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- PDB-8i7r: In situ structure of axonemal doublet microtubules in mouse sperm... -

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基本情報

登録情報
データベース: PDB / ID: 8i7r
タイトルIn situ structure of axonemal doublet microtubules in mouse sperm with 48-nm repeat
要素
  • (Cilia- and flagella-associated protein ...) x 10
  • (EF-hand domain-containing family member ...) x 2
  • (Piercer of microtubule wall ...) x 2
  • Cilia and flagella-associated protein 77
  • Coiled-coil domain-containing protein 105
  • Detyrosinated tubulin alpha-3 chain
  • Dual specificity phosphatase 21
  • 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 FAM166A
  • Protein FAM166C
  • 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
  • Testis-expressed protein 43
  • Tubulin beta-4B chain
キーワードSTRUCTURAL PROTEIN / microtubules / axoneme / sperm / filament
機能・相同性
機能・相同性情報


male germ-line stem cell population maintenance / 9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly ...male germ-line stem cell population maintenance / 9+0 motile cilium / sperm flagellum assembly / outer acrosomal membrane / regulation of brood size / establishment of left/right asymmetry / protein localization to motile cilium / manchette assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / left/right pattern formation / axonemal B tubule inner sheath / axonemal A tubule inner sheath / epithelial cilium movement involved in determination of left/right asymmetry / regulation of calcineurin-NFAT signaling cascade / inner dynein arm assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / positive regulation of feeding behavior / cerebrospinal fluid circulation / sperm axoneme assembly / COPI-independent Golgi-to-ER retrograde traffic / cilium-dependent cell motility / sperm principal piece / MAP kinase tyrosine/serine/threonine phosphatase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / regulation of store-operated calcium entry / epithelial cilium movement involved in extracellular fluid movement / 9+2 motile cilium / intraciliary transport / PKR-mediated signaling / COPI-mediated anterograde transport / protein localization to organelle / calcium ion sensor activity / Aggrephagy / 転移酵素; リンを含む基を移すもの / acrosomal membrane / Kinesins / ciliary transition zone / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cilium movement / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / axoneme assembly / axonemal microtubule / left/right axis specification / cilium organization / COPI-dependent Golgi-to-ER retrograde traffic / gamma-tubulin ring complex / flagellated sperm motility / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / 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 / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / positive regulation of cilium assembly / MHC class II antigen presentation / protein targeting to mitochondrion / CTP biosynthetic process / UTP biosynthetic process / motile cilium / positive regulation of cell motility / determination of left/right symmetry / protein targeting to membrane / GTP biosynthetic process / microtubule organizing center / intermediate filament / regulation of neuron projection development / ciliary base / nucleoside diphosphate kinase activity / tubulin complex / myosin phosphatase activity / extrinsic component of membrane / intercellular bridge / protein-serine/threonine phosphatase / beta-tubulin binding / AMP binding / regulation of cell division / receptor clustering / phosphatase activity / cytoplasmic microtubule / axoneme / microtubule-based process / centriolar satellite / spermatid development / mitotic cytokinesis / alpha-tubulin binding
類似検索 - 分子機能
