arm assembly / regulation of calcineurin-NFAT signaling cascade / regulation of microtubule nucleation / positive regulation of feeding behavior / COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / 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 / protein tyrosine/serine/threonine phosphatase activity / epithelial cilium movement involved in extracellular fluid movement / cilium movement involved in cell motility / COPI-mediated anterograde transport / Aggrephagy / regulation of store-operated calcium entry / Kinesins / 9+2 motile cilium / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / intraciliary transport / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / acrosomal membrane / RHO GTPases activate IQGAPs / Recycling pathway of L1 / axoneme assembly / cilium movement / microtubule sliding / ciliary transition zone / left/right axis specification / COPI-dependent Golgi-to-ER retrograde traffic / calcium ion sensor activity / axonemal microtubule / RHO GTPases Activate Formins / Separation of Sister Chromatids / organelle transport along microtubule / Hedgehog 'off' state / cilium organization / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / forebrain morphogenesis / AURKA Activation by TPX2 / gamma-tubulin ring complex / Regulation of PLK1 Activity at G2/M Transition / manchette / cerebellar cortex morphogenesis / dentate gyrus development / glial cell differentiation / positive regulation of cilium assembly / neuron projection arborization / flagellated sperm motility / cell projection organization / MHC class II antigen presentation / UTP biosynthetic process / CTP biosynthetic process / centrosome cycle / determination of left/right symmetry / response to L-glutamate / intermediate filament / pyramidal neuron differentiation / positive regulation of cell motility / nucleoside diphosphate kinase activity / regulation of focal adhesion assembly / GTP biosynthetic process / smoothened signaling pathway / tubulin complex / regulation of synapse organization / AMP binding / protein-serine/threonine phosphatase / receptor clustering / ciliary base / startle response / negative regulation of epidermal growth factor receptor signaling pathway / motor behavior
類似検索 - 分子機能
Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / Tektin bundle interacting protein 1 / DJBP, EF-hand domain / EF-hand domain / Atypical dual specificity phosphatase, subfamily A / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 ...Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / Tektin bundle interacting protein 1 / DJBP, EF-hand domain / EF-hand domain / Atypical dual specificity phosphatase, subfamily A / 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 / Protein Flattop / Ciliary microtubule inner protein 2B-like / 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 / Dual specificity phosphatase, catalytic domain / EF hand / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / 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 / EF-hand domain pair / Mir domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Tyrosine specific protein phosphatases active site. / Beta tubulin / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Protein-tyrosine phosphatase-like / 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.
類似検索 - ドメイン・相同性
