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- PDB-5okz: Crystal Strucrure of the Mpp6 Exosome complex -

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基本情報

登録情報
データベース: PDB / ID: 5okz
タイトルCrystal Strucrure of the Mpp6 Exosome complex
要素
  • (Exosome complex component ...) x 9
  • M-phase phosphoprotein 6 homolog
キーワードRNA BINDING PROTEIN / RNA degradation Exosome Ribosome biogenesis KH-domain
機能・相同性
機能・相同性情報


nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / mRNA decay by 3' to 5' exoribonuclease / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent mRNA catabolic process / nuclear mRNA surveillance of mRNA 3'-end processing / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / U5 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / exosome (RNase complex) / U4 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear mRNA surveillance / rRNA catabolic process / mRNA 3'-UTR AU-rich region binding / RNA catabolic process / poly(U) RNA binding / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA metabolic process / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / mRNA processing / manganese ion binding / protein-containing complex binding / nucleolus / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
類似検索 - 分子機能
M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain ...M-phase phosphoprotein 6 / M-phase phosphoprotein 6 / : / Exosome complex component CSL4, N-terminal domain / Exosome complex exonuclease Rrp40, N-terminal / Exosome complex exonuclease Rrp40 N-terminal domain / Exosome complex component RRP45 / Rrp40, S1 domain / : / Exosome complex component RRP40, S1 domain / Exosome complex component CSL4, C-terminal / Exosome complex component, N-terminal domain / Exosome complex component Csl4 / Exosome component EXOSC1/CSL4 / Exosome complex exonuclease RRP4 N-terminal region / RRP4, S1 domain / : / KH domain / Exosome complex RNA-binding protein 1/RRP40/RRP4 / GHMP Kinase, N-terminal domain / : / : / K Homology domain, type 1 / Exoribonuclease, phosphorolytic domain 2 / 3' exoribonuclease family, domain 2 / Exoribonuclease, phosphorolytic domain 1 / PNPase/RNase PH domain superfamily / Exoribonuclease, PH domain 2 superfamily / 3' exoribonuclease family, domain 1 / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / K Homology domain, type 1 superfamily / Ribosomal Protein S5; domain 2 / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Exosome complex component RRP43 / Exosome complex component RRP4 / Exosome complex component SKI6 / Exosome complex component MTR3 / Exosome complex component RRP46 / M-phase phosphoprotein 6 homolog / Exosome complex component CSL4 / Exosome complex component RRP45 / Exosome complex component RRP40 / Exosome complex component RRP42
類似検索 - 構成要素
生物種Saccharomyces cerevisiae (パン酵母)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.20003898551 Å
データ登録者Falk, S. / Ebert, J. / Conti, E.
資金援助 ベルギー, ドイツ, 4件
組織認可番号国
European Research Council294371 ベルギー
German Research FoundationSFB1035 ドイツ
German Research FoundationGRK1721 ドイツ
German Research FoundationCluster of Excellence CIPSM ドイツ
引用ジャーナル: Cell Rep / 年: 2017
タイトル: Mpp6 Incorporation in the Nuclear Exosome Contributes to RNA Channeling through the Mtr4 Helicase.
著者: Falk, S. / Bonneau, F. / Ebert, J. / Kogel, A. / Conti, E.
履歴
登録2017年7月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年8月30日Provider: repository / タイプ: Initial release
改定 1.12017年9月20日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22024年1月17日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.32024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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
m: Exosome complex component CSL4
A: Exosome complex component RRP45
B: Exosome complex component SKI6
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: M-phase phosphoprotein 6 homolog
K: Exosome complex component RRP45
L: Exosome complex component SKI6
M: Exosome complex component RRP43
N: Exosome complex component RRP46
O: Exosome complex component RRP42
P: Exosome complex component MTR3
Q: Exosome complex component RRP40
R: Exosome complex component RRP4
S: Exosome complex component CSL4
T: M-phase phosphoprotein 6 homolog
U: Exosome complex component RRP45
V: Exosome complex component SKI6
W: Exosome complex component RRP43
X: Exosome complex component RRP46
Y: Exosome complex component RRP42
Z: Exosome complex component MTR3
a: Exosome complex component RRP40
b: Exosome complex component RRP4
c: Exosome complex component CSL4
d: M-phase phosphoprotein 6 homolog
e: Exosome complex component RRP45
f: Exosome complex component SKI6
g: Exosome complex component RRP43
h: Exosome complex component RRP46
i: Exosome complex component RRP42
j: Exosome complex component MTR3
k: Exosome complex component RRP40
l: Exosome complex component RRP4
n: M-phase phosphoprotein 6 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)1,211,38253
ポリマ－1,210,43240
非ポリマー95013
水2,522140
1
m: Exosome complex component CSL4
e: Exosome complex component RRP45
f: Exosome complex component SKI6
g: Exosome complex component RRP43
h: Exosome complex component RRP46
i: Exosome complex component RRP42
j: Exosome complex component MTR3
k: Exosome complex component RRP40
l: Exosome complex component RRP4
n: M-phase phosphoprotein 6 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,86614
ポリマ－302,60810
非ポリマー2584
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area31280 Å2
ΔGint-176 kcal/mol
Surface area89130 Å2
手法PISA
2
A: Exosome complex component RRP45
B: Exosome complex component SKI6
C: Exosome complex component RRP43
D: Exosome complex component RRP46
E: Exosome complex component RRP42
F: Exosome complex component MTR3
G: Exosome complex component RRP40
H: Exosome complex component RRP4
I: Exosome complex component CSL4
J: M-phase phosphoprotein 6 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,84213
ポリマ－302,60810
非ポリマー2343
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area31470 Å2
ΔGint-172 kcal/mol
Surface area88760 Å2
手法PISA
3
K: Exosome complex component RRP45
L: Exosome complex component SKI6
M: Exosome complex component RRP43
N: Exosome complex component RRP46
O: Exosome complex component RRP42
P: Exosome complex component MTR3
Q: Exosome complex component RRP40
R: Exosome complex component RRP4
S: Exosome complex component CSL4
T: M-phase phosphoprotein 6 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,86614
ポリマ－302,60810
非ポリマー2584
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
4
U: Exosome complex component RRP45
V: Exosome complex component SKI6
W: Exosome complex component RRP43
X: Exosome complex component RRP46
Y: Exosome complex component RRP42
Z: Exosome complex component MTR3
a: Exosome complex component RRP40
b: Exosome complex component RRP4
c: Exosome complex component CSL4
d: M-phase phosphoprotein 6 homolog
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,80712
ポリマ－302,60810
非ポリマー1992
水1267
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area31160 Å2
ΔGint-153 kcal/mol
Surface area90560 Å2
手法PISA
単位格子
Length a, b, c (Å)161.779, 237.430, 201.895
Angle α, β, γ (deg.)90.00, 110.37, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43
14
24
15
25
35
45
16
26
36
46
17
27
37
47
18
28
38
19
29
39
49
110
210
310

