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- PDB-8snb: atomic model of sea urchin sperm doublet microtubule (48-nm perio... -

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基本情報

登録情報
データベース: PDB / ID: 8snb
タイトルatomic model of sea urchin sperm doublet microtubule (48-nm periodicity)
要素
  • (Cilia- and flagella-associated protein ...) x 6
  • (Coiled-coil domain-containing protein ...) x 2
  • (Meiosis-specific nuclear structural protein ...) x 2
  • (Outer dense fiber protein ...) x 2
  • (Trichohyalin-plectin-homology domain-containing ...) x 2
  • ATP6V1FNB
  • C20Orf85
  • C4orf45
  • CFA20 domain-containing protein
  • CFAP107
  • CFAP144(FAM183A)
  • CFAP21
  • CFAP276
  • CFAP68(UPF0686, C11orf1)
  • CFAP90(C5orf49)
  • CFAP96(C4orf47)
  • EF-hand domain-containing family member C2
  • Enkurin domain-containing protein
  • FAM166C
  • Flagellar FliJ protein
  • Flagellar protofilament ribbon protein rib74
  • HeLo_like_N(LOC577943)
  • Nucleoside diphosphate kinase
  • PACRG
  • Pierce1
  • Protein FAM166B
  • Protein phosphatase 1 regulatory subunit 32
  • RIB35
  • RIB43A-like with coiled-coils protein 2
  • SAXO3(LOC115918676)
  • SPATA45
  • SPATA48
  • Sperm-associated antigen 8
  • TEPP protein
  • Tektin A1
  • Tektin B1
  • Tektin C1
  • Testicular haploid expressed gene protein-like
  • Tex26(LOC100888047)
  • Tex33
  • Tex36(CFAP95, C9orf135)
  • Tex43
  • Tex49
  • Tex49_homologue(LOC580808)
  • Tubulin alpha chain
  • Tubulin beta chain
キーワードSTRUCTURAL PROTEIN / sperm / doublet microtubule / DMT / microtubule inner protein / cilia / flagella / FAP / CFAP / MIP / MAP / cytoskeleton / tublin / sea urchin / TEX / Tektin / SAXO / ODF / SPATA / RIB
機能・相同性
機能・相同性情報


: / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process ...: / cilium-dependent cell motility / regulation of cilium beat frequency involved in ciliary motility / cilium movement involved in cell motility / axoneme assembly / axonemal microtubule / cilium organization / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / motile cilium / positive regulation of cell motility / GTP biosynthetic process / nucleoside diphosphate kinase activity / ciliary base / regulation of neuron projection development / axoneme / microtubule-based process / mitotic cytokinesis / cilium assembly / alpha-tubulin binding / sperm flagellum / phosphatase binding / Hsp70 protein binding / phosphorylation / mitotic spindle organization / acrosomal vesicle / ciliary basal body / Hsp90 protein binding / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / protein-folding chaperone binding / spermatogenesis / microtubule binding / vesicle / microtubule / calmodulin binding / cytoskeleton / hydrolase activity / neuron projection / GTPase activity / centrosome / calcium ion binding / GTP binding / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
類似検索 - 分子機能
Coiled-coil domain-containing protein 81 / Testicular haploid expressed repeat / Uncharacterised protein family C20orf85 / Protein of unknown function DUF4562 / Testis-expressed protein 33 / Protein of unknown function DUF4586 / Hemingway/CFA97 / CFAP97 domain-containing protein 1/2 / Testicular haploid expressed gene protein-like / Hemingway/CFA97 ...Coiled-coil domain-containing protein 81 / Testicular haploid expressed repeat / Uncharacterised protein family C20orf85 / Protein of unknown function DUF4562 / Testis-expressed protein 33 / Protein of unknown function DUF4586 / Hemingway/CFA97 / CFAP97 domain-containing protein 1/2 / Testicular haploid expressed gene protein-like / Hemingway/CFA97 / Testicular haploid expressed repeat / Normal lung function maintenance, Low in Lung Cancer 1 protein / Domain of unknown function (DUF4562) / Cilia-and flagella-associated protein 96 / Testis-expressed sequence 33 protein family / Repeats in THEG (testicular haploid expressed gene) and several fly proteins. / Protein phosphatase 1 regulatory subunit 32 / Testis, prostate and placenta-expressed protein / Testis-expressed protein 49 / Protein phosphatase 1 regulatory subunit 32 / Protein of unknown function DUF1143 / Protein of unknown function DUF4541 / Protein of unknown function DUF4513 / CCDC81, HU domain 1 / CCDC81, HU domain 2 / Cilia- and flagella-associated protein 68 / CCDC81 eukaryotic HU domain 1 / Sperm-associated microtubule inner protein 10 / Cilia and flagella associated protein 90 / CCDC81 eukaryotic HU domain 2 / Sperm-tail PG-rich repeat / Coiled-coil domain-containing protein 105 / Sperm-tail PG-rich repeat / 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 / 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 / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / 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. / 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
類似検索 - ドメイン・相同性
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 97 / Uncharacterized protein / Uncharacterized protein / Protein FAM166B / Uncharacterized protein ...GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Cilia- and flagella-associated protein 97 / Uncharacterized protein / Uncharacterized protein / Protein FAM166B / Uncharacterized protein / Flagellar FliJ protein / TEPP protein / Sperm-associated antigen 8 / Cilia- and flagella-associated protein 126 / Cilia- and flagella-associated protein 45 / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Tubulin beta chain / Cilia- and flagella-associated protein 52 / Protein phosphatase 1 regulatory subunit 32 / Coiled-coil domain-containing protein 81 / Cilia- and flagella-associated protein 161 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Coiled-coil domain-containing protein 105 / Outer dense fiber protein 3 / RIB43A-like with coiled-coils protein 2 / Uncharacterized protein / Meiosis-specific nuclear structural protein 1 / Uncharacterized protein / Trichohyalin-plectin-homology domain-containing protein / Uncharacterized protein / EF-hand domain-containing protein / Uncharacterized protein / Testicular haploid expressed gene protein-like / Enkurin domain-containing protein / Tubulin alpha chain / Uncharacterized protein / Uncharacterized protein / Trichohyalin-plectin-homology domain-containing protein / EF-hand domain-containing family member C2 / Uncharacterized protein / Uncharacterized protein / Outer dense fiber protein 3 / CFA20 domain-containing protein / Nucleoside diphosphate kinase / Tektin / Uncharacterized protein / Cilia- and flagella-associated protein 77 / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Tektin / Flagellar protofilament ribbon protein rib74 / Tektin
類似検索 - 構成要素
生物種Strongylocentrotus purpuratus (ムラサキウニ)
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: 3.3 Å
データ登録者Zeng, J. / Zhang, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138854 米国
引用ジャーナル: Cell / 年: 2023
タイトル: Structural specializations of the sperm tail.
著者: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / ...著者: Miguel Ricardo Leung / Jianwei Zeng / Xiangli Wang / Marc C Roelofs / Wei Huang / Riccardo Zenezini Chiozzi / Johannes F Hevler / Albert J R Heck / Susan K Dutcher / Alan Brown / Rui Zhang / Tzviya Zeev-Ben-Mordehai /
要旨: Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule- ...Sperm motility is crucial to reproductive success in sexually reproducing organisms. Impaired sperm movement causes male infertility, which is increasing globally. Sperm are powered by a microtubule-based molecular machine-the axoneme-but it is unclear how axonemal microtubules are ornamented to support motility in diverse fertilization environments. Here, we present high-resolution structures of native axonemal doublet microtubules (DMTs) from sea urchin and bovine sperm, representing external and internal fertilizers. We identify >60 proteins decorating sperm DMTs; at least 15 are sperm associated and 16 are linked to infertility. By comparing DMTs across species and cell types, we define core microtubule inner proteins (MIPs) and analyze evolution of the tektin bundle. We identify conserved axonemal microtubule-associated proteins (MAPs) with unique tubulin-binding modes. Additionally, we identify a testis-specific serine/threonine kinase that links DMTs to outer dense fibers in mammalian sperm. Our study provides structural foundations for understanding sperm evolution, motility, and dysfunction at a molecular level.
履歴
登録2023年4月26日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02023年6月28日Provider: repository / タイプ: Initial release