Atypical dual specificity phosphatase, subfamily B / Protein of unknown function DUF4513 / Sperm-associated microtubule inner protein 10 / DJBP, EF-hand domain / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / EF-hand domain / Tektin bundle interacting protein 1 / Sperm-associated antigen 8 / Sperm acrosome-associated protein 9 ...Atypical dual specificity phosphatase, subfamily B / Protein of unknown function DUF4513 / Sperm-associated microtubule inner protein 10 / DJBP, EF-hand domain / Tektin bundle interacting protein 1 / Coiled-coil domain-containing protein 105 / EF-hand domain / Tektin bundle interacting protein 1 / Sperm-associated antigen 8 / Sperm acrosome-associated protein 9 / Cilia- and flagella-associated protein 95 / NDPK7, first NDPk domain / Cilia- and flagella-associated protein 107 / : / Sperm acrosome-associated protein 9 / Protein CFAP95 / Tektin / Cilia- and flagella-associated protein 276 / Tektin family / Protein of unknown function (DUF3695) / Cilia- and flagella-associated protein 77 / Cilia- and flagella-associated protein 77 / Uncharacterised protein FAM166/UPF0605 / Protein Flattop / Ciliary microtubule inner protein 2B-like / 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 / Dual specificity phosphatase, catalytic domain / Nucleoside diphosphate kinase (NDPK)-like domain profile. / EF hand / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / EF-hand domain pair / Mir domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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. / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / 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 / Protein-tyrosine phosphatase-like / 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 / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat
類似検索 - ドメイン・相同性
GUANOSINE-5'-TRIPHOSPHATE / Cilia and flagella associated protein 77 / Cilia- and flagella- associated protein 210 / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-3 chain / Tubulin beta-4B chain / Tektin-4 / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 107 ...GUANOSINE-5'-TRIPHOSPHATE / Cilia and flagella associated protein 77 / Cilia- and flagella- associated protein 210 / Tektin bundle-interacting protein 1 / Tektin-5 / Tubulin alpha-3 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 / Ciliary microtubule inner protein 2A / Tektin-like protein 1 / RIB43A-like with coiled-coils protein 2 / Dual specificity phosphatase 21 / Cilia- and flagella-associated protein 141 / Sperm-associated microtubule inner protein 10 / 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 / Ciliary microtubule inner protein 2C / 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: 6.5 Å
データ登録者Zhu, Y. / Yin, G.L. / Tai, L.H. / Sun, F.
資金援助 中国, 1件
組織認可番号国
National Natural Science Foundation of China (NSFC)31925026 中国
引用ジャーナル: Cell Discov / 年: 2023
タイトル: In-cell structural insight into the stability of sperm microtubule doublet.
著者: Linhua Tai / Guoliang Yin / Xiaojun Huang / Fei Sun / Yun Zhu /
要旨: The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. ...The propulsion for mammalian sperm swimming is generated by flagella beating. Microtubule doublets (DMTs) along with microtubule inner proteins (MIPs) are essential structural blocks of flagella. However, the intricate molecular architecture of intact sperm DMT remains elusive. Here, by in situ cryo-electron tomography, we solved the in-cell structure of mouse sperm DMT at 4.5-7.5 Å resolutions, and built its model with 36 kinds of MIPs in 48 nm periodicity. We identified multiple copies of Tektin5 that reinforce Tektin bundle, and multiple MIPs with different periodicities that anchor the Tektin bundle to tubulin wall. This architecture contributes to a superior stability of A-tubule than B-tubule of DMT, which was revealed by structural comparison of DMTs from the intact and deformed axonemes. Our work provides an overall molecular picture of intact sperm DMT in 48 nm periodicity that is essential to understand the molecular mechanism of sperm motility as well as the related ciliopathies.