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSMETMET(chain A and (resseq 3:13 or (resid 14 and (name...AB3 - 2963 - 296
211LYSLYSMETMET(chain K and (resseq 3:13 or (resid 14 and (name...KL3 - 2963 - 296
311LYSLYSMETMET(chain U and (resseq 3:13 or (resid 14 and (name...UV3 - 2963 - 296
411LYSLYSMETMET(chain e and ((resid 3 and (name N or name...eFA3 - 2963 - 296
112ARGARGPHEPHE(chain F and (resseq 8:19 or (resid 20 and (name...FG8 - 208 - 20
122GLNGLNASPASP(chain F and (resseq 8:19 or (resid 20 and (name...FG44 - 14644 - 146
132SERSERMETMET(chain F and (resseq 8:19 or (resid 20 and (name...FG163 - 246163 - 246
212ARGARGPHEPHE(chain P and (resseq 8:19 or (resid 20 and (name...PQ8 - 208 - 20
222GLNGLNASPASP(chain P and (resseq 8:19 or (resid 20 and (name...PQ44 - 14644 - 146
232SERSERMETMET(chain P and (resseq 8:19 or (resid 20 and (name...PQ163 - 246163 - 246
312ARGARGPHEPHE(chain Z and (resseq 8:15 or (resid 16 and (name...ZAA8 - 208 - 20
322GLNGLNASPASP(chain Z and (resseq 8:15 or (resid 16 and (name...ZAA44 - 14644 - 146
332SERSERMETMET(chain Z and (resseq 8:15 or (resid 16 and (name...ZAA163 - 246163 - 246
412ARGARGPHEPHE(chain j and (resseq 8:15 or (resid 16 and (name...jKA8 - 208 - 20
422GLNGLNASPASP(chain j and (resseq 8:15 or (resid 16 and (name...jKA44 - 14644 - 146
432SERSERMETMET(chain j and (resseq 8:15 or (resid 16 and (name...jKA163 - 246163 - 246
113SERSERPROPRO(chain H and (resseq 52:56 or (resid 57 and (name...HI52 - 1449 - 101
123LEULEUARGARG(chain H and (resseq 52:56 or (resid 57 and (name...HI157 - 243114 - 200
133GLNGLNGLNGLN(chain H and (resseq 52:56 or (resid 57 and (name...HI279 - 316236 - 273
143ARGARGMETMET(chain H and (resseq 52:56 or (resid 57 and (name...HI318 - 354275 - 311
213SERSERPROPRO(chain R and (resseq 52:56 or (resid 57 and (name...RS52 - 1449 - 101
223LEULEUARGARG(chain R and (resseq 52:56 or (resid 57 and (name...RS157 - 243114 - 200
233GLNGLNGLNGLN(chain R and (resseq 52:56 or (resid 57 and (name...RS279 - 316236 - 273
243ARGARGMETMET(chain R and (resseq 52:56 or (resid 57 and (name...RS318 - 354275 - 311
313SERSERPROPRO(chain b and (resseq 52:56 or (resid 57 and (name...bCA52 - 1449 - 101
323LEULEUARGARG(chain b and (resseq 52:56 or (resid 57 and (name...bCA157 - 243114 - 200
343GLNGLNGLNGLN(chain b and (resseq 52:56 or (resid 57 and (name...bCA279 - 316236 - 273
353ARGARGMETMET(chain b and (resseq 52:56 or (resid 57 and (name...bCA318 - 354275 - 311
413SERSERPROPRO(chain l and (resseq 52:65 or (resid 66 and (name...lMA52 - 1449 - 101
423LEULEUARGARG(chain l and (resseq 52:65 or (resid 66 and (name...lMA157 - 243114 - 200
433GLNGLNGLNGLN(chain l and (resseq 52:65 or (resid 66 and (name...lMA279 - 316236 - 273
443ARGARGMETMET(chain l and (resseq 52:65 or (resid 66 and (name...lMA318 - 354275 - 311
114ILEILETHRTHRchain TTU109 - 114113 - 118
214ILEILETHRTHRchain ddEA109 - 114113 - 118
115VALVALCYSCYS(chain C and ((resid 21 and (name N or name...CD21 - 4221 - 42
125LYSLYSTHRTHR(chain C and ((resid 21 and (name N or name...CD45 - 9945 - 99
135GLUGLUPROPRO(chain C and ((resid 21 and (name N or name...CD121 - 190121 - 190
145LYSLYSPHEPHE(chain C and ((resid 21 and (name N or name...CD206 - 247206 - 247
155ARGARGGLYGLY(chain C and ((resid 21 and (name N or name...CD256 - 263256 - 263
165ILEILELEULEU(chain C and ((resid 21 and (name N or name...CD274 - 302274 - 302
175ASNASNPHEPHE(chain C and ((resid 21 and (name N or name...CD327 - 392327 - 392
215VALVALCYSCYS(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN21 - 4221 - 42
225LYSLYSTHRTHR(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN45 - 9945 - 99
235GLUGLUPROPRO(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN121 - 190121 - 190
245LYSLYSPHEPHE(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN206 - 247206 - 247
255ARGARGGLYGLY(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN256 - 263256 - 263
265ILEILELEULEU(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN274 - 302274 - 302
275ASNASNPHEPHE(chain M and (resseq 21:43 or resseq 45:69 or (resid...MN327 - 392327 - 392
315VALVALCYSCYS(chain W and ((resid 21 and (name N or name...WX21 - 4221 - 42
325LYSLYSTHRTHR(chain W and ((resid 21 and (name N or name...WX45 - 9945 - 99
335GLUGLUPROPRO(chain W and ((resid 21 and (name N or name...WX121 - 190121 - 190
345LYSLYSPHEPHE(chain W and ((resid 21 and (name N or name...WX206 - 247206 - 247
355ARGARGGLYGLY(chain W and ((resid 21 and (name N or name...WX256 - 263256 - 263
365ILEILELEULEU(chain W and ((resid 21 and (name N or name...WX274 - 302274 - 302
375ASNASNPHEPHE(chain W and ((resid 21 and (name N or name...WX327 - 392327 - 392
415VALVALCYSCYS(chain g and ((resid 21 and (name N or name...gHA21 - 4221 - 42
425LYSLYSTHRTHR(chain g and ((resid 21 and (name N or name...gHA45 - 9945 - 99
435GLUGLUPROPRO(chain g and ((resid 21 and (name N or name...gHA121 - 190121 - 190
445LYSLYSPHEPHE(chain g and ((resid 21 and (name N or name...gHA206 - 247206 - 247
455ARGARGGLYGLY(chain g and ((resid 21 and (name N or name...gHA256 - 263256 - 263
465ILEILELEULEU(chain g and ((resid 21 and (name N or name...gHA274 - 302274 - 302
475ASNASNPHEPHE(chain g and ((resid 21 and (name N or name...gHA327 - 392327 - 392