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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
1A: CFAP96(C4orf47)
1B: CFAP96(C4orf47)
1E: Coiled-coil domain-containing protein 105
1F: Coiled-coil domain-containing protein 105
1G: Coiled-coil domain-containing protein 105
1H: Coiled-coil domain-containing protein 105
1K: Coiled-coil domain-containing protein 81
1L: Coiled-coil domain-containing protein 81
1M: Coiled-coil domain-containing protein 81
1P: FAM166C
1Q: FAM166C
1T: Protein FAM166B
1U: Protein FAM166B
1V: Protein FAM166B
1W: Protein FAM166B
1Y: CFAP144(FAM183A)
1a: Outer dense fiber protein 3
1b: Outer dense fiber protein 3
1d: Tex33
1f: C20Orf85
1g: C20Orf85
1i: ATP6V1FNB
1j: ATP6V1FNB
1l: Tex26(LOC100888047)
1m: Tex26(LOC100888047)
1o: Meiosis-specific nuclear structural protein 1
1p: Meiosis-specific nuclear structural protein 1
1q: Meiosis-specific nuclear structural protein 1
1r: Meiosis-specific nuclear structural protein 1
1v: Coiled-coil domain-containing protein 81
1w: Coiled-coil domain-containing protein 81
1x: Coiled-coil domain-containing protein 81
1y: Coiled-coil domain-containing protein 81
1z: Coiled-coil domain-containing protein 81
2A: Enkurin domain-containing protein
2B: Enkurin domain-containing protein
2C: Enkurin domain-containing protein
2D: Enkurin domain-containing protein
2G: CFAP107
2J: Cilia- and flagella-associated protein 126
2K: Cilia- and flagella-associated protein 126
2L: Cilia- and flagella-associated protein 126
2O: Flagellar FliJ protein
2R: Meiosis-specific nuclear structural protein 1
2S: Meiosis-specific nuclear structural protein 1
2V: Cilia- and flagella-associated protein 161
2W: Cilia- and flagella-associated protein 161
2a: Coiled-coil domain-containing protein 81
3A: CFA20 domain-containing protein
3B: CFA20 domain-containing protein
3C: CFA20 domain-containing protein
3D: CFA20 domain-containing protein
3E: CFA20 domain-containing protein
3F: CFA20 domain-containing protein
3G: CFA20 domain-containing protein
3J: CFAP21
3K: CFAP21
3N: Trichohyalin-plectin-homology domain-containing protein
3O: Trichohyalin-plectin-homology domain-containing protein
3R: CFAP276
3S: CFAP276
3T: CFAP276
3W: Cilia- and flagella-associated protein 45
3X: Cilia- and flagella-associated protein 45
3Y: Cilia- and flagella-associated protein 45
3Z: Cilia- and flagella-associated protein 45
4A: Cilia- and flagella-associated protein 52
4B: Cilia- and flagella-associated protein 52
4C: Cilia- and flagella-associated protein 52
4F: Trichohyalin-plectin-homology domain-containing protein
4G: Trichohyalin-plectin-homology domain-containing protein
4J: Nucleoside diphosphate kinase
4K: Nucleoside diphosphate kinase
4N: Cilia- and flagella-associated protein 77
4O: Cilia- and flagella-associated protein 77
4P: Cilia- and flagella-associated protein 77
4Q: Cilia- and flagella-associated protein 77
4T: Cilia- and flagella-associated protein 97
4U: Cilia- and flagella-associated protein 97
4V: Cilia- and flagella-associated protein 97