Cilia- and flagella- associated protein 210 / Ciliary microtubule inner protein 2B / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 / Piercer of microtubule wall 1 protein ...Cilia- and flagella- associated protein 210 / Ciliary microtubule inner protein 2B / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-1A chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 / Piercer of microtubule wall 1 protein / Cilia- and flagella-associated protein 52 / Meiosis-specific nuclear structural protein 1 / EF-hand calcium-binding domain-containing protein 6 / Protein Flattop / Cilia- and flagella-associated protein 161 / Enkurin / Tektin-3 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 20 / EF-hand domain-containing family member B / Tektin-2 / Cilia- and flagella-associated protein 95 / Cilia- and flagella-associated protein 53 / EF-hand domain-containing family member C2 / Tektin-like protein 1 / RIB43A-like with coiled-coils protein 2 / Dual specificity protein phosphatase 3 / Cilia- and flagella-associated protein 141 / EF-hand domain-containing protein 1 / Cilia- and flagella-associated protein 45 / Cilia- and flagella-associated protein 276 / Tektin-1 / Parkin coregulated gene protein homolog / Nucleoside diphosphate kinase homolog 7 / Piercer of microtubule wall 2 protein
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法電子顕微鏡法 / サブトモグラム平均法 / クライオ電子顕微鏡法 / 解像度: 7.7 Å
データ登録者Chen, Z. / Shiozak, M. / Hass, K.M. / Skinner, W. / Zhao, S. / Guo, C. / Polacco, B.J. / Yu, Z. / Krogan, N.J. / Kaake, R.M. ...Chen, Z. / Shiozak, M. / Hass, K.M. / Skinner, W. / Zhao, S. / Guo, C. / Polacco, B.J. / Yu, Z. / Krogan, N.J. / Kaake, R.M. / Vale, R.D. / Agard, D.A.
資金援助 米国, 3件
組織認可番号国
Howard Hughes Medical Institute (HHMI) 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118106 米国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118099 米国
引用ジャーナル: Cell / 年: 2023
タイトル: De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking.
著者: Zhen Chen / Momoko Shiozaki / Kelsey M Haas / Will M Skinner / Shumei Zhao / Caiying Guo / Benjamin J Polacco / Zhiheng Yu / Nevan J Krogan / Polina V Lishko / Robyn M Kaake / Ronald D Vale / David A Agard /
要旨: To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their ...To understand the molecular mechanisms of cellular pathways, contemporary workflows typically require multiple techniques to identify proteins, track their localization, and determine their structures in vitro. Here, we combined cellular cryoelectron tomography (cryo-ET) and AlphaFold2 modeling to address these questions and understand how mammalian sperm are built in situ. Our cellular cryo-ET and subtomogram averaging provided 6.0-Å reconstructions of axonemal microtubule structures. The well-resolved tertiary structures allowed us to unbiasedly match sperm-specific densities with 21,615 AlphaFold2-predicted protein models of the mouse proteome. We identified Tektin 5, CCDC105, and SPACA9 as novel microtubule-associated proteins. These proteins form an extensive interaction network crosslinking the lumen of axonemal doublet microtubules, suggesting their roles in modulating the mechanical properties of the filaments. Indeed, Tekt5 -/- sperm possess more deformed flagella with 180° bends. Together, our studies presented a cellular visual proteomics workflow and shed light on the in vivo functions of Tektin 5.
履歴
登録2023年8月2日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年11月1日Provider: repository / タイプ: Initial release
改定 1.12023年11月22日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: Cilia- and flagella-associated protein 95
L: Tektin-1
M: Tektin-1
N: Detyrosinated tubulin alpha-1A chain
O: Tubulin beta-4B chain
P: Detyrosinated tubulin alpha-1A chain
Q: Tubulin beta-4B chain
R: Detyrosinated tubulin alpha-1A chain
S: Tubulin beta-4B chain
T: Detyrosinated tubulin alpha-1A chain
U: Tubulin beta-4B chain
V: Detyrosinated tubulin alpha-1A chain
W: Tubulin beta-4B chain
