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- PDB-5els: Structure of the KH domain of T-STAR in complex with AAAUAA RNA -

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基本情報

登録情報
データベース: PDB / ID: 5els
タイトルStructure of the KH domain of T-STAR in complex with AAAUAA RNA
要素
  • KH domain-containing, RNA-binding, signal transduction-associated protein 3
  • RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
キーワードRNA BINDING PROTEIN / Protein - RNA complexes STAR protein Alternative splicing KH domain
機能・相同性
機能・相同性情報


PTK6 Regulates Proteins Involved in RNA Processing / regulation of alternative mRNA splicing, via spliceosome / mRNA processing / SH3 domain binding / protein domain specific binding / mRNA binding / protein-containing complex / RNA binding / nucleoplasm / identical protein binding / nucleus
類似検索 - 分子機能
Sam68, tyrosine-rich domain / KHDRBS, Qua1 domain / Qua1 domain / Tyrosine-rich domain of Sam68 / KH domain-containing BBP-like / KH domain / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
類似検索 - ドメイン・相同性
RNA / KH domain-containing, RNA-binding, signal transduction-associated protein 3
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
synthetic construct (人工物)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.873 Å
データ登録者Dominguez, C. / Feracci, M.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (United Kingdom)G1000526 英国
引用ジャーナル: Nat Commun / 年: 2016
タイトル: Structural basis of RNA recognition and dimerization by the STAR proteins T-STAR and Sam68.
著者: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / ...著者: Feracci, M. / Foot, J.N. / Grellscheid, S.N. / Danilenko, M. / Stehle, R. / Gonchar, O. / Kang, H.S. / Dalgliesh, C. / Meyer, N.H. / Liu, Y. / Lahat, A. / Sattler, M. / Eperon, I.C. / Elliott, D.J. / Dominguez, C.
履歴
登録2015年11月5日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年1月13日Provider: repository / タイプ: Initial release
改定 1.12016年1月27日Group: Database references
改定 1.22017年9月13日Group: Author supporting evidence / Data collection
カテゴリ: diffrn_radiation_wavelength / pdbx_audit_support
Item: _pdbx_audit_support.funding_organization
改定 1.32024年5月8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 / 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

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: KH domain-containing, RNA-binding, signal transduction-associated protein 3
B: KH domain-containing, RNA-binding, signal transduction-associated protein 3
C: KH domain-containing, RNA-binding, signal transduction-associated protein 3
D: KH domain-containing, RNA-binding, signal transduction-associated protein 3
E: KH domain-containing, RNA-binding, signal transduction-associated protein 3
F: KH domain-containing, RNA-binding, signal transduction-associated protein 3
H: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)81,19111
ポリマ－80,9038
非ポリマー2883
水00
1
A: KH domain-containing, RNA-binding, signal transduction-associated protein 3
C: KH domain-containing, RNA-binding, signal transduction-associated protein 3
H: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
I: RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)29,6075
ポリマ－29,5114
非ポリマー961
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: KH domain-containing, RNA-binding, signal transduction-associated protein 3
F: KH domain-containing, RNA-binding, signal transduction-associated protein 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)25,8884
ポリマ－25,6962
非ポリマー1922
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
D: KH domain-containing, RNA-binding, signal transduction-associated protein 3
E: KH domain-containing, RNA-binding, signal transduction-associated protein 3