4Y: HeLo_like_N(LOC577943)
5A: Outer dense fiber protein 3
5B: Outer dense fiber protein 3
5E: Outer dense fiber protein 3
5F: Outer dense fiber protein 3
5G: Outer dense fiber protein 3
5H: Outer dense fiber protein 3
5I: Outer dense fiber protein 3
5J: Outer dense fiber protein 3
5K: Outer dense fiber protein 3
5L: Outer dense fiber protein 3
5M: Outer dense fiber protein 3
5N: Outer dense fiber protein 3
5O: Outer dense fiber protein 3
6A: PACRG
6B: PACRG
6C: PACRG
6D: PACRG
6E: PACRG
6F: PACRG
6I: Pierce1
6J: Pierce1
6M: Protein phosphatase 1 regulatory subunit 32
6N: Protein phosphatase 1 regulatory subunit 32
6Q: RIB35
6R: RIB35
6U: RIB43A-like with coiled-coils protein 2
6V: RIB43A-like with coiled-coils protein 2
6W: RIB43A-like with coiled-coils protein 2
6X: RIB43A-like with coiled-coils protein 2
7A: EF-hand domain-containing family member C2
7B: EF-hand domain-containing family member C2
7C: EF-hand domain-containing family member C2
7D: EF-hand domain-containing family member C2
7G: Flagellar protofilament ribbon protein rib74
7H: Flagellar protofilament ribbon protein rib74
7I: Flagellar protofilament ribbon protein rib74
7M: SAXO3(LOC115918676)
7N: SAXO3(LOC115918676)
7Q: TEPP protein
7R: TEPP protein
7U: SPATA48
7V: SPATA48
7Y: Sperm-associated antigen 8
7Z: Sperm-associated antigen 8
8A: Testicular haploid expressed gene protein-like
8D: Tektin A1
8E: Tektin A1
8F: Tektin A1
8G: Tektin A1
8J: Tektin B1
8K: Tektin B1
8L: Tektin B1
8M: Tektin B1
8N: Tektin B1
8Q: Tektin C1
8R: Tektin C1
8S: Tektin C1
8T: Tektin C1
8U: Tektin C1
8X: Tex43
8Y: Tex43
8Z: Tex43
9A: Tex36(CFAP95, C9orf135)
9D: CFAP90(C5orf49)
9G: Tex49
9J: Tex49_homologue(LOC580808)
9M: ATP6V1FNB
9N: ATP6V1FNB
9O: ATP6V1FNB
9R: CFAP68(UPF0686, C11orf1)
9T: SPATA45
9V: C4orf45
9W: C4orf45
9Y: Outer dense fiber protein 3
9Z: Outer dense fiber protein 3
AA: Tubulin alpha chain
AB: Tubulin alpha chain
AC: Tubulin beta chain
AD: Tubulin beta chain
AE: Tubulin alpha chain
AF: Tubulin beta chain
AG: Tubulin alpha chain
AH: Tubulin beta chain
AI: Tubulin alpha chain
AJ: Tubulin beta chain
AK: Tubulin alpha chain
AL: Tubulin beta chain
AM: Tubulin alpha chain
BA: Tubulin alpha chain
BB: Tubulin alpha chain
BC: Tubulin beta chain
BD: Tubulin beta chain
BE: Tubulin alpha chain
BF: Tubulin beta chain
BG: Tubulin alpha chain
BH: Tubulin beta chain
BI: Tubulin alpha chain
BJ: Tubulin beta chain
BK: Tubulin alpha chain
BL: Tubulin beta chain
BM: Tubulin alpha chain
CA: Tubulin alpha chain
CB: Tubulin alpha chain
CC: Tubulin beta chain
CD: Tubulin beta chain
CE: Tubulin alpha chain
CF: Tubulin beta chain
CG: Tubulin alpha chain
CH: Tubulin beta chain
CI: Tubulin alpha chain
CJ: Tubulin beta chain
CK: Tubulin alpha chain
CL: Tubulin beta chain
CM: Tubulin alpha chain
DA: Tubulin alpha chain
DB: Tubulin alpha chain
DC: Tubulin beta chain
DD: Tubulin beta chain
DE: Tubulin alpha chain
DF: Tubulin beta chain
DG: Tubulin alpha chain
DH: Tubulin beta chain
DI: Tubulin alpha chain
DJ: Tubulin beta chain
DK: Tubulin alpha chain