X: Detyrosinated tubulin alpha-1A chain
Y: Tubulin beta-4B chain
Z: Detyrosinated tubulin alpha-1A chain
b: Tektin-2
e: Tektin-2
f: Tektin-2
g: Tektin-2
h: Tektin-2
i: Tektin-2
j: Tektin-2
k: Tektin-2
l: Tektin-2
m: Tektin-2
n: Detyrosinated tubulin alpha-1A chain
1: EF-hand domain-containing family member B
o: Tubulin beta-4B chain
p: Detyrosinated tubulin alpha-1A chain
q: Tubulin beta-4B chain
r: Detyrosinated tubulin alpha-1A chain
s: Tubulin beta-4B chain
t: Detyrosinated tubulin alpha-1A chain
u: Tubulin beta-4B chain
v: Detyrosinated tubulin alpha-1A chain
w: Tubulin beta-4B chain
x: Detyrosinated tubulin alpha-1A chain
y: Tubulin beta-4B chain
z: Detyrosinated tubulin alpha-1A chain
AC: Tektin-3
AD: Tektin-3
AE: Tektin-3
AF: Tektin-3
AG: Tektin-3
AH: Tektin-3
AI: Tektin-3
AJ: Tektin-3
AK: Tektin-3
a: Meiosis-specific nuclear structural protein 1
BQ: Detyrosinated tubulin alpha-1A chain
BR: Tubulin beta-4B chain
BS: Detyrosinated tubulin alpha-1A chain
BT: Tubulin beta-4B chain
2: EF-hand domain-containing family member B
BU: Detyrosinated tubulin alpha-1A chain
BV: Tubulin beta-4B chain
BW: Detyrosinated tubulin alpha-1A chain
BX: Tubulin beta-4B chain
BY: Detyrosinated tubulin alpha-1A chain
BZ: Tubulin beta-4B chain
AV: Tubulin beta-4B chain
AW: Detyrosinated tubulin alpha-1A chain
AX: Tubulin beta-4B chain
AY: Detyrosinated tubulin alpha-1A chain
Aa: Tektin-4
Ab: Tektin-4
Ac: Tektin-4
Ad: Tektin-4
Af: Tektin-4
Ag: Tektin-4
Ah: Tektin-4
Ai: Tektin-4
Aj: Detyrosinated tubulin alpha-1A chain
Ak: Tubulin beta-4B chain
Al: Detyrosinated tubulin alpha-1A chain
Am: Tubulin beta-4B chain
An: Detyrosinated tubulin alpha-1A chain
Ao: Tubulin beta-4B chain
Ap: Detyrosinated tubulin alpha-1A chain
3: Cilia- and flagella-associated protein 53
Aq: Tubulin beta-4B chain
Ar: Detyrosinated tubulin alpha-1A chain
As: Tubulin beta-4B chain
At: Detyrosinated tubulin alpha-1A chain
Au: Tubulin beta-4B chain
Av: Detyrosinated tubulin alpha-1A chain
Aw: Tubulin beta-4B chain
Az: Tektin bundle-interacting protein 1
A1: Tektin bundle-interacting protein 1
A2: Tektin bundle-interacting protein 1
A3: Tektin bundle-interacting protein 1
A4: Tubulin beta-4B chain
A5: Detyrosinated tubulin alpha-1A chain
A6: Tubulin beta-4B chain
A7: Detyrosinated tubulin alpha-1A chain
A8: Tubulin beta-4B chain
A9: Detyrosinated tubulin alpha-1A chain
A0: Tubulin beta-4B chain
BA: Detyrosinated tubulin alpha-1A chain
BB: Tubulin beta-4B chain
BC: Detyrosinated tubulin alpha-1A chain
BD: Tubulin beta-4B chain
BE: Detyrosinated tubulin alpha-1A chain
BF: Tubulin beta-4B chain
BI: Tektin-3
BJ: Tektin-3
4: Cilia- and flagella-associated protein 53
BK: Tektin-3
BL: Tektin-3
BM: Tektin-3
BN: Tubulin beta-4B chain
BO: Detyrosinated tubulin alpha-1A chain
BP: Tubulin beta-4B chain
AB: Cilia- and flagella-associated protein 141
CX: Detyrosinated tubulin alpha-1A chain
CY: Tubulin beta-4B chain
Cb: Tubulin beta-4B chain
Cc: Detyrosinated tubulin alpha-1A chain
Cd: Tubulin beta-4B chain
Ce: Detyrosinated tubulin alpha-1A chain
Cf: Tubulin beta-4B chain
Cg: Detyrosinated tubulin alpha-1A chain
Ch: Tubulin beta-4B chain
Ci: Detyrosinated tubulin alpha-1A chain
Bb: Tubulin beta-4B chain
Bc: Detyrosinated tubulin alpha-1A chain
Bd: Tubulin beta-4B chain
Be: Detyrosinated tubulin alpha-1A chain
Bf: Tubulin beta-4B chain
Bg: Detyrosinated tubulin alpha-1A chain
Bh: Tubulin beta-4B chain
Bi: Detyrosinated tubulin alpha-1A chain
Bj: Tubulin beta-4B chain
5: Nucleoside diphosphate kinase 7
Bk: Detyrosinated tubulin alpha-1A chain
Bl: Tubulin beta-4B chain
Bm: Detyrosinated tubulin alpha-1A chain
Bn: Tubulin beta-4B chain