116SERSERLEULEU(chain D and ((resid 2 and (name N or name...DE2 - 2215 - 224
216SERSERLEULEU(chain N and ((resid 2 and (name N or name...NO2 - 2215 - 224
316SERSERLEULEU(chain X and ((resid 2 and (name N or name...XY2 - 2215 - 224
416SERSERLEULEU(chain h and (resseq 2:10 or (resid 11 and (name...hIA2 - 2215 - 224
117METMETALAALA(chain E and (resseq 1:11 or (resid 12 and (name...EF1 - 1604 - 163
127LEULEULEULEU(chain E and (resseq 1:11 or (resid 12 and (name...EF169 - 244172 - 247
137GLNGLNVALVAL(chain E and (resseq 1:11 or (resid 12 and (name...EF246 - 259249 - 262
147SERSERLEULEU(chain E and (resseq 1:11 or (resid 12 and (name...EF261 - 262264 - 265
217METMETALAALA(chain O and ((resid 1 and (name N or name...OP1 - 1604 - 163
227LEULEULEULEU(chain O and ((resid 1 and (name N or name...OP169 - 244172 - 247
237GLNGLNVALVAL(chain O and ((resid 1 and (name N or name...OP246 - 259249 - 262
247SERSERLEULEU(chain O and ((resid 1 and (name N or name...OP261 - 262264 - 265
317METMETALAALA(chain Y and ((resid 1 and (name N or name...YZ1 - 1604 - 163
327LEULEULEULEU(chain Y and ((resid 1 and (name N or name...YZ169 - 244172 - 247
337GLNGLNVALVAL(chain Y and ((resid 1 and (name N or name...YZ246 - 259249 - 262
347SERSERLEULEU(chain Y and ((resid 1 and (name N or name...YZ261 - 262264 - 265
417METMETALAALA(chain i and ((resid 1 and (name N or name...iJA1 - 1604 - 163
427LEULEULEULEU(chain i and ((resid 1 and (name N or name...iJA169 - 244172 - 247
437GLNGLNVALVAL(chain i and ((resid 1 and (name N or name...iJA246 - 259249 - 262
447SERSERLEULEU(chain i and ((resid 1 and (name N or name...iJA261 - 262264 - 265
118SERSERHISHIS(chain G and (resseq 2:3 or (resid 4 and (name...GH2 - 436 - 47
128GLNGLNASNASN(chain G and (resseq 2:3 or (resid 4 and (name...GH53 - 10457 - 108
138LYSLYSTHRTHR(chain G and (resseq 2:3 or (resid 4 and (name...GH108 - 140112 - 144
148GLYGLYCYSCYS(chain G and (resseq 2:3 or (resid 4 and (name...GH146 - 198150 - 202
158LEULEUILEILE(chain G and (resseq 2:3 or (resid 4 and (name...GH201 - 234205 - 238
218SERSERHISHIS(chain a and ((resid 2 and (name N or name...aBA2 - 436 - 47
228GLNGLNASNASN(chain a and ((resid 2 and (name N or name...aBA53 - 10457 - 108
238LYSLYSTHRTHR(chain a and ((resid 2 and (name N or name...aBA108 - 140112 - 144
248GLYGLYCYSCYS(chain a and ((resid 2 and (name N or name...aBA146 - 198150 - 202
258LEULEUILEILE(chain a and ((resid 2 and (name N or name...aBA201 - 234205 - 238
318SERSERHISHIS(chain k and (resseq 2:3 or (resid 4 and (name...kLA2 - 436 - 47
328GLNGLNASNASN(chain k and (resseq 2:3 or (resid 4 and (name...kLA53 - 10457 - 108
338LYSLYSTHRTHR(chain k and (resseq 2:3 or (resid 4 and (name...kLA108 - 140112 - 144
348GLYGLYCYSCYS(chain k and (resseq 2:3 or (resid 4 and (name...kLA146 - 198150 - 202
358LEULEUILEILE(chain k and (resseq 2:3 or (resid 4 and (name...kLA201 - 234205 - 238
119LEULEUPROPRO(chain B and (resseq 4:9 or (resid 10 and (name...BC4 - 337 - 36
129ALAALALYSLYS(chain B and (resseq 4:9 or (resid 10 and (name...BC35 - 8338 - 86
139ARGARGARGARG(chain B and (resseq 4:9 or (resid 10 and (name...BC96 - 23999 - 242
219LEULEUPROPRO(chain L and ((resid 4 and (name N or name...LM4 - 337 - 36
229ALAALALYSLYS(chain L and ((resid 4 and (name N or name...LM35 - 8338 - 86
239ARGARGARGARG(chain L and ((resid 4 and (name N or name...LM96 - 23999 - 242
319LEULEUPROPRO(chain V and (resseq 4:9 or (resid 10 and (name...VW4 - 337 - 36
329ALAALALYSLYS(chain V and (resseq 4:9 or (resid 10 and (name...VW35 - 8338 - 86
339ARGARGARGARG(chain V and (resseq 4:9 or (resid 10 and (name...VW96 - 23999 - 242
419LEULEUPROPRO(chain f and ((resid 4 and (name N or name...fGA4 - 337 - 36
429ALAALALYSLYS(chain f and ((resid 4 and (name N or name...fGA35 - 8338 - 86
439ARGARGARGARG(chain f and ((resid 4 and (name N or name...fGA96 - 23999 - 242
1110PROPROPROPRO(chain S and (resseq 8:19 or resseq 37:45 or (resid...ST8 - 1911 - 22
1210PROPROARGARG(chain S and (resseq 8:19 or resseq 37:45 or (resid...ST37 - 6540 - 68
1310SERSERPROPRO(chain S and (resseq 8:19 or resseq 37:45 or (resid...ST109 - 112112 - 115
1410ASNASNLYSLYS(chain S and (resseq 8:19 or resseq 37:45 or (resid...ST126 - 161129 - 164
1510THRTHRPROPRO(chain S and (resseq 8:19 or resseq 37:45 or (resid...ST187 - 291190 - 294
2210PROPROPROPRO(chain c and (resseq 8:19 or resseq 37:45 or (resid...cDA8 - 1911 - 22
2310PROPROARGARG(chain c and (resseq 8:19 or resseq 37:45 or (resid...cDA37 - 6540 - 68
2410SERSERPROPRO(chain c and (resseq 8:19 or resseq 37:45 or (resid...cDA109 - 112112 - 115
2510ASNASNLYSLYS(chain c and (resseq 8:19 or resseq 37:45 or (resid...cDA126 - 161129 - 164
2610THRTHRPROPRO(chain c and (resseq 8:19 or resseq 37:45 or (resid...cDA187 - 291190 - 294
3110PROPROPROPRO(chain m and (resseq 8:19 or resseq 37:45 or (resid...mA8 - 1911 - 22
3210PROPROARGARG(chain m and (resseq 8:19 or resseq 37:45 or (resid...mA37 - 6540 - 68
3310SERSERPROPRO(chain m and (resseq 8:19 or resseq 37:45 or (resid...mA109 - 112112 - 115
3410ASNASNLYSLYS(chain m and (resseq 8:19 or resseq 37:45 or (resid...mA126 - 161129 - 164
3510THRTHRPROPRO(chain m and (resseq 8:19 or resseq 37:45 or (resid...mA187 - 291190 - 294