DL: Tubulin beta chain
DM: Tubulin alpha chain
EA: Tubulin alpha chain
EB: Tubulin beta chain
EC: Tubulin alpha chain
ED: Tubulin beta chain
EE: Tubulin alpha chain
EF: Tubulin beta chain
EG: Tubulin alpha chain
EH: Tubulin beta chain
EI: Tubulin alpha chain
EJ: Tubulin beta chain
EK: Tubulin alpha chain
EL: Tubulin beta chain
EM: Tubulin beta chain
FA: Tubulin alpha chain
FB: Tubulin alpha chain
FC: Tubulin beta chain
FD: Tubulin beta chain
FE: Tubulin alpha chain
FF: Tubulin beta chain
FG: Tubulin alpha chain
FH: Tubulin beta chain
FI: Tubulin alpha chain
FJ: Tubulin beta chain
FK: Tubulin alpha chain
FL: Tubulin beta chain
FM: Tubulin beta chain
GA: Tubulin alpha chain
GB: Tubulin alpha chain
GC: Tubulin beta chain
GD: Tubulin beta chain
GE: Tubulin alpha chain
GF: Tubulin beta chain
GG: Tubulin alpha chain
GH: Tubulin beta chain
GI: Tubulin alpha chain
GJ: Tubulin beta chain
GK: Tubulin alpha chain
GL: Tubulin beta chain
GM: Tubulin beta chain
HA: Tubulin alpha chain
HB: Tubulin alpha chain
HC: Tubulin beta chain
HD: Tubulin beta chain
HE: Tubulin alpha chain
HF: Tubulin beta chain
HG: Tubulin alpha chain
HH: Tubulin beta chain
HI: Tubulin alpha chain
HJ: Tubulin beta chain
HK: Tubulin alpha chain
HL: Tubulin beta chain
HM: Tubulin beta chain
IA: Tubulin alpha chain
IB: Tubulin alpha chain
IC: Tubulin beta chain
ID: Tubulin beta chain
IE: Tubulin alpha chain
IF: Tubulin beta chain
IG: Tubulin alpha chain
IH: Tubulin beta chain
II: Tubulin alpha chain
IJ: Tubulin beta chain
IK: Tubulin alpha chain
IL: Tubulin beta chain
IM: Tubulin alpha chain
JA: Tubulin alpha chain
JB: Tubulin alpha chain
JC: Tubulin beta chain
JD: Tubulin beta chain
JE: Tubulin alpha chain
JF: Tubulin beta chain
JG: Tubulin alpha chain
JH: Tubulin beta chain
JI: Tubulin alpha chain
JJ: Tubulin beta chain
JK: Tubulin alpha chain
JL: Tubulin beta chain
JM: Tubulin beta chain
KA: Tubulin alpha chain
KB: Tubulin alpha chain
KC: Tubulin beta chain
KD: Tubulin beta chain
KE: Tubulin alpha chain
KF: Tubulin beta chain
KG: Tubulin alpha chain
KH: Tubulin beta chain
KI: Tubulin alpha chain
KJ: Tubulin beta chain
KK: Tubulin alpha chain
KL: Tubulin beta chain
KM: Tubulin beta chain
LA: Tubulin alpha chain
LB: Tubulin alpha chain
LC: Tubulin beta chain
LD: Tubulin beta chain
LE: Tubulin alpha chain
LF: Tubulin beta chain
LG: Tubulin alpha chain
LH: Tubulin beta chain
LI: Tubulin alpha chain
LJ: Tubulin beta chain
LK: Tubulin alpha chain
LL: Tubulin beta chain
LM: Tubulin beta chain
MA: Tubulin alpha chain
MB: Tubulin alpha chain
MC: Tubulin beta chain
MD: Tubulin beta chain
ME: Tubulin alpha chain
MF: Tubulin beta chain
MG: Tubulin alpha chain
MH: Tubulin beta chain
MI: Tubulin alpha chain
MJ: Tubulin beta chain
MK: Tubulin alpha chain
ML: Tubulin alpha chain
MM: Tubulin beta chain
NA: Tubulin alpha chain
NB: Tubulin alpha chain
NC: Tubulin beta chain
ND: Tubulin beta chain
NE: Tubulin alpha chain
NF: Tubulin beta chain
NG: Tubulin alpha chain
NH: Tubulin beta chain
NI: Tubulin alpha chain
NJ: Tubulin beta chain