Br: Detyrosinated tubulin alpha-1A chain
Bs: Tubulin beta-4B chain
Bt: Detyrosinated tubulin alpha-1A chain
Bu: Tubulin beta-4B chain
Bv: Detyrosinated tubulin alpha-1A chain
Bw: Tubulin beta-4B chain
Bx: Detyrosinated tubulin alpha-1A chain
By: Tubulin beta-4B chain
Bz: Detyrosinated tubulin alpha-1A chain
B1: Tubulin beta-4B chain
B2: Detyrosinated tubulin alpha-1A chain
B3: Tubulin beta-4B chain
B4: Detyrosinated tubulin alpha-1A chain
B6: Protein FAM166B
B7: Tubulin beta-4B chain
B8: Detyrosinated tubulin alpha-1A chain
B9: Tubulin beta-4B chain
B0: Detyrosinated tubulin alpha-1A chain
CA: Tubulin beta-4B chain
CB: Detyrosinated tubulin alpha-1A chain
CC: Tubulin beta-4B chain
CD: Detyrosinated tubulin alpha-1A chain
6: Nucleoside diphosphate kinase 7
CE: Tubulin beta-4B chain
CF: Detyrosinated tubulin alpha-1A chain
CG: Tubulin beta-4B chain
CH: Detyrosinated tubulin alpha-1A chain
CI: Tubulin beta-4B chain
CJ: Detyrosinated tubulin alpha-1A chain
CM: Tubulin beta-4B chain
CN: Detyrosinated tubulin alpha-1A chain
CO: Tubulin beta-4B chain
CP: Detyrosinated tubulin alpha-1A chain
CQ: Tubulin beta-4B chain
CR: Detyrosinated tubulin alpha-1A chain
CS: Tubulin beta-4B chain
CT: Detyrosinated tubulin alpha-1A chain
CU: Tubulin beta-4B chain
CV: Detyrosinated tubulin alpha-1A chain
CW: Tubulin beta-4B chain
AZ: Sperm-associated antigen 8
Di: Tubulin beta-4B chain
Dj: Detyrosinated tubulin alpha-1A chain
Dk: Tubulin beta-4B chain
Dl: Detyrosinated tubulin alpha-1A chain
Dm: Tubulin beta-4B chain
Do: RIB43A-like with coiled-coils protein 2
Dp: Detyrosinated tubulin alpha-1A chain
Dq: Tubulin beta-4B chain
7: Cilia- and flagella-associated protein 95
Dr: Detyrosinated tubulin alpha-1A chain
Ds: Tubulin beta-4B chain
Cj: Tubulin beta-4B chain
Ck: Detyrosinated tubulin alpha-1A chain
Cl: Tubulin beta-4B chain
Cm: Detyrosinated tubulin alpha-1A chain
Cn: Tubulin beta-4B chain
Co: Detyrosinated tubulin alpha-1A chain
Cr: Tubulin beta-4B chain
Cs: Detyrosinated tubulin alpha-1A chain
Ct: Tubulin beta-4B chain
Cu: Detyrosinated tubulin alpha-1A chain
Cv: Tubulin beta-4B chain
Cw: Detyrosinated tubulin alpha-1A chain
Cx: Tubulin beta-4B chain
Cy: Detyrosinated tubulin alpha-1A chain
Cz: Tubulin beta-4B chain
C1: Detyrosinated tubulin alpha-1A chain
C2: Tubulin beta-4B chain
C3: Detyrosinated tubulin alpha-1A chain
C4: Tubulin beta-4B chain
C7: Tubulin beta-4B chain
C8: Detyrosinated tubulin alpha-1A chain
C9: Tubulin beta-4B chain
C0: Detyrosinated tubulin alpha-1A chain
DA: Tubulin beta-4B chain
8: Cilia- and flagella-associated protein 107
DB: Detyrosinated tubulin alpha-1A chain
DC: Tubulin beta-4B chain
DD: Detyrosinated tubulin alpha-1A chain
DE: Tubulin beta-4B chain
DF: Detyrosinated tubulin alpha-1A chain
DG: Tubulin beta-4B chain
DH: Detyrosinated tubulin alpha-1A chain
DI: Tubulin beta-4B chain
DL: Tubulin beta-4B chain
DM: Detyrosinated tubulin alpha-1A chain
DN: Tubulin beta-4B chain
DO: Detyrosinated tubulin alpha-1A chain
DP: Tubulin beta-4B chain
DQ: Detyrosinated tubulin alpha-1A chain
DR: Tubulin beta-4B chain
DS: Detyrosinated tubulin alpha-1A chain
DT: Tubulin beta-4B chain
DU: Detyrosinated tubulin alpha-1A chain
DV: Tubulin beta-4B chain
DW: Detyrosinated tubulin alpha-1A chain
DX: Tubulin beta-4B chain
Db: Detyrosinated tubulin alpha-1A chain
Dc: Tubulin beta-4B chain
Dd: Detyrosinated tubulin alpha-1A chain
De: Tubulin beta-4B chain
Df: Detyrosinated tubulin alpha-1A chain
9: Cilia- and flagella-associated protein 107
Dg: Tubulin beta-4B chain
Dh: Detyrosinated tubulin alpha-1A chain
Ay: Cilia- and flagella-associated protein 161