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9
10

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要素

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Exosome complex component ... , 9種, 36分子 mIScAKUeBLVfCMWgDNXhEOYiFPZjGQ...

#1: タンパク質
Exosome complex component CSL4 / CEP1 synthetic lethal protein 4


分子量: 31911.594 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: CSL4, SKI4, YNL232W, N1154 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P53859
#2: タンパク質
Exosome complex component RRP45 / Ribosomal RNA-processing protein 45


分子量: 34001.859 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: RRP45, YDR280W, D9954.1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q05636
#3: タンパク質
Exosome complex component SKI6 / Extracellular mutant protein 20 / Ribosomal RNA-processing protein 41 / Superkiller protein 6


分子量: 27892.041 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: SKI6, ECM20, RRP41, YGR195W, G7587 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P46948
#4: タンパク質
Exosome complex component RRP43 / Ribosomal RNA-processing protein 43


分子量: 44093.000 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: RRP43, YCR035C, YCR35C, YCR522 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P25359
#5: タンパク質
Exosome complex component RRP46 / Ribosomal RNA-processing protein 46


分子量: 24659.428 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: RRP46, YGR095C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P53256
#6: タンパク質
Exosome complex component RRP42 / Ribosomal RNA-processing protein 42


分子量: 29391.516 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: RRP42, YDL111C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q12277
#7: タンパク質
Exosome complex component MTR3 / mRNA transport regulator 3


分子量: 27573.896 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: MTR3, YGR158C, G6676 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P48240
#8: タンパク質
Exosome complex component RRP40 / Ribosomal RNA-processing protein 40


分子量: 26939.688 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: RRP40, YOL142W / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q08285
#9: タンパク質
Exosome complex component RRP4 / Ribosomal RNA-processing protein 4


分子量: 34603.148 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (パン酵母)
遺伝子: RRP4, YHR069C / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P38792

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タンパク質 , 1種, 4分子 JTdn

#10: タンパク質
M-phase phosphoprotein 6 homolog / Exosome-associated RNA-binding protein MPP6


分子量: 21541.881 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母)
遺伝子: MPP6, YNR024W, N3230 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P53725

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非ポリマー , 4種, 153分子

#11: 化合物
ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / 3-アミノ-3-(2-ヒドロキシエチル)-1,5-ペンタンジオ-ル


分子量: 163.215 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C7H17NO3 / コメント: pH緩衝剤*YM
#12: 化合物
ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 7 / 由来タイプ: 合成 / 式: Cl
#13: 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: 2 / 由来タイプ: 合成 / 式: Mg
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 140 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.68 Å3/Da / 溶媒含有率: 66.57 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5
詳細: 0.1 M Tris/Mops pH 7.5 30 mM MgCl2, 30 mM CaCl2 30% PEG 8000/Ethylene glycol

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X10SA / 波長: 1.25 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年10月10日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1.25 Å / 相対比: 1
反射解像度: 3.2→151.66 Å / Num. obs: 229497 / % possible obs: 97.7 % / 冗長度: 4.3 % / Biso Wilson estimate: 72.3570397634 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.114 / Net I/σ(I): 5.7
反射 シェル解像度: 3.2→3.25 Å / 冗長度: 2.8 % / Rmerge(I) obs: 1.881 / Mean I/σ(I) obs: 0.6 / Num. unique all: 9275 / CC1/2: 0.243 / Rpim(I) all: 1.298 / % possible all: 79.9

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
DIALSdata processing
Aimlessデータ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5jea