履歴
登録2023年2月2日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年10月11日Provider: repository / タイプ: Initial release
改定 1.12023年12月6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_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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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
A: Meiosis-specific nuclear structural protein 1
A1: Tektin-1
A2: Tektin-1
A3: Tektin-1
A4: Tektin-1
AB: Tubulin beta-4B chain
AC: Detyrosinated tubulin alpha-3 chain
AD: Tubulin beta-4B chain
AE: Detyrosinated tubulin alpha-3 chain
AF: Tubulin beta-4B chain
AG: Detyrosinated tubulin alpha-3 chain
AH: Tubulin beta-4B chain
AI: Detyrosinated tubulin alpha-3 chain
AJ: Tubulin beta-4B chain
AK: Detyrosinated tubulin alpha-3 chain
AL: Tubulin beta-4B chain
AM: Detyrosinated tubulin alpha-3 chain
B: Meiosis-specific nuclear structural protein 1
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
BB: Tubulin beta-4B chain
BC: Detyrosinated tubulin alpha-3 chain
BD: Tubulin beta-4B chain
BE: Detyrosinated tubulin alpha-3 chain
BF: Tubulin beta-4B chain
BG: Detyrosinated tubulin alpha-3 chain
BH: Tubulin beta-4B chain
BI: Detyrosinated tubulin alpha-3 chain
BJ: Tubulin beta-4B chain
BK: Detyrosinated tubulin alpha-3 chain
BL: Tubulin beta-4B chain
BM: Detyrosinated tubulin alpha-3 chain
C: Nucleoside diphosphate kinase 7
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
CB: Tubulin beta-4B chain
CC: Detyrosinated tubulin alpha-3 chain
CD: Tubulin beta-4B chain
CE: Detyrosinated tubulin alpha-3 chain
CF: Tubulin beta-4B chain
CG: Detyrosinated tubulin alpha-3 chain
CH: Tubulin beta-4B chain
CI: Detyrosinated tubulin alpha-3 chain
CJ: Tubulin beta-4B chain
CK: Detyrosinated tubulin alpha-3 chain
CL: Tubulin beta-4B chain
CM: Detyrosinated tubulin alpha-3 chain
Ca: Tektin-3
Cb: Tektin-3
Cc: Tektin-3
Cd: Tektin-3
D: Nucleoside diphosphate kinase 7
D1: Tektin-4
D2: Tektin-4
D3: Tektin-4
D4: Tektin-4
D5: Tektin-4
D6: Tektin-4
D7: Tektin-4
D8: Tektin-4
D9: Tektin-4
DA: Detyrosinated tubulin alpha-3 chain
DB: Tubulin beta-4B chain
DC: Detyrosinated tubulin alpha-3 chain
DD: Tubulin beta-4B chain
DE: Detyrosinated tubulin alpha-3 chain
DF: Tubulin beta-4B chain
DG: Detyrosinated tubulin alpha-3 chain
DH: Tubulin beta-4B chain
DI: Detyrosinated tubulin alpha-3 chain
DJ: Tubulin beta-4B chain
DK: Detyrosinated tubulin alpha-3 chain
DL: Tubulin beta-4B chain
Da: Tektin-4
E: EF-hand domain-containing family member B
E1: Tektin bundle-interacting protein 1
E2: Tektin bundle-interacting protein 1
E3: Tektin bundle-interacting protein 1
E4: Tektin bundle-interacting protein 1
EA: Detyrosinated tubulin alpha-3 chain
EB: Tubulin beta-4B chain
EC: Detyrosinated tubulin alpha-3 chain
ED: Tubulin beta-4B chain
EE: Detyrosinated tubulin alpha-3 chain
EF: Tubulin beta-4B chain
EG: Detyrosinated tubulin alpha-3 chain
EH: Tubulin beta-4B chain
EI: Detyrosinated tubulin alpha-3 chain
EJ: Tubulin beta-4B chain
EK: Detyrosinated tubulin alpha-3 chain
EL: Tubulin beta-4B chain
F: EF-hand domain-containing family member B
F1: Tektin-5
F2: Tektin-5
F3: Tektin-5
F4: Tektin-5
F5: Tektin-5
F6: Tektin-5
F7: Tektin-5
F8: Tektin-5
F9: Tektin-5
FA: Detyrosinated tubulin alpha-3 chain
FB: Tubulin beta-4B chain
FC: Detyrosinated tubulin alpha-3 chain
FD: Tubulin beta-4B chain
FE: Detyrosinated tubulin alpha-3 chain