Er: Tubulin beta-4B chain
Es: Detyrosinated tubulin alpha-1A chain
Et: Tubulin beta-4B chain
Eu: Detyrosinated tubulin alpha-1A chain
Ev: Tubulin beta-4B chain
Ew: Detyrosinated tubulin alpha-1A chain
Ex: Tubulin beta-4B chain
Ey: Detyrosinated tubulin alpha-1A chain
E1: EF-hand domain-containing protein 1
E3: Detyrosinated tubulin alpha-1A chain
Dt: Detyrosinated tubulin alpha-1A chain
Du: Tubulin beta-4B chain
Dv: Detyrosinated tubulin alpha-1A chain
Dw: Tubulin beta-4B chain
Dx: Detyrosinated tubulin alpha-1A chain
Dy: Tubulin beta-4B chain
Dz: Detyrosinated tubulin alpha-1A chain
D1: Tubulin beta-4B chain
D2: Detyrosinated tubulin alpha-1A chain
D5: Detyrosinated tubulin alpha-1A chain
D6: Tubulin beta-4B chain
D7: Detyrosinated tubulin alpha-1A chain
D8: Tubulin beta-4B chain
A: Meiosis-specific nuclear structural protein 1
D9: Detyrosinated tubulin alpha-1A chain
D0: Tubulin beta-4B chain
EA: Detyrosinated tubulin alpha-1A chain
EB: Tubulin beta-4B chain
EC: Detyrosinated tubulin alpha-1A chain
ED: Tubulin beta-4B chain
EE: Detyrosinated tubulin alpha-1A chain
EF: Tubulin beta-4B chain
EG: Detyrosinated tubulin alpha-1A chain
EJ: Detyrosinated tubulin alpha-1A chain
EK: Tubulin beta-4B chain
EL: Detyrosinated tubulin alpha-1A chain
EM: Tubulin beta-4B chain
EN: Detyrosinated tubulin alpha-1A chain
EO: Tubulin beta-4B chain
EP: Detyrosinated tubulin alpha-1A chain
EQ: Tubulin beta-4B chain
ER: Detyrosinated tubulin alpha-1A chain
ES: Tubulin beta-4B chain
ET: Detyrosinated tubulin alpha-1A chain
EU: Tubulin beta-4B chain
EV: Detyrosinated tubulin alpha-1A chain
EY: Detyrosinated tubulin alpha-1A chain
EZ: Tubulin beta-4B chain
Ea: Detyrosinated tubulin alpha-1A chain
Eb: Tubulin beta-4B chain
AL: Tektin-3
Ec: Detyrosinated tubulin alpha-1A chain
Ed: Tubulin beta-4B chain
Ee: Detyrosinated tubulin alpha-1A chain
Ef: Tubulin beta-4B chain
Eg: Detyrosinated tubulin alpha-1A chain
Eh: Tubulin beta-4B chain
Ei: Detyrosinated tubulin alpha-1A chain
Ej: Tubulin beta-4B chain
Ek: Detyrosinated tubulin alpha-1A chain
Em: EF-hand domain-containing protein 1
Eo: Detyrosinated tubulin alpha-1A chain
Ep: Tubulin beta-4B chain
Eq: Detyrosinated tubulin alpha-1A chain
BH: Cilia- and flagella-associated protein 161
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
F9: Sperm acrosome-associated protein 9
F0: Sperm acrosome-associated protein 9
E4: Tubulin beta-4B chain
E5: Detyrosinated tubulin alpha-1A chain
AM: Detyrosinated tubulin alpha-1A chain
E6: Tubulin beta-4B chain
E7: Detyrosinated tubulin alpha-1A chain
E8: Tubulin beta-4B chain
E9: Detyrosinated tubulin alpha-1A chain
E0: Tubulin beta-4B chain
FA: Detyrosinated tubulin alpha-1A chain
FB: Tubulin beta-4B chain
FC: Detyrosinated tubulin alpha-1A chain
FD: Tubulin beta-4B chain
FE: EF-hand domain-containing protein 1
FG: Detyrosinated tubulin alpha-1A chain
FH: Tubulin beta-4B chain
FI: Detyrosinated tubulin alpha-1A chain
FJ: Tubulin beta-4B chain
FK: Detyrosinated tubulin alpha-1A chain
FL: Tubulin beta-4B chain
FM: Detyrosinated tubulin alpha-1A chain
FN: Tubulin beta-4B chain
FO: Detyrosinated tubulin alpha-1A chain
FP: Tubulin beta-4B chain
FQ: Detyrosinated tubulin alpha-1A chain
FR: Tubulin beta-4B chain
FU: Detyrosinated tubulin alpha-1A chain
FV: Tubulin beta-4B chain
FW: Detyrosinated tubulin alpha-1A chain
FX: Tubulin beta-4B chain
AN: Tubulin beta-4B chain
FY: Detyrosinated tubulin alpha-1A chain
FZ: Tubulin beta-4B chain
Fa: Detyrosinated tubulin alpha-1A chain
Fb: Tubulin beta-4B chain
Fc: Detyrosinated tubulin alpha-1A chain
Fd: Tubulin beta-4B chain
Fe: Detyrosinated tubulin alpha-1A chain
Ff: Tubulin beta-4B chain