分子量 (理論値)分子数
合計 (水以外)25,6962
ポリマ－25,6962
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)93.730, 162.220, 113.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 48:51 or resseq 53:58 or resseq...
21(chain B and (resseq 48:51 or resseq 53:58 or resseq...
31(chain C and (resseq 48:51 or resseq 53:58 or resseq...
41(chain D and (resseq 48:51 or resseq 53:58 or resseq...
51(chain E and (resseq 48:51 or resseq 53:58 or resseq...
61(chain F and (resseq 48:51 or resseq 53:58 or resseq...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASNASN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA48 - 511 - 4
12ASNASNGLNGLN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA53 - 586 - 11
13VALVALVALVAL(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA60 - 6413 - 17
14PHEPHEPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA67 - 6820 - 21
15PHEPHEGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA70 - 7423 - 27
16LEULEUPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA76 - 7929 - 32
17GLYGLYLEULEU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA81 - 8434 - 37
18LEULEUGLNGLN(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA87 - 8840 - 41
19THRTHRLYSLYS(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA91 - 9444 - 47
110SERSERGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA96 - 9949 - 52
111GLYGLYMETMET(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA101 - 10354 - 56
112ASPASPASPASP(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA10558
113ALAALAALAALA(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA10760
114GLUGLUGLUGLU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA109 - 11062 - 63
115LEULEUARGARG(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA112 - 11365 - 66
116SERSERGLYGLY(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA115 - 11668 - 69
117ALAALAALAALA(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA118 - 14271 - 95
118METMETLEULEU(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA144 - 14897 - 101
119GLUGLULYSLYS(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA150 - 152103 - 105
120PHEPHEPROPRO(chain A and (resseq 48:51 or resseq 53:58 or resseq...AA154 - 157107 - 110
21GLYGLYASNASN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB48 - 511 - 4
22ASNASNGLNGLN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB53 - 586 - 11
23VALVALVALVAL(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB60 - 6413 - 17
24PHEPHEPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB67 - 6820 - 21
25PHEPHEGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB70 - 7423 - 27
26LEULEUPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB76 - 7929 - 32
27GLYGLYLEULEU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB81 - 8434 - 37
28LEULEUGLNGLN(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB87 - 8840 - 41
29THRTHRLYSLYS(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB91 - 9444 - 47
210SERSERGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB96 - 9949 - 52
211GLYGLYMETMET(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB101 - 10354 - 56
212ASPASPASPASP(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB10558
213ALAALAALAALA(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB10760
214GLUGLUGLUGLU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB109 - 11062 - 63
215LEULEUARGARG(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB112 - 11365 - 66
216SERSERGLYGLY(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB115 - 11668 - 69
217ALAALAALAALA(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB118 - 14271 - 95
218METMETLEULEU(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB144 - 14897 - 101
219GLUGLULYSLYS(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB150 - 152103 - 105
220PHEPHEPROPRO(chain B and (resseq 48:51 or resseq 53:58 or resseq...BB154 - 157107 - 110
31GLYGLYASNASN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC48 - 511 - 4
32ASNASNGLNGLN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC53 - 586 - 11
33VALVALVALVAL(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC60 - 6413 - 17
34PHEPHEPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC67 - 6820 - 21
35PHEPHEGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC70 - 7423 - 27
36LEULEUPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC76 - 7929 - 32
37GLYGLYLEULEU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC81 - 8434 - 37
38LEULEUGLNGLN(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC87 - 8840 - 41
39THRTHRLYSLYS(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC91 - 9444 - 47
310SERSERGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC96 - 9949 - 52
311GLYGLYMETMET(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC101 - 10354 - 56
312ASPASPASPASP(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC10558
313ALAALAALAALA(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC10760
314GLUGLUGLUGLU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC109 - 11062 - 63
315LEULEUARGARG(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC112 - 11365 - 66
316SERSERGLYGLY(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC115 - 11668 - 69
317ALAALAALAALA(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC118 - 14271 - 95
318METMETLEULEU(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC144 - 14897 - 101
319GLUGLULYSLYS(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC150 - 152103 - 105
320PHEPHEPROPRO(chain C and (resseq 48:51 or resseq 53:58 or resseq...CC154 - 157107 - 110
41GLYGLYASNASN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD48 - 511 - 4
42ASNASNGLNGLN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD53 - 586 - 11
43VALVALVALVAL(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD60 - 6413 - 17
44PHEPHEPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD67 - 6820 - 21
45PHEPHEGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD70 - 7423 - 27
46LEULEUPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD76 - 7929 - 32
47GLYGLYLEULEU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD81 - 8434 - 37
48LEULEUGLNGLN(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD87 - 8840 - 41
49THRTHRLYSLYS(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD91 - 9444 - 47
410SERSERGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD96 - 9949 - 52
411GLYGLYMETMET(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD101 - 10354 - 56
412ASPASPASPASP(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD10558
413ALAALAALAALA(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD10760
414GLUGLUGLUGLU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD109 - 11062 - 63
415LEULEUARGARG(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD112 - 11365 - 66
416SERSERGLYGLY(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD115 - 11668 - 69
417ALAALAALAALA(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD118 - 14271 - 95
418METMETLEULEU(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD144 - 14897 - 101
419GLUGLULYSLYS(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD150 - 152103 - 105
420PHEPHEPROPRO(chain D and (resseq 48:51 or resseq 53:58 or resseq...DD154 - 157107 - 110
51GLYGLYASNASN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE48 - 511 - 4
52ASNASNGLNGLN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE53 - 586 - 11
53VALVALVALVAL(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE60 - 6413 - 17
54PHEPHEPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE67 - 6820 - 21
55PHEPHEGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE70 - 7423 - 27
56LEULEUPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE76 - 7929 - 32
57GLYGLYLEULEU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE81 - 8434 - 37
58LEULEUGLNGLN(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE87 - 8840 - 41
59THRTHRLYSLYS(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE91 - 9444 - 47
510SERSERGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE96 - 9949 - 52
511GLYGLYMETMET(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE101 - 10354 - 56
512ASPASPASPASP(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE10558
513ALAALAALAALA(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE10760
514GLUGLUGLUGLU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE109 - 11062 - 63
515LEULEUARGARG(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE112 - 11365 - 66
516SERSERGLYGLY(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE115 - 11668 - 69
517ALAALAALAALA(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE118 - 14271 - 95
518METMETLEULEU(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE144 - 14897 - 101
519GLUGLULYSLYS(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE150 - 152103 - 105
520PHEPHEPROPRO(chain E and (resseq 48:51 or resseq 53:58 or resseq...EE154 - 157107 - 110
61GLYGLYASNASN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF48 - 511 - 4
62ASNASNGLNGLN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF53 - 586 - 11
63VALVALVALVAL(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF60 - 6413 - 17
64PHEPHEPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF67 - 6820 - 21
65PHEPHEGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF70 - 7423 - 27
66LEULEUPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF76 - 7929 - 32
67GLYGLYLEULEU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF81 - 8434 - 37
68LEULEUGLNGLN(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF87 - 8840 - 41
69THRTHRLYSLYS(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF91 - 9444 - 47
610SERSERGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF96 - 9949 - 52
611GLYGLYMETMET(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF101 - 10354 - 56
612ASPASPASPASP(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF10558
613ALAALAALAALA(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF10760
614GLUGLUGLUGLU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF109 - 11062 - 63
615LEULEUARGARG(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF112 - 11365 - 66
616SERSERGLYGLY(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF115 - 11668 - 69
617ALAALAALAALA(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF118 - 14271 - 95
618METMETLEULEU(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF144 - 14897 - 101
619GLUGLULYSLYS(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF150 - 152103 - 105
620PHEPHEPROPRO(chain F and (resseq 48:51 or resseq 53:58 or resseq...FF154 - 157107 - 110