FF: Tubulin beta-4B chain
FG: Detyrosinated tubulin alpha-3 chain
FH: Tubulin beta-4B chain
FI: Detyrosinated tubulin alpha-3 chain
FJ: Tubulin beta-4B chain
FK: Detyrosinated tubulin alpha-3 chain
FL: Tubulin beta-4B chain
Fa: Tektin-5
Fb: Tektin-5
Fc: Tektin-5
Fd: Tektin-5
Fe: Tektin-5
Ff: Tektin-5
Fg: Tektin-5
Fh: Tektin-5
Fi: Tektin-5
Fj: Tektin-5
Fk: Tektin-5
Fl: Tektin-5
Fm: Tektin-5
G: Cilia- and flagella-associated protein 53
G1: EF-hand domain-containing protein 1
G2: EF-hand domain-containing protein 1
G3: EF-hand domain-containing protein 1
G4: EF-hand domain-containing family member C2
G5: EF-hand domain-containing family member C2
G6: EF-hand domain-containing family member C2
GA: Detyrosinated tubulin alpha-3 chain
GB: Tubulin beta-4B chain
GC: Detyrosinated tubulin alpha-3 chain
GD: Tubulin beta-4B chain
GE: Detyrosinated tubulin alpha-3 chain
GF: Tubulin beta-4B chain
GG: Detyrosinated tubulin alpha-3 chain
GH: Tubulin beta-4B chain
GI: Detyrosinated tubulin alpha-3 chain
GJ: Tubulin beta-4B chain
GK: Detyrosinated tubulin alpha-3 chain
GL: Tubulin beta-4B chain
H: Cilia- and flagella-associated protein 53
H1: Protein FAM166A
H2: Protein FAM166A
H3: Protein FAM166A
H4: Protein FAM166A
H5: Protein FAM166A
H6: Protein FAM166A
HA: Detyrosinated tubulin alpha-3 chain
HB: Tubulin beta-4B chain
HC: Detyrosinated tubulin alpha-3 chain
HD: Tubulin beta-4B chain
HE: Detyrosinated tubulin alpha-3 chain
HF: Tubulin beta-4B chain
HG: Detyrosinated tubulin alpha-3 chain
HH: Tubulin beta-4B chain
HI: Detyrosinated tubulin alpha-3 chain
HJ: Tubulin beta-4B chain
HK: Detyrosinated tubulin alpha-3 chain
HL: Tubulin beta-4B chain
I: Cilia- and flagella-associated protein 95
I1: Protein FAM166C
I2: Protein FAM166C
I3: Protein FAM166C
IA: Detyrosinated tubulin alpha-3 chain
IB: Tubulin beta-4B chain
IC: Detyrosinated tubulin alpha-3 chain
ID: Tubulin beta-4B chain
IE: Detyrosinated tubulin alpha-3 chain
IF: Tubulin beta-4B chain
IG: Detyrosinated tubulin alpha-3 chain
IH: Tubulin beta-4B chain
II: Detyrosinated tubulin alpha-3 chain
IJ: Tubulin beta-4B chain
IK: Detyrosinated tubulin alpha-3 chain
IL: Tubulin beta-4B chain
IM: Detyrosinated tubulin alpha-3 chain
J: Cilia- and flagella-associated protein 107
J1: Dual specificity phosphatase 21
J2: Dual specificity phosphatase 21
J3: Dual specificity phosphatase 21
JA: Detyrosinated tubulin alpha-3 chain
JB: Tubulin beta-4B chain
JC: Detyrosinated tubulin alpha-3 chain
JD: Tubulin beta-4B chain
JE: Detyrosinated tubulin alpha-3 chain
JF: Tubulin beta-4B chain
JG: Detyrosinated tubulin alpha-3 chain
JH: Tubulin beta-4B chain
JI: Detyrosinated tubulin alpha-3 chain
JJ: Tubulin beta-4B chain
JK: Detyrosinated tubulin alpha-3 chain
JL: Tubulin beta-4B chain
K: Cilia- and flagella-associated protein 161
K1: Coiled-coil domain-containing protein 105
K2: Coiled-coil domain-containing protein 105
K3: Coiled-coil domain-containing protein 105
K4: Coiled-coil domain-containing protein 105
K5: Coiled-coil domain-containing protein 105
KA: Detyrosinated tubulin alpha-3 chain
KB: Tubulin beta-4B chain
KC: Detyrosinated tubulin alpha-3 chain
KD: Tubulin beta-4B chain
KE: Detyrosinated tubulin alpha-3 chain
KF: Tubulin beta-4B chain
KG: Detyrosinated tubulin alpha-3 chain
KH: Tubulin beta-4B chain
KI: Detyrosinated tubulin alpha-3 chain
KJ: Tubulin beta-4B chain
KK: Detyrosinated tubulin alpha-3 chain
KL: Tubulin beta-4B chain
L: Cilia- and flagella-associated protein 161
L1: Enkurin
L2: Enkurin
L3: Enkurin
L4: Enkurin
LA: Detyrosinated tubulin alpha-3 chain
LB: Tubulin beta-4B chain
LC: Detyrosinated tubulin alpha-3 chain
LD: Tubulin beta-4B chain
LE: Detyrosinated tubulin alpha-3 chain
LF: Tubulin beta-4B chain
LG: Detyrosinated tubulin alpha-3 chain