Fg: EF-hand domain-containing family member C2
Fh: Cilia- and flagella-associated protein 20
Fi: Cilia- and flagella-associated protein 20
Fj: Cilia- and flagella-associated protein 20
Fk: Cilia- and flagella-associated protein 20
Fl: Cilia- and flagella-associated protein 20
Fm: Cilia- and flagella-associated protein 20
Fn: Cilia- and flagella-associated protein 20
Fp: Parkin coregulated gene protein homolog
Fq: Parkin coregulated gene protein homolog
Fr: Parkin coregulated gene protein homolog
Fs: Parkin coregulated gene protein homolog
Ft: Parkin coregulated gene protein homolog
Fx: Dual specificity protein phosphatase 3
Fy: Dual specificity protein phosphatase 3
Fz: Dual specificity protein phosphatase 3
G: Piercer of microtubule wall 2 protein
GA: Sperm acrosome-associated protein 9
AO: Detyrosinated tubulin alpha-1A chain
GB: Sperm acrosome-associated protein 9
GC: Sperm acrosome-associated protein 9
GD: Sperm acrosome-associated protein 9
GE: Sperm acrosome-associated protein 9
GF: Sperm acrosome-associated protein 9
GG: Sperm acrosome-associated protein 9
GH: Sperm acrosome-associated protein 9
GI: Sperm acrosome-associated protein 9
GJ: Sperm acrosome-associated protein 9
GK: Sperm acrosome-associated protein 9
GL: Sperm acrosome-associated protein 9
GM: Sperm acrosome-associated protein 9
GN: Sperm acrosome-associated protein 9
GO: Sperm acrosome-associated protein 9
GP: Sperm acrosome-associated protein 9
GQ: Sperm acrosome-associated protein 9
GR: Tektin-5
GS: Tektin-5
GT: Tektin-5
GU: Tektin-5
GV: Tektin-5
GW: Tektin-5
GX: Tektin-5
GY: Tektin-5
GZ: Tektin-5
Ga: Tektin-5
AP: Tubulin beta-4B chain
Gb: Tektin-5
Gc: Tektin-5
Gd: Tektin-5
Ge: Tektin-5
z0: Tektin-5
z1: Tektin-5
z3: Tektin-5
z4: Tektin-5
Gf: Tektin-5
Gg: Tektin-5
Gh: Tektin-5
Gi: Tektin-5
Gj: Tektin-5
Bq: Tubulin beta-4B chain
CL: Protein FAM166B
Ca: Protein FAM166B
Cq: Protein FAM166B
C6: Protein FAM166B
DK: Protein FAM166B
Da: Tubulin beta-4B chain
DZ: RIB43A-like with coiled-coils protein 2
D4: RIB43A-like with coiled-coils protein 2
EI: RIB43A-like with coiled-coils protein 2
EX: RIB43A-like with coiled-coils protein 2
AQ: Detyrosinated tubulin alpha-1A chain
En: Tubulin beta-4B chain
E2: Tubulin beta-4B chain
FF: Tubulin beta-4B chain
FT: Tubulin beta-4B chain
FS: EF-hand domain-containing family member C2
Fo: EF-hand domain-containing family member C2
Fv: EF-hand domain-containing family member C2
B: Cilia- and flagella-associated protein 45
AA: Cilia- and flagella-associated protein 45
c: Cilia- and flagella-associated protein 45
Ax: Cilia- and flagella-associated protein 45
BG: Cilia- and flagella-associated protein 52
Ba: Cilia- and flagella-associated protein 52
Bo: Cilia- and flagella-associated protein 52
B5: Enkurin
CK: Enkurin
CZ: Enkurin
Cp: Enkurin
C5: Protein Flattop
DJ: Protein Flattop
DY: Protein Flattop
Dn: Cilia- and flagella- associated protein 210
D3: Cilia- and flagella- associated protein 210
EH: Cilia- and flagella-associated protein 276
EW: Cilia- and flagella-associated protein 276
El: Cilia- and flagella-associated protein 276
AR: Tubulin beta-4B chain
Ez: EF-hand calcium-binding domain-containing protein 6
d: Cilia- and flagella-associated protein 45
C: Coiled-coil domain-containing protein 105
D: Coiled-coil domain-containing protein 105
E: Coiled-coil domain-containing protein 105
Fw: Piercer of microtubule wall 1 protein
AS: Detyrosinated tubulin alpha-1A chain
AT: Tubulin beta-4B chain
AU: Detyrosinated tubulin alpha-1A chain
F: Coiled-coil domain-containing protein 105
H: Coiled-coil domain-containing protein 105
I: Tektin-1
J: Tektin-1
K: Tektin-1