NK: Tubulin beta chain
NL: Tubulin alpha chain
NM: Tubulin beta chain
OA: Tubulin alpha chain
OB: Tubulin alpha chain
OC: Tubulin beta chain
OD: Tubulin beta chain
OE: Tubulin alpha chain
OF: Tubulin beta chain
OG: Tubulin alpha chain
OH: Tubulin beta chain
OI: Tubulin alpha chain
OJ: Tubulin beta chain
OK: Tubulin alpha chain
OL: Tubulin alpha chain
OM: Tubulin beta chain
PA: Tubulin alpha chain
PB: Tubulin alpha chain
PC: Tubulin beta chain
PD: Tubulin beta chain
PE: Tubulin alpha chain
PF: Tubulin beta chain
PG: Tubulin alpha chain
PH: Tubulin beta chain
PI: Tubulin alpha chain
PJ: Tubulin beta chain
PK: Tubulin alpha chain
PL: Tubulin alpha chain
PM: Tubulin beta chain
QA: Tubulin alpha chain
QB: Tubulin alpha chain
QC: Tubulin beta chain
QD: Tubulin beta chain
QE: Tubulin alpha chain
QF: Tubulin beta chain
QG: Tubulin alpha chain
QH: Tubulin beta chain
QI: Tubulin alpha chain
QJ: Tubulin beta chain
QK: Tubulin alpha chain
QL: Tubulin alpha chain
QM: Tubulin beta chain
RA: Tubulin alpha chain
RB: Tubulin alpha chain
RC: Tubulin beta chain
RD: Tubulin beta chain
RE: Tubulin alpha chain
RF: Tubulin beta chain
RG: Tubulin alpha chain
RH: Tubulin beta chain
RI: Tubulin alpha chain
RJ: Tubulin beta chain
RK: Tubulin alpha chain
RL: Tubulin alpha chain
RM: Tubulin beta chain
SA: Tubulin alpha chain
SB: Tubulin alpha chain
SC: Tubulin beta chain
SD: Tubulin beta chain
SE: Tubulin alpha chain
SF: Tubulin beta chain
SG: Tubulin alpha chain
SH: Tubulin beta chain
SI: Tubulin alpha chain
SJ: Tubulin beta chain
SK: Tubulin alpha chain
SL: Tubulin beta chain
SM: Tubulin beta chain
TA: Tubulin alpha chain
TB: Tubulin alpha chain
TC: Tubulin beta chain
TD: Tubulin beta chain
TE: Tubulin alpha chain
TF: Tubulin beta chain
TG: Tubulin alpha chain
TH: Tubulin beta chain
TI: Tubulin alpha chain
TJ: Tubulin beta chain
TK: Tubulin alpha chain
TL: Tubulin beta chain
TM: Tubulin beta chain
UA: Tubulin alpha chain
UB: Tubulin alpha chain
UC: Tubulin beta chain
UD: Tubulin beta chain
UE: Tubulin alpha chain
UF: Tubulin beta chain
UG: Tubulin alpha chain
UH: Tubulin beta chain
UI: Tubulin alpha chain
UJ: Tubulin beta chain
UK: Tubulin alpha chain
UL: Tubulin beta chain
UM: Tubulin beta chain
VA: Tubulin alpha chain
VB: Tubulin alpha chain
VC: Tubulin beta chain
VD: Tubulin beta chain
VE: Tubulin alpha chain
VF: Tubulin beta chain
VG: Tubulin alpha chain
VH: Tubulin beta chain
VI: Tubulin alpha chain
VJ: Tubulin beta chain
VK: Tubulin alpha chain
VL: Tubulin beta chain
VM: Tubulin beta chain
WA: Tubulin alpha chain
WB: Tubulin alpha chain
WC: Tubulin beta chain
WD: Tubulin beta chain
WE: Tubulin alpha chain
WF: Tubulin beta chain
WG: Tubulin alpha chain
WH: Tubulin beta chain
WI: Tubulin alpha chain
WJ: Tubulin beta chain
WK: Tubulin alpha chain
WL: Tubulin beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)21,164,643900
ポリマ－21,017,135454
非ポリマー147,508446
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 , 41種, 395分子 1A1B1P1Q1T1U1V1W1Y1d1f1g1i1j9M9N9O1l1m2A2B2C2D2G2O3A3B3C3D3E...