LH: Tubulin beta-4B chain
LI: Detyrosinated tubulin alpha-3 chain
LJ: Tubulin beta-4B chain
LK: Detyrosinated tubulin alpha-3 chain
LL: Tubulin beta-4B chain
M: Piercer of microtubule wall 1 protein
M1: Testis-expressed protein 43
M2: Testis-expressed protein 43
M3: Testis-expressed protein 43
MB: Tubulin beta-4B chain
MC: Detyrosinated tubulin alpha-3 chain
MD: Tubulin beta-4B chain
ME: Detyrosinated tubulin alpha-3 chain
MF: Tubulin beta-4B chain
MG: Detyrosinated tubulin alpha-3 chain
MH: Tubulin beta-4B chain
MI: Detyrosinated tubulin alpha-3 chain
MJ: Tubulin beta-4B chain
MK: Detyrosinated tubulin alpha-3 chain
ML: Tubulin beta-4B chain
MM: Detyrosinated tubulin alpha-3 chain
N: Piercer of microtubule wall 2 protein
N1: Cilia- and flagella-associated protein 276
N2: Cilia- and flagella-associated protein 276
N3: Cilia- and flagella-associated protein 276
N4: Cilia- and flagella-associated protein 276
NA: Detyrosinated tubulin alpha-3 chain
NB: Tubulin beta-4B chain
NC: Detyrosinated tubulin alpha-3 chain
ND: Tubulin beta-4B chain
NE: Detyrosinated tubulin alpha-3 chain
NF: Tubulin beta-4B chain
NG: Detyrosinated tubulin alpha-3 chain
NH: Tubulin beta-4B chain
NI: Detyrosinated tubulin alpha-3 chain
NJ: Tubulin beta-4B chain
NK: Detyrosinated tubulin alpha-3 chain
NL: Tubulin beta-4B chain
O: RIB43A-like with coiled-coils protein 2
O1: Protein Flattop
O2: Protein Flattop
O3: Protein Flattop
OA: Detyrosinated tubulin alpha-3 chain
OB: Tubulin beta-4B chain
OC: Detyrosinated tubulin alpha-3 chain
OD: Tubulin beta-4B chain
OE: Detyrosinated tubulin alpha-3 chain
OF: Tubulin beta-4B chain
OG: Detyrosinated tubulin alpha-3 chain
OH: Tubulin beta-4B chain
OI: Detyrosinated tubulin alpha-3 chain
OJ: Tubulin beta-4B chain
OK: Detyrosinated tubulin alpha-3 chain
OL: Tubulin beta-4B chain
P: RIB43A-like with coiled-coils protein 2
P1: Cilia- and flagella-associated protein 52
P2: Cilia- and flagella-associated protein 52
P3: Cilia- and flagella-associated protein 52
PA: Detyrosinated tubulin alpha-3 chain
PB: Tubulin beta-4B chain
PC: Detyrosinated tubulin alpha-3 chain
PD: Tubulin beta-4B chain
PE: Detyrosinated tubulin alpha-3 chain
PF: Tubulin beta-4B chain
PG: Detyrosinated tubulin alpha-3 chain
PH: Tubulin beta-4B chain
PI: Detyrosinated tubulin alpha-3 chain
PJ: Tubulin beta-4B chain
PK: Detyrosinated tubulin alpha-3 chain
PL: Tubulin beta-4B chain
PM: Detyrosinated tubulin alpha-3 chain
Q: RIB43A-like with coiled-coils protein 2
Q1: EF-hand calcium-binding domain-containing protein 6
Q2: EF-hand calcium-binding domain-containing protein 6
Q3: EF-hand calcium-binding domain-containing protein 6
QB: Tubulin beta-4B chain
QC: Detyrosinated tubulin alpha-3 chain
QD: Tubulin beta-4B chain
QE: Detyrosinated tubulin alpha-3 chain
QF: Tubulin beta-4B chain
QG: Detyrosinated tubulin alpha-3 chain
QH: Tubulin beta-4B chain
QI: Detyrosinated tubulin alpha-3 chain
QJ: Tubulin beta-4B chain
QK: Detyrosinated tubulin alpha-3 chain
QL: Tubulin beta-4B chain
QM: Detyrosinated tubulin alpha-3 chain
R: RIB43A-like with coiled-coils protein 2
R1: Cilia and flagella-associated protein 77
R2: Cilia and flagella-associated protein 77
R3: Cilia and flagella-associated protein 77
RB: Tubulin beta-4B chain
RC: Detyrosinated tubulin alpha-3 chain
RD: Tubulin beta-4B chain
RE: Detyrosinated tubulin alpha-3 chain
RF: Tubulin beta-4B chain
RG: Detyrosinated tubulin alpha-3 chain
RH: Tubulin beta-4B chain
RI: Detyrosinated tubulin alpha-3 chain
RJ: Tubulin beta-4B chain
RK: Detyrosinated tubulin alpha-3 chain
RL: Tubulin beta-4B chain
RM: Detyrosinated tubulin alpha-3 chain
S: Sperm-associated antigen 8
SB: Tubulin beta-4B chain
SC: Detyrosinated tubulin alpha-3 chain
SD: Tubulin beta-4B chain