5jea


解像度: 3.20003898551→80.76 Å / SU ML: 0.520726703071 / 交差検証法: FREE R-VALUE / 位相誤差: 29.4475207363
Rfactor反射数%反射
Rfree0.26152374451 11365 4.9721137382 %
Rwork0.222533890933 --
obs0.224490359891 229006 95.764203604 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 95.2736983465 Å2
精密化ステップサイクル: LAST / 解像度: 3.20003898551→80.76 Å
タンパク質核酸リガンド溶媒全体
原子数66971 0 53 140 67164
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.4040962650875010.39233541441411017X-RAY DIFFRACTION73.7199180748
3.2364-3.27450.4134288536216000.37903648363411344X-RAY DIFFRACTION77.6997137653
3.2745-3.31440.4059483899126430.37233981951512162X-RAY DIFFRACTION82.3896538412
3.3144-3.35640.396515864736670.37196138240912695X-RAY DIFFRACTION86.2732438017
3.3564-3.40050.3974223748237740.35367580062913029X-RAY DIFFRACTION89.5658944909
3.4005-3.44710.3764997025257780.34053190113913696X-RAY DIFFRACTION92.7761040959
3.4471-3.49640.3642609299197860.32703372577714126X-RAY DIFFRACTION96.4366552415
3.4964-3.54860.3555625386766870.30980335821614602X-RAY DIFFRACTION98.8747332342
3.5486-3.6040.3472204831947840.31017141103114690X-RAY DIFFRACTION99.3834296724
3.604-3.66310.3405750064268260.32314971054114480X-RAY DIFFRACTION99.3057808344
3.6631-3.72630.3377391607768170.30968688001814542X-RAY DIFFRACTION99.2375783421
3.7263-3.7940.3365280942997780.29182553487214555X-RAY DIFFRACTION99.1016028956
3.794-3.8670.2984103069517590.26150613591114585X-RAY DIFFRACTION99.0894413949
3.867-3.94590.2823718308747560.23577329057614605X-RAY DIFFRACTION98.7528126005
3.9459-4.03170.2737592072987130.22353877996814493X-RAY DIFFRACTION98.3888709156
4.0317-4.12550.2514995996317180.20906485609714389X-RAY DIFFRACTION97.6914123125
4.1255-4.22870.2288019233177140.18854453485514667X-RAY DIFFRACTION99.1491007542
4.2287-4.3430.2144329256137570.1745527327714657X-RAY DIFFRACTION99.419504644
4.343-4.47080.1962728816427980.1690096637314609X-RAY DIFFRACTION99.2655112428
4.4708-4.61510.2134429361347090.16386817251614599X-RAY DIFFRACTION99.2994291645
4.6151-4.78010.2044027723878270.15600206714414564X-RAY DIFFRACTION98.9456766313
4.7801-4.97150.1992942846587400.15808122588214390X-RAY DIFFRACTION98.3809090318
4.9715-5.19770.2167710473917210.16492206103514597X-RAY DIFFRACTION98.343605547
5.1977-5.47170.2203005435177340.1734031577614637X-RAY DIFFRACTION99.4757960135
5.4717-5.81450.2429734695267310.1945724237114699X-RAY DIFFRACTION99.5483870968
5.8145-6.26330.2730667367327410.20001130773614644X-RAY DIFFRACTION99.3157317152
6.2633-6.89350.2523321436867440.20566354881214400X-RAY DIFFRACTION98.0003882741
6.8935-7.89050.2258915294687670.18989107360314648X-RAY DIFFRACTION99.5543787135
7.8905-9.93960.1858380990817700.14274023932814500X-RAY DIFFRACTION98.5670023238
9.9396-94.67540.2184152973427870.20773969087914274X-RAY DIFFRACTION97.1426728586
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.324621009222-0.1226392676410.1061174035540.247374873914-0.1996911824620.185157354592-0.4789989413860.8635103795450.3811834771180.762462457289-0.003525680726830.330984258315-1.051988149620.07004271237780.0001202416734051.47146765088-0.05205551541860.06218542938081.504413756440.06051765107191.1987875110477.555322541919.259625543761.6399750588
20.01622067823940.002045179918860.0139531866480.0179486989383-0.004521425002860.00512396425471-0.7901722158-0.5245355228620.222529981477-0.076926324254-0.3623831071330.5724885833330.5669568575280.465782667957-0.0007569442186961.44880421506-0.200795627792-0.363209960231.465453189480.2792266422350.86354497683476.874337756320.236836052280.9748403212
30.1135582040620.0987288486318-0.1358732612340.0993835637221-0.003862448283220.3575990500940.5377901938680.9546955349570.6582414294670.002049902565170.249812380107-0.3595082308550.03566201840521.274814860770.009918916160951.44696506357-0.248405499630.1970694637791.358847036180.2777784775932.3828341416190.290407304617.56307533296.9950256154
40.09948257057020.03477682492580.08498945197770.005129507782830.01269267310320.02841881555340.2572587907460.347954693705-0.6259454615460.7008490050610.3008767721310.3246003817990.656949288170.09227184375929.77964554798E-51.46331808491-0.0112361912153-0.01382698441811.58293966316-0.02475619674571.5206243594680.801753353415.493216209691.9166178972
50.57090578455-0.06367477571750.6028517049250.0644280391419-0.06465286214130.5543925311-0.1701473102040.5862586028220.809972417935-0.2824205345810.266118788007-0.717500997997-1.008613632330.266288616353-2.71926611899E-51.86923566375-0.1842493320870.2480624884521.19803561735-0.1906209531412.4246855593191.425671659423.2610210184105.564180955
62.735712925360.0771872315314-0.2657698749132.56250392167-0.4753605372540.605960663068-0.05309717742550.06920843140670.291302584831-0.111801312181-0.0789186103224-0.2231270368450.0678976652461-0.152961613767-0.000138333574580.6269013997980.06355669465490.01027175299770.530077426138-0.0375394167710.54654270688785.3815201839-78.9475984008110.463613968
71.45009606798-0.7258830350.09174617281880.946197383656-0.6794600760271.55448875363-0.123130630042-0.4324393403980.6741012107080.256258125852-0.107775187145-0.0654457205294-0.048680306114-0.09894632441783.1721929119E-50.7122663403730.145096544025-0.03202990049720.560320564326-0.1219955271580.57421036209280.9034349685-71.3864948827113.358908786
80.0486704235518-0.00346183308546-0.01293644007560.0430309883426-0.03111000818360.17230323686-0.8681601799-0.3239181492021.0686215635-0.636956807061-0.136040653334-0.593470102905-0.7544755106420.65909104352-2.6543428702E-50.670550393229-0.186482835158-0.04566051575720.792753811932-0.03062763287061.3587181000175.0713481785-48.997223693286.0599285196