#1: タンパク質 CFAP96(C4orf47)


分子量: 33406.297 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7TH36
#4: タンパク質 FAM166C


分子量: 23728.354 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHZ2
#5: タンパク質
Protein FAM166B


分子量: 48701.172 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7HL38
#6: タンパク質 CFAP144(FAM183A)


分子量: 16431.441 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7GGZ7
#8: タンパク質 Tex33


分子量: 40544.223 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NRA7
#9: タンパク質 C20Orf85


分子量: 23738.551 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7HL88
#10: タンパク質
ATP6V1FNB


分子量: 21973.307 Da / 分子数: 5 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7GIN5
#11: タンパク質 Tex26(LOC100888047)


分子量: 19625.033 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7GGC2
#13: タンパク質
Enkurin domain-containing protein


分子量: 30122.543 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RFW1
#14: タンパク質 CFAP107


分子量: 27343.648 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RF95
#16: タンパク質 Flagellar FliJ protein


分子量: 14037.033 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7LW98
#19: タンパク質
CFA20 domain-containing protein


分子量: 22892.596 Da / 分子数: 7 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7SUA7
#20: タンパク質 CFAP21


分子量: 66165.797 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RFU1
#22: タンパク質 CFAP276


分子量: 19508.793 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RBR2
#26: タンパク質 Nucleoside diphosphate kinase


分子量: 42906.504 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7SX53
#29: タンパク質 HeLo_like_N(LOC577943)


分子量: 34673.039 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHW6
#31: タンパク質
PACRG


分子量: 26652.809 Da / 分子数: 6 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7REU1
#32: タンパク質 Pierce1


分子量: 13920.258 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7GRL1
#33: タンパク質 Protein phosphatase 1 regulatory subunit 32


分子量: 52795.879 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7P181
#34: タンパク質 RIB35


分子量: 34957.242 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7THB5
#35: タンパク質
RIB43A-like with coiled-coils protein 2


分子量: 45162.070 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RDQ5
#36: タンパク質
EF-hand domain-containing family member C2


分子量: 85763.664 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHU7
#37: タンパク質 Flagellar protofilament ribbon protein rib74


分子量: 74127.648 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: Q6TXM2
#38: タンパク質 SAXO3(LOC115918676)


分子量: 37032.676 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7THD0
#39: タンパク質 TEPP protein


分子量: 21414.076 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7N5A5
#40: タンパク質 SPATA48


分子量: 23009.598 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
#41: タンパク質 Sperm-associated antigen 8


分子量: 23161.557 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7N7W6
#42: タンパク質 Testicular haploid expressed gene protein-like


分子量: 30135.172 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RFU8
#43: タンパク質
Tektin A1


分子量: 53036.789 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: Q9U0E3
#44: タンパク質
Tektin B1


分子量: 49845.398 Da / 分子数: 5 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7SXG5
#45: タンパク質
Tektin C1


分子量: 46691.652 Da / 分子数: 5 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: Q26623
#46: タンパク質 Tex43


分子量: 14191.163 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7G0R8
#47: タンパク質 Tex36(CFAP95, C9orf135)


分子量: 25701.264 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RBC4
#48: タンパク質 CFAP90(C5orf49)


分子量: 19712.092 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7SYJ8
#49: タンパク質 Tex49


分子量: 17482.893 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RDT3
#50: タンパク質 Tex49_homologue(LOC580808)