SE: Detyrosinated tubulin alpha-3 chain
SF: Tubulin beta-4B chain
SG: Detyrosinated tubulin alpha-3 chain
SH: Tubulin beta-4B chain
SI: Detyrosinated tubulin alpha-3 chain
SJ: Tubulin beta-4B chain
SK: Detyrosinated tubulin alpha-3 chain
SL: Tubulin beta-4B chain
SM: Detyrosinated tubulin alpha-3 chain
T: Sperm-associated antigen 8
TB: Tubulin beta-4B chain
TC: Detyrosinated tubulin alpha-3 chain
TD: Tubulin beta-4B chain
TE: Detyrosinated tubulin alpha-3 chain
TF: Tubulin beta-4B chain
TG: Detyrosinated tubulin alpha-3 chain
TH: Tubulin beta-4B chain
TI: Detyrosinated tubulin alpha-3 chain
TJ: Tubulin beta-4B chain
TK: Detyrosinated tubulin alpha-3 chain
TL: Tubulin beta-4B chain
TM: Detyrosinated tubulin alpha-3 chain
TN: Tubulin beta-4B chain
U: Cilia- and flagella-associated protein 45
UA: Detyrosinated tubulin alpha-3 chain
UB: Tubulin beta-4B chain
UC: Detyrosinated tubulin alpha-3 chain
UD: Tubulin beta-4B chain
UE: Detyrosinated tubulin alpha-3 chain
UF: Tubulin beta-4B chain
UG: Detyrosinated tubulin alpha-3 chain
UH: Tubulin beta-4B chain
UI: Detyrosinated tubulin alpha-3 chain
UJ: Tubulin beta-4B chain
UK: Detyrosinated tubulin alpha-3 chain
UL: Tubulin beta-4B chain
V: Cilia- and flagella-associated protein 45
VA: Detyrosinated tubulin alpha-3 chain
VB: Tubulin beta-4B chain
VC: Detyrosinated tubulin alpha-3 chain
VD: Tubulin beta-4B chain
VE: Detyrosinated tubulin alpha-3 chain
VF: Tubulin beta-4B chain
VG: Detyrosinated tubulin alpha-3 chain
VH: Tubulin beta-4B chain
VI: Detyrosinated tubulin alpha-3 chain
VJ: Tubulin beta-4B chain
VK: Detyrosinated tubulin alpha-3 chain
VL: Tubulin beta-4B chain
W: Cilia- and flagella-associated protein 45
WA: Detyrosinated tubulin alpha-3 chain
WB: Tubulin beta-4B chain
WC: Detyrosinated tubulin alpha-3 chain
WD: Tubulin beta-4B chain
WE: Detyrosinated tubulin alpha-3 chain
WF: Tubulin beta-4B chain
WG: Detyrosinated tubulin alpha-3 chain
WH: Tubulin beta-4B chain
WI: Detyrosinated tubulin alpha-3 chain
WJ: Tubulin beta-4B chain
WK: Detyrosinated tubulin alpha-3 chain
WL: Tubulin beta-4B chain
X: Cilia- and flagella-associated protein 45
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
XH: Parkin coregulated gene protein homolog
XI: Parkin coregulated gene protein homolog
XJ: Parkin coregulated gene protein homolog
XK: Parkin coregulated gene protein homolog
XL: Parkin coregulated gene protein homolog
XM: Parkin coregulated gene protein homolog
Y: Cilia- and flagella-associated protein 210
YA: Sperm acrosome-associated protein 9
YB: Sperm acrosome-associated protein 9
YC: Sperm acrosome-associated protein 9
YD: Sperm acrosome-associated protein 9
YE: Sperm acrosome-associated protein 9
YF: Sperm acrosome-associated protein 9
YG: Sperm acrosome-associated protein 9
YH: Sperm acrosome-associated protein 9
YI: Sperm acrosome-associated protein 9
YJ: Sperm acrosome-associated protein 9
YK: Sperm acrosome-associated protein 9
YL: Sperm acrosome-associated protein 9
YM: Sperm acrosome-associated protein 9
YN: Sperm acrosome-associated protein 9
YO: Sperm acrosome-associated protein 9
YP: Sperm acrosome-associated protein 9
YQ: Sperm acrosome-associated protein 9
YR: Sperm acrosome-associated protein 9
YS: Sperm acrosome-associated protein 9
YT: Sperm acrosome-associated protein 9
YU: Sperm acrosome-associated protein 9
YV: Sperm acrosome-associated protein 9
YW: Sperm acrosome-associated protein 9
Z: Cilia- and flagella-associated protein 210
a: Cilia- and flagella-associated protein 141
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,412,304729
ポリマ－21,266,337450
非ポリマー145,967279
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 , 24種, 416分子 ABA1A2A3A4ABADAFAHAJALBBBDBFBHBJBLCBCDCFCHCJCLDBDDDFDHDJDL...