90.403834558583-0.124533787579-0.02872968303680.0439452941340.04622326363530.1632925313080.0090031537780.6222590488330.058479406887-0.4385893216960.124447563196-0.5085129587390.2395419684280.0929385214342-8.10526030196E-60.93942937642-0.193488027648-0.1608657017130.7201725217460.1105865034540.58512330697267.3692990232-73.978321316173.7033135701
100.620426810548-0.1592067111680.1196508891810.4045091810320.6334083110031.1124467290.123431952922-0.288202967782-0.190021781898-0.00701324266015-0.1717964614420.4578389097370.1330864507270.0887057669552.24528440019E-50.661252614876-0.06891353119-0.1184060861460.5894061528410.0292697270580.80714167936370.9371187208-83.522794094982.427104789
110.0499502004245-0.001078178938250.0182043651454-0.002255171056970.007431365261870.01618947173340.680337154476-1.102721880930.211606947764-0.1921991653550.513323099642-0.3167320170350.137211123302-0.2923033591188.78787962835E-50.775127794246-0.1869040650190.009487074897961.0560642469-0.1797358464250.70505904655289.9155671981-72.859946579580.366912569
121.67563625949-1.01090192008-0.3028197684121.216231921870.3842378510371.53896091857-0.21625753123-0.162762646253-0.00688494752771-0.04056891060310.00896972831218-0.08661860932970.380972654932-0.06800836965917.27829197454E-50.593700636569-0.1253096513830.02815954267810.560726836345-0.01647970404180.44048818539270.5875095257-79.902003162686.9159671967
130.836029397675-0.8268510148340.2807075501790.8937701425680.2521079964681.1681937537-0.3244094781060.188405215030.372510890885-0.314814641620.0899755871137-0.608164750418-0.2357097143240.06248649532244.24739996167E-50.456779973492-0.0117071361605-0.03270684981960.5353268840630.01766992595550.84954156370770.8113895261-64.092613619790.9170512366
140.09706077759730.06792619808390.1365578007070.554575260506-0.2969731127340.268283576484-0.2596620573620.3396272226370.5233679308060.184764486538-0.0171700594474-0.186144251674-0.1914789859040.0102160159185-1.25248676092E-50.5949868889750.0242851966367-0.002853884847650.653433674705-0.01729834426310.73451737283369.9235663876-64.7480396035100.054524139
151.35770283036-0.6508441505590.1723330434271.25572938634-0.7735339276330.562721220708-0.2151446680590.4055840680520.481503013581-0.707050729481-0.3866023235910.382940901475-0.490362056654-0.248884820635-0.0002867753079540.5568706734860.0423935594585-0.03578371154130.751919651830.03614746694560.93692703778859.0557039173-66.917932980982.4252336059
162.12184603122-0.1891879323450.6397537028441.26543144314-0.04853513046332.188606344860.01171726983330.37905319655-0.0868687296421-0.163464794068-0.117213483978-0.24531555853-0.0209315819720.112091211231-1.90414382941E-50.6049729892360.1923126463780.1879194420370.7763829848280.02608584810020.909334227689114.565181837-103.17657396693.8219716671
170.986576750022-0.183945170039-0.3080551660340.295510072270.5905537970681.526788266780.05701074494820.4639767895740.6316732139860.0801905140696-0.0352977975504-0.500905965524-0.4691161970.1794679993863.54769432408E-60.7747420096120.2053853048890.1054736114790.7057645475110.2358250319111.26968715525120.448634464-89.686087536790.2436957721
180.0526606139993-0.349827605797-0.02031616287280.479608676115-0.0214504392692-0.127171669127-0.1951553523330.4187193413690.0769004845953-0.198297331468-0.171612237295-0.862968939999-0.132630468980.287762746742-0.0001884306856660.9281075163230.007292795803680.2943446135150.8336854998560.1875630538341.59265687298121.848067878-76.370807137188.5229496355
191.17446112701-0.752072260090.7818994023111.14433676964-0.1369205747322.037033762870.00456554654180.085112850406-0.2660136591910.0875522925921-0.0382686519572-0.3195898126230.2865683095570.149848947446-4.39149041428E-50.7307044092680.2092614504820.005819851638190.59324859638-0.037821994240.808858212156116.197420565-115.265473834105.922939502
200.3398975356630.438391606484-0.250920538030.492864716679-0.3077681080290.179191893106-0.57566266754-0.2475764198730.8740914685941.174937018920.3543447155910.3218609955060.1744071877550.115711837865-0.00578325842840.9893987195540.098799103175-0.03739432732370.572385332677-0.08285998470570.51126314852788.4329651584-95.3271843375123.870106991
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1630.110390564258-0.09938242063240.1506075807650.7507354633610.308795538690.583308292022-0.4705180434260.1013481004450.07387642978210.2356636900770.331763211392-0.04993083319950.258402864481-0.455280620006-0.0001692550526810.8835117018280.0242743136994-0.1143505088430.854803213629-0.02865132249950.68258913720777.9866662041-15.600334114126.047304556
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1670.712043823653-0.5657002984750.100636402690.4641646126590.0906280389730.437104040803-0.077055073903-0.96598372342-1.075856333230.4886499846370.280532474205-0.2154098410680.138729405702-0.1717063769560.0009592501910810.7399228262890.140539438393-0.07077592135570.8416092363080.0538863416890.72374820543255.3616149997-13.0289484275124.156689355
1680.6495631404580.150295364562-0.6400840608350.383124611757-0.120045882880.901491745523-0.0319643108658-0.788525851637-0.1092561450420.6151227773610.1180243933240.355658732139-0.13323062917-0.02487729779370.008394795593541.019119224450.184502722425-0.1187049807340.801147938978-0.1552721571020.61193160148665.615412727-3.40563755901129.915942258
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1732.77595732485-0.879727363357-0.619060810762.460949536250.7499803277583.10698366740.08464223384030.3190793255690.347732403943-0.3067003705290.03104583944440.272769164954-0.46347133364-0.480217451191.23700398311E-50.8163232194830.130066231546-0.120201401480.8206648472050.06444253445480.65207757079369.13743045430.057904928537570.8693103838
1742.942131968511.93284721019-0.5582618394291.32218338661-0.3052185058011.889712000320.622590460614-1.390180308852.088381886330.6301843921460.1461728246290.645423129235-0.775621406817-0.2586369814850.9640871590971.430633062970.615090888463-0.3921724053430.919993394218-1.149286857790.99686955153782.133963420911.5037608152133.684562548