分子量: 20695.467 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RFU3
#51: タンパク質 CFAP68(UPF0686, C11orf1)


分子量: 17679.635 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RBK2
#52: タンパク質 SPATA45


分子量: 9870.922 Da / 分子数: 1 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHE9
#53: タンパク質 C4orf45


分子量: 32467.586 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHI6
#54: タンパク質 ...
Tubulin alpha chain


分子量: 50184.496 Da / 分子数: 148 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RGW6
#55: タンパク質 ...
Tubulin beta chain


分子量: 50097.988 Da / 分子数: 150 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NS69

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Coiled-coil domain-containing protein ... , 2種, 13分子 1E1F1G1H1K1L1M1v1w1x1y1z2a

#2: タンパク質
Coiled-coil domain-containing protein 105


分子量: 49945.527 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RBY5
#3: タンパク質
Coiled-coil domain-containing protein 81


分子量: 79691.844 Da / 分子数: 9 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7PGM9

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Outer dense fiber protein ... , 2種, 17分子 1a1b5E5F5G5H5I5J5K5L5M5N5O5A5B9Y9Z

#7: タンパク質
Outer dense fiber protein 3


分子量: 27280.830 Da / 分子数: 13 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RI41
#30: タンパク質
Outer dense fiber protein 3


分子量: 30624.738 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RDG4

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Meiosis-specific nuclear structural protein ... , 2種, 6分子 1o1p1q1r2R2S

#12: タンパク質
Meiosis-specific nuclear structural protein 1


分子量: 17323.562 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NFX5
#17: タンパク質 Meiosis-specific nuclear structural protein 1


分子量: 61705.172 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7REB1

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Cilia- and flagella-associated protein ... , 6種, 19分子 2J2K2L2V2W3W3X3Y3Z4A4B4C4N4O4P4Q4T4U4V

#15: タンパク質 Cilia- and flagella-associated protein 126


分子量: 15883.667 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NA77
#18: タンパク質 Cilia- and flagella-associated protein 161


分子量: 32480.740 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RAY9
#23: タンパク質
Cilia- and flagella-associated protein 45


分子量: 64116.262 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NFL8
#24: タンパク質 Cilia- and flagella-associated protein 52


分子量: 70455.148 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7NV05
#27: タンパク質
Cilia- and flagella-associated protein 77


分子量: 27690.299 Da / 分子数: 4 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7TG06
#28: タンパク質 Cilia- and flagella-associated protein 97


分子量: 27701.848 Da / 分子数: 3 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7GHD6

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Trichohyalin-plectin-homology domain-containing ... , 2種, 4分子 3N3O4F4G

#21: タンパク質 Trichohyalin-plectin-homology domain-containing protein


分子量: 65783.406 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7REW2
#25: タンパク質 Trichohyalin-plectin-homology domain-containing protein


分子量: 62040.836 Da / 分子数: 2 / 由来タイプ: 天然
由来: (天然) Strongylocentrotus purpuratus (ムラサキウニ)
参照: UniProt: A0A7M7RHS4

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非ポリマー , 3種, 446分子

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


分子量: 523.180 Da / 分子数: 148 / 由来タイプ: 合成 / 式: C10H16N5O14P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: GTP, エネルギー貯蔵分子*YM
#57: 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: 148 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#58: 化合物...
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP


タイプ: RNA linking / 分子量: 443.201 Da / 分子数: 150 / 由来タイプ: 合成 / 式: C10H15N5O11P2 / タイプ: SUBJECT OF INVESTIGATION / 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Y

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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: sea urchin sperm doublet microtubule / タイプ: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#55 / 由来: NATURAL
由来(天然)生物種: Strongylocentrotus purpuratus (ムラサキウニ)
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）: 2500 nm / 最小 デフォーカス（公称値）: 500 nm
撮影電子線照射量: 34 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

ソフトウェア名称: UCSF ChimeraX / バージョン: 1.5/v9 / 分類: モデル構築 / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / タイプ: package
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
3次元再構成解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 127673 / 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://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