#1: 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
#2: タンパク質
Tektin-1


分子量: 48713.035 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: Q9DAJ2
#3: タンパク質 ...
Tubulin beta-4B chain / Tubulin beta-2C chain


分子量: 47897.918 Da / 分子数: 139 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P68372
#4: タンパク質 ...
Detyrosinated tubulin alpha-3 chain


分子量: 48689.090 Da / 分子数: 140 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P05214
#5: タンパク質
Tektin-2 / Tektin-t / Testicular tektin


分子量: 50385.066 Da / 分子数: 9 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q922G7
#6: 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
#7: タンパク質
Tektin-3


分子量: 56754.777 Da / 分子数: 13 / 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
Tektin-4 / Testicular microtubules-related protein 4


分子量: 52121.449 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: Q149S1
#10: 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
#11: タンパク質 ...
Tektin-5


分子量: 62817.535 Da / 分子数: 22 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: G5E8A8
#13: 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
#15: タンパク質
Protein FAM166A


分子量: 36659.566 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: Q9D4K5
#17: タンパク質 Protein FAM166C


分子量: 23097.957 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: Q9DAS2
#19: タンパク質 Dual specificity phosphatase 21


分子量: 21527.574 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: Q9D9D8, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#21: 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
#22: 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
#24: タンパク質 Testis-expressed protein 43


分子量: 16305.608 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: Q9D9I1
#27: タンパク質
RIB43A-like with coiled-coils protein 2


分子量: 45328.156 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: Q9D4Q1
#28: タンパク質 Protein Flattop / Cilia- and flagella-associated protein 126


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
#30: 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: 3 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q6P1E8
#31: タンパク質 Cilia and flagella-associated protein 77


分子量: 32786.020 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: A0A087WRI3
#32: 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: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q3V0Q6
#35: 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: 6 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q9DAK2
#37: 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: 23 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q7TPM5

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EF-hand domain-containing family member ... , 2種, 5分子 EFG4G5G6

#9: 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
#14: タンパク質 EF-hand domain-containing family member C2


分子量: 87758.023 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: Q9D485

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Cilia- and flagella-associated protein ... , 10種, 27分子 GHIJKLN1N2N3N4P1P2P3UVWXXAXBXCXDXEXFXGYZa

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


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


分子量: 26633.035 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: Q9CQC3
#18: タンパク質 Cilia- and flagella-associated protein 107


分子量: 23062.510 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: Q4KKZ1
#20: 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
#26: タンパク質
Cilia- and flagella-associated protein 276


分子量: 18960.092 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: Q9DAD0
#29: 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
#33: 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: 65962.016 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: Q9D9U9
#34: 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
#36: タンパク質 Cilia- and flagella-associated protein 210 / Coiled-coil domain-containing protein 173


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
#38: 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

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

#23: 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
#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

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非ポリマー , 1種, 279分子

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


分子量: 523.180 Da / 分子数: 279 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / コメント: GTP, 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: 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: #1-#38 / 由来: NATURAL
由来(天然)生物種: Mus musculus (ハツカネズミ)
緩衝液pH: 7
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: SPOT SCAN
電子レンズモード: BRIGHT FIELD / 最大 デフォーカス（公称値）: 5000 nm / 最小 デフォーカス（公称値）: 1000 nm / Cs: 2.7 mm
撮影電子線照射量: 3 e/Å2 / Avg electron dose per subtomogram: 117 e/Å2 / 検出モード: SUPER-RESOLUTION
フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k)

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解析

ソフトウェア名称: UCSF ChimeraX / バージョン: 1.6/v9 / 分類: モデル構築 / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / タイプ: package
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: 6.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 17450 / 対称性のタイプ: POINT
EM volume selectionNum. of tomograms: 689 / Num. of volumes extracted: 17450

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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://pdbjlvh1.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