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1791.26409371234-0.0616717563376-0.1422525098630.8686876987210.232638400660.7168869251390.0678575408634-0.3671422475370.7852691083940.104217373355-0.176268570710.357501264485-0.7495940607110.100600006662-0.002091831119770.855656524991-0.288892693815-0.1359081598950.7506699874390.08428999293011.20402430695112.7139201655.6704059944377.6725638845
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精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'm' and (resid 8 through 109 )
2X-RAY DIFFRACTION2chain 'm' and (resid 110 through 131 )
3X-RAY DIFFRACTION3chain 'm' and (resid 132 through 159 )
4X-RAY DIFFRACTION4chain 'm' and (resid 160 through 201 )
5X-RAY DIFFRACTION5chain 'm' and (resid 202 through 291 )
6X-RAY DIFFRACTION6chain 'A' and (resid 3 through 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 297 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 22 )
9X-RAY DIFFRACTION9chain 'B' and (resid 23 through 37 )
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 92 )
12X-RAY DIFFRACTION12chain 'B' and (resid 93 through 149 )
13X-RAY DIFFRACTION13chain 'B' and (resid 150 through 190 )
14X-RAY DIFFRACTION14chain 'B' and (resid 191 through 209 )
15X-RAY DIFFRACTION15chain 'B' and (resid 210 through 244 )
16X-RAY DIFFRACTION16chain 'C' and (resid 16 through 175 )
17X-RAY DIFFRACTION17chain 'C' and (resid 176 through 240 )
18X-RAY DIFFRACTION18chain 'C' and (resid 241 through 291 )
19X-RAY DIFFRACTION19chain 'C' and (resid 292 through 393 )
20X-RAY DIFFRACTION20chain 'D' and (resid 2 through 14 )
21X-RAY DIFFRACTION21chain 'D' and (resid 15 through 31 )
22X-RAY DIFFRACTION22chain 'D' and (resid 32 through 45 )
23X-RAY DIFFRACTION23chain 'D' and (resid 46 through 60 )
24X-RAY DIFFRACTION24chain 'D' and (resid 61 through 77 )
25X-RAY DIFFRACTION25chain 'D' and (resid 78 through 96 )
26X-RAY DIFFRACTION26chain 'D' and (resid 97 through 150 )
27X-RAY DIFFRACTION27chain 'D' and (resid 151 through 167 )
28X-RAY DIFFRACTION28chain 'D' and (resid 168 through 187 )
29X-RAY DIFFRACTION29chain 'D' and (resid 188 through 222 )
30X-RAY DIFFRACTION30chain 'E' and (resid 0 through 16 )
31X-RAY DIFFRACTION31chain 'E' and (resid 17 through 103 )
32X-RAY DIFFRACTION32chain 'E' and (resid 104 through 119 )
33X-RAY DIFFRACTION33chain 'E' and (resid 120 through 176 )
34X-RAY DIFFRACTION34chain 'E' and (resid 177 through 202 )
35X-RAY DIFFRACTION35chain 'E' and (resid 203 through 263 )
36X-RAY DIFFRACTION36chain 'F' and (resid 6 through 44 )
37X-RAY DIFFRACTION37chain 'F' and (resid 45 through 247 )
38X-RAY DIFFRACTION38chain 'G' and (resid 0 through 18 )
39X-RAY DIFFRACTION39chain 'G' and (resid 19 through 94 )
40X-RAY DIFFRACTION40chain 'G' and (resid 95 through 125 )
41X-RAY DIFFRACTION41chain 'G' and (resid 126 through 219 )
42X-RAY DIFFRACTION42chain 'G' and (resid 220 through 237 )
43X-RAY DIFFRACTION43chain 'H' and (resid 52 through 99 )
44X-RAY DIFFRACTION44chain 'H' and (resid 100 through 127 )
45X-RAY DIFFRACTION45chain 'H' and (resid 128 through 161 )
46X-RAY DIFFRACTION46chain 'H' and (resid 162 through 242 )
47X-RAY DIFFRACTION47chain 'H' and (resid 243 through 290 )
48X-RAY DIFFRACTION48chain 'H' and (resid 291 through 355 )
49X-RAY DIFFRACTION49chain 'I' and (resid 11 through 37 )
50X-RAY DIFFRACTION50chain 'I' and (resid 38 through 58 )
51X-RAY DIFFRACTION51chain 'I' and (resid 59 through 137 )
52X-RAY DIFFRACTION52chain 'I' and (resid 138 through 149 )
53X-RAY DIFFRACTION53chain 'I' and (resid 150 through 194 )
54X-RAY DIFFRACTION54chain 'I' and (resid 195 through 209 )
55X-RAY DIFFRACTION55chain 'I' and (resid 210 through 236 )
56X-RAY DIFFRACTION56chain 'I' and (resid 237 through 261 )
57X-RAY DIFFRACTION57chain 'I' and (resid 262 through 290 )
58X-RAY DIFFRACTION58chain 'J' and (resid 90 through 94 )
59X-RAY DIFFRACTION59chain 'J' and (resid 95 through 99 )
60X-RAY DIFFRACTION60chain 'J' and (resid 108 through 117 )
61X-RAY DIFFRACTION61chain 'K' and (resid 3 through 161 )
62X-RAY DIFFRACTION62chain 'K' and (resid 162 through 176 )
63X-RAY DIFFRACTION63chain 'K' and (resid 177 through 224 )
64X-RAY DIFFRACTION64chain 'K' and (resid 225 through 297 )
65X-RAY DIFFRACTION65chain 'L' and (resid 2 through 29 )
66X-RAY DIFFRACTION66chain 'L' and (resid 30 through 78 )
67X-RAY DIFFRACTION67chain 'L' and (resid 79 through 109 )
68X-RAY DIFFRACTION68chain 'L' and (resid 110 through 166 )
69X-RAY DIFFRACTION69chain 'L' and (resid 167 through 241 )
70X-RAY DIFFRACTION70chain 'M' and (resid 19 through 51 )
71X-RAY DIFFRACTION71chain 'M' and (resid 52 through 175 )
72X-RAY DIFFRACTION72chain 'M' and (resid 176 through 240 )
73X-RAY DIFFRACTION73chain 'M' and (resid 241 through 264 )
74X-RAY DIFFRACTION74chain 'M' and (resid 272 through 335 )
75X-RAY DIFFRACTION75chain 'M' and (resid 336 through 370 )
76X-RAY DIFFRACTION76chain 'M' and (resid 371 through 393 )
77X-RAY DIFFRACTION77chain 'N' and (resid 2 through 31 )
78X-RAY DIFFRACTION78chain 'N' and (resid 32 through 45 )
79X-RAY DIFFRACTION79chain 'N' and (resid 46 through 85 )
80X-RAY DIFFRACTION80chain 'N' and (resid 86 through 105 )
81X-RAY DIFFRACTION81chain 'N' and (resid 106 through 139 )
82X-RAY DIFFRACTION82chain 'N' and (resid 140 through 150 )
83X-RAY DIFFRACTION83chain 'N' and (resid 151 through 223 )
84X-RAY DIFFRACTION84chain 'O' and (resid 0 through 15 )
85X-RAY DIFFRACTION85chain 'O' and (resid 16 through 82 )
86X-RAY DIFFRACTION86chain 'O' and (resid 83 through 102 )
87X-RAY DIFFRACTION87chain 'O' and (resid 103 through 119 )
88X-RAY DIFFRACTION88chain 'O' and (resid 120 through 199 )