分子量 (理論値)分子数
合計 (水以外)22,692,158471
ポリマ－22,692,158471
非ポリマー00
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, not applicable
タイプ名称対称操作数
identity operation1_5551

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要素

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Cilia- and flagella-associated protein ... , 9種, 27分子 0734AB89AyBHFhFiFjFkFlFmFnBAAcAxdBGBaBoEHEWEl

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


分子量: 26633.035 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9CQC3
#10: タンパク質 Cilia- and flagella-associated protein 53


分子量: 62036.609 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D439
#12: タンパク質 Cilia- and flagella-associated protein 141


分子量: 12278.145 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D9D9
#17: タンパク質 Cilia- and flagella-associated protein 107


分子量: 23062.510 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q4KKZ1
#18: タンパク質 Cilia- and flagella-associated protein 161


分子量: 34433.383 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6P8Y0
#22: タンパク質
Cilia- and flagella-associated protein 20 / Gene trap locus 3 protein


分子量: 22781.389 Da / 分子数: 7 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q8BTU1
#27: タンパク質
Cilia- and flagella-associated protein 45


分子量: 65962.016 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D9U9
#28: タンパク質 Cilia- and flagella-associated protein 52 / WD repeat-containing protein 16


分子量: 68322.164 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q5F201
#32: タンパク質 Cilia- and flagella-associated protein 276


分子量: 18960.092 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9DAD0

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タンパク質 , 22種, 436分子 LMIJKNPRTVXZnprtvxzBQBSBUBWBYAWAYAjAlAnAp...

#2: タンパク質
Tektin-1


分子量: 48713.035 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9DAJ2
#3: タンパク質 ...
Detyrosinated tubulin alpha-1A chain


分子量: 50188.441 Da / 分子数: 149 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P68369
#4: 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) Mus musculus (ハツカネズミ) / 参照: UniProt: P68372
#5: タンパク質
Tektin-2 / Tektin-t / Testicular tektin


分子量: 50385.066 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q922G7
#7: タンパク質
Tektin-3


分子量: 56754.777 Da / 分子数: 15 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6X6Z7
#8: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 60353.012 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q61884
#9: タンパク質
Tektin-4


分子量: 52121.449 Da / 分子数: 8 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q149S1
#11: タンパク質
Tektin bundle-interacting protein 1


分子量: 23987.262 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: A6H6Q4
#13: タンパク質 Nucleoside diphosphate kinase 7 / NDK 7 / NDP kinase 7 / nm23-M7


分子量: 44489.828 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9QXL8, nucleoside-diphosphate kinase
#14: タンパク質
Protein FAM166B


分子量: 30290.346 Da / 分子数: 6 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: A2AIP0
#15: タンパク質 Sperm-associated antigen 8 / Sperm membrane protein 1 / SMP-1 / Sperm membrane protein BS-84


分子量: 50591.805 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q3V0Q6
#16: タンパク質
RIB43A-like with coiled-coils protein 2


分子量: 45328.156 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D4Q1
#19: タンパク質 EF-hand domain-containing protein 1 / Myoclonin-1


分子量: 75235.422 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D9T8
#20: タンパク質 ...
Sperm acrosome-associated protein 9 / Acrosome and sperm tail protein / MAST


分子量: 19512.373 Da / 分子数: 27 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q7TPM5
#23: タンパク質
Parkin coregulated gene protein homolog / Hypertension-related protein 1-like protein / PARK2 coregulated gene protein


分子量: 27763.268 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9DAK2
#24: タンパク質 Dual specificity protein phosphatase 3 / T-DSP11 / Vaccinia H1-related phosphatase / VHR


分子量: 20494.127 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ)
参照: UniProt: Q9D7X3, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#26: タンパク質 ...
Tektin-5


分子量: 62817.535 Da / 分子数: 23 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: G5E8A8
#29: タンパク質
Enkurin


分子量: 29587.521 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6SP97
#30: タンパク質 Protein Flattop


分子量: 20575.123 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6P8X9
#31: タンパク質 Cilia- and flagella- associated protein 210


分子量: 65266.520 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: A0JLY1
#33: タンパク質 EF-hand calcium-binding domain-containing protein 6 / DJ-1-binding protein / DJBP


分子量: 176028.312 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6P1E8
#34: タンパク質
Coiled-coil domain-containing protein 105


分子量: 57406.484 Da / 分子数: 5 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D4K7

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

#6: タンパク質 EF-hand domain-containing family member B / Cilia- and flagella-associated protein 21


分子量: 95891.961 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q8CDU5
#21: タンパク質
EF-hand domain-containing family member C2


分子量: 87758.023 Da / 分子数: 4 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9D485

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Piercer of microtubule wall ... , 2種, 2分子 GFw

#25: タンパク質 Piercer of microtubule wall 2 protein


分子量: 13728.513 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: V9GXK1
#35: タンパク質 Piercer of microtubule wall 1 protein / Pierce1 / p53-induced expression in RB-null cells protein 1


分子量: 18862.852 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q5BN45

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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: CELL / ３次元再構成法: サブトモグラム平均法

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試料調製

構成要素名称: Mouse sperm / タイプ: CELL / Entity ID: all / 由来: NATURAL
由来(天然)生物種: Mus musculus (ハツカネズミ)
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
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 / 最大 デフォーカス（公称値）: 6000 nm / 最小 デフォーカス（公称値）: 2000 nm
撮影電子線照射量: 4 e/Å2 / Avg electron dose per subtomogram: 100 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ソフトウェア名称: RELION / バージョン: 4.0-beta2 / カテゴリ: ３次元再構成
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C1 (非対称)
3次元再構成解像度: 7.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 12848 / 対称性のタイプ: POINT
EM volume selection詳細: 32288 particles were initially picked every 24 nm along the microtubules.
Num. of tomograms: 76 / Num. of volumes extracted: 32288

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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