89X-RAY DIFFRACTION89chain 'O' and (resid 200 through 265 )
90X-RAY DIFFRACTION90chain 'P' and (resid 5 through 44 )
91X-RAY DIFFRACTION91chain 'P' and (resid 45 through 247 )
92X-RAY DIFFRACTION92chain 'Q' and (resid 2 through 24 )
93X-RAY DIFFRACTION93chain 'Q' and (resid 25 through 79 )
94X-RAY DIFFRACTION94chain 'Q' and (resid 80 through 125 )
95X-RAY DIFFRACTION95chain 'Q' and (resid 126 through 140 )
96X-RAY DIFFRACTION96chain 'Q' and (resid 141 through 168 )
97X-RAY DIFFRACTION97chain 'Q' and (resid 169 through 200 )
98X-RAY DIFFRACTION98chain 'Q' and (resid 201 through 235 )
99X-RAY DIFFRACTION99chain 'R' and (resid 50 through 99 )
100X-RAY DIFFRACTION100chain 'R' and (resid 100 through 127 )
101X-RAY DIFFRACTION101chain 'R' and (resid 128 through 158 )
102X-RAY DIFFRACTION102chain 'R' and (resid 159 through 355 )
103X-RAY DIFFRACTION103chain 'S' and (resid 1 through 111 )
104X-RAY DIFFRACTION104chain 'S' and (resid 112 through 291 )
105X-RAY DIFFRACTION105chain 'T' and (resid 109 through 115 )
106X-RAY DIFFRACTION106chain 'U' and (resid 3 through 161 )
107X-RAY DIFFRACTION107chain 'U' and (resid 162 through 201 )
108X-RAY DIFFRACTION108chain 'U' and (resid 202 through 224 )
109X-RAY DIFFRACTION109chain 'U' and (resid 225 through 297 )
110X-RAY DIFFRACTION110chain 'V' and (resid 3 through 90 )
111X-RAY DIFFRACTION111chain 'V' and (resid 91 through 109 )
112X-RAY DIFFRACTION112chain 'V' and (resid 110 through 166 )
113X-RAY DIFFRACTION113chain 'V' and (resid 167 through 243 )
114X-RAY DIFFRACTION114chain 'W' and (resid 15 through 240 )
115X-RAY DIFFRACTION115chain 'W' and (resid 241 through 301 )
116X-RAY DIFFRACTION116chain 'W' and (resid 302 through 394 )
117X-RAY DIFFRACTION117chain 'X' and (resid 1 through 14 )
118X-RAY DIFFRACTION118chain 'X' and (resid 15 through 31 )
119X-RAY DIFFRACTION119chain 'X' and (resid 32 through 45 )
120X-RAY DIFFRACTION120chain 'X' and (resid 46 through 96 )
121X-RAY DIFFRACTION121chain 'X' and (resid 97 through 139 )
122X-RAY DIFFRACTION122chain 'X' and (resid 140 through 150 )
123X-RAY DIFFRACTION123chain 'X' and (resid 151 through 167 )
124X-RAY DIFFRACTION124chain 'X' and (resid 168 through 223 )
125X-RAY DIFFRACTION125chain 'Y' and (resid 1 through 38 )
126X-RAY DIFFRACTION126chain 'Y' and (resid 39 through 82 )
127X-RAY DIFFRACTION127chain 'Y' and (resid 83 through 103 )
128X-RAY DIFFRACTION128chain 'Y' and (resid 104 through 132 )
129X-RAY DIFFRACTION129chain 'Y' and (resid 133 through 185 )
130X-RAY DIFFRACTION130chain 'Y' and (resid 186 through 265 )
131X-RAY DIFFRACTION131chain 'Z' and (resid 5 through 44 )
132X-RAY DIFFRACTION132chain 'Z' and (resid 45 through 247 )
133X-RAY DIFFRACTION133chain 'a' and (resid 1 through 18 )
134X-RAY DIFFRACTION134chain 'a' and (resid 19 through 33 )
135X-RAY DIFFRACTION135chain 'a' and (resid 34 through 94 )
136X-RAY DIFFRACTION136chain 'a' and (resid 95 through 125 )
137X-RAY DIFFRACTION137chain 'a' and (resid 126 through 140 )
138X-RAY DIFFRACTION138chain 'a' and (resid 141 through 153 )
139X-RAY DIFFRACTION139chain 'a' and (resid 154 through 168 )
140X-RAY DIFFRACTION140chain 'a' and (resid 169 through 188 )
141X-RAY DIFFRACTION141chain 'a' and (resid 189 through 200 )
142X-RAY DIFFRACTION142chain 'a' and (resid 201 through 235 )
143X-RAY DIFFRACTION143chain 'b' and (resid 51 through 140 )
144X-RAY DIFFRACTION144chain 'b' and (resid 141 through 355 )
145X-RAY DIFFRACTION145chain 'c' and (resid 1 through 40 )
146X-RAY DIFFRACTION146chain 'c' and (resid 41 through 111 )
147X-RAY DIFFRACTION147chain 'c' and (resid 112 through 137 )
148X-RAY DIFFRACTION148chain 'c' and (resid 138 through 190 )
149X-RAY DIFFRACTION149chain 'c' and (resid 191 through 201 )
150X-RAY DIFFRACTION150chain 'c' and (resid 202 through 276 )
151X-RAY DIFFRACTION151chain 'c' and (resid 277 through 291 )
152X-RAY DIFFRACTION152chain 'd' and (resid 109 through 115 )
153X-RAY DIFFRACTION153chain 'e' and (resid 3 through 161 )
154X-RAY DIFFRACTION154chain 'e' and (resid 162 through 240 )
155X-RAY DIFFRACTION155chain 'e' and (resid 241 through 297 )
156X-RAY DIFFRACTION156chain 'f' and (resid 3 through 78 )
157X-RAY DIFFRACTION157chain 'f' and (resid 79 through 109 )
158X-RAY DIFFRACTION158chain 'f' and (resid 110 through 166 )
159X-RAY DIFFRACTION159chain 'f' and (resid 167 through 244 )
160X-RAY DIFFRACTION160chain 'g' and (resid 14 through 226 )
161X-RAY DIFFRACTION161chain 'g' and (resid 227 through 291 )
162X-RAY DIFFRACTION162chain 'g' and (resid 292 through 393 )
163X-RAY DIFFRACTION163chain 'h' and (resid 1 through 31 )
164X-RAY DIFFRACTION164chain 'h' and (resid 32 through 46 )
165X-RAY DIFFRACTION165chain 'h' and (resid 47 through 96 )
166X-RAY DIFFRACTION166chain 'h' and (resid 97 through 139 )
167X-RAY DIFFRACTION167chain 'h' and (resid 140 through 167 )
168X-RAY DIFFRACTION168chain 'h' and (resid 168 through 223 )
169X-RAY DIFFRACTION169chain 'i' and (resid 1 through 103 )
170X-RAY DIFFRACTION170chain 'i' and (resid 104 through 132 )
171X-RAY DIFFRACTION171chain 'i' and (resid 133 through 265 )
172X-RAY DIFFRACTION172chain 'j' and (resid 5 through 44 )
173X-RAY DIFFRACTION173chain 'j' and (resid 45 through 247 )
174X-RAY DIFFRACTION174chain 'k' and (resid 2 through 33 )
175X-RAY DIFFRACTION175chain 'k' and (resid 34 through 94 )
176X-RAY DIFFRACTION176chain 'k' and (resid 95 through 135 )
177X-RAY DIFFRACTION177chain 'k' and (resid 136 through 235 )
178X-RAY DIFFRACTION178chain 'l' and (resid 52 through 140 )
179X-RAY DIFFRACTION179chain 'l' and (resid 141 through 196 )
180X-RAY DIFFRACTION180chain 'l' and (resid 197 through 355 )
181X-RAY DIFFRACTION181chain 'n' and (resid 108 through 117 )

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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