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要素

#1: タンパク質
KH domain-containing, RNA-binding, signal transduction-associated protein 3 / RNA-binding protein T-Star / Sam68-like mammalian protein 2 / SLM-2 / Sam68-like phosphotyrosine protein


分子量: 12848.066 Da / 分子数: 6 / 断片: RNA binding protein, UNP residues 50-160 / 由来タイプ: 組換発現 / 詳細: N-terminus GA residues from tag. / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KHDRBS3, SALP, SLM2 / プラスミド: pLEICS 03 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O75525
#2: RNA鎖 RNA (5'-R(P*AP*AP*AP*UP*AP*A)-3')


分子量: 1907.237 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#3: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.66 Å3/Da / 溶媒含有率: 53.68 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7 / 詳細: Lithium sulphate, Tris

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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: Diamond / ビームライン: I04-1 / 波長: 0.9173 Å
検出器タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2012年2月3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: 0.9173 Å / 相対比: 1
Reflection twinOperator: 1/2*h+1/2*k,3/2*h-1/2*k,-l / Fraction: 0.25
反射解像度: 2.873→46.865 Å / Num. all: 20014 / Num. obs: 20014 / % possible obs: 99.8 % / 冗長度: 6.9 % / Rpim(I) all: 0.078 / Rrim(I) all: 0.206 / Rsym value: 0.174 / Net I/av σ(I): 3.5 / Net I/σ(I): 8.1 / Num. measured all: 137466
反射 シェル

Diffraction-ID: 1 / Rejects: _

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.87-2.957.20.74511069014750.3210.7452.4100
2.95-3.037.20.5991.31030914350.2580.5993.199.8
3.03-3.127.10.511.5976613680.2220.513.699.8
3.12-3.217.20.4261.8965513440.1860.4264.299.9
3.21-3.326.90.3582.1892713000.1590.3584.7100
3.32-3.436.60.2832.7830112510.130.2835.899.6
3.43-3.5660.2333.3738612230.1150.2336.499.6
3.56-3.7160.1864704011740.0930.1867.899.8
3.71-3.877.30.1784.2841111500.0780.1789.5100
3.87-4.067.20.1534.8782110860.0670.15310.899.8
4.06-4.287.20.1394.8737010290.0640.13911.499.9
4.28-4.547.10.1315.567839550.0580.13111.8100
4.54-4.867.10.1235.765859280.0550.12312.399.9
4.86-5.256.90.1345.460878830.060.13411.299.9
5.25-5.756.70.1245.851617730.0580.12411.1100
5.75-6.426.50.1225.647347310.0570.12211.399.6
6.42-7.425.50.1016.535656440.0530.10111.899.5
7.42-9.087.30.0827.740795580.0350.08215.9100
9.08-12.857.10.0689.431154410.0280.06817100
12.85-46.8656.30.0628.316812660.0280.0621798.7

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX精密化
SCALA3.3.20データスケーリング
PHASER位相決定
PDB_EXTRACT3.15データ抽出
xia2データ削減
精密化構造決定の手法: 分子置換 / 解像度: 2.873→46.865 Å / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.47 / 立体化学のターゲット値: TWIN_LSQ_F
Rfactor反射数%反射Selection details
Rfree0.2358 1021 5.11 %RAMDOM
Rwork0.1875 18918 --
obs0.1897 19995 99.76 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 198.12 Å2 / Biso mean: 52.3359 Å2 / Biso min: 11.2 Å2
精密化ステップサイクル: final / 解像度: 2.873→46.865 Å
タンパク質核酸リガンド溶媒全体
原子数5356 260 15 0 5631
Biso mean--58.75 --
残基数----684
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0135760
X-RAY DIFFRACTIONf_angle_d1.4617756
X-RAY DIFFRACTIONf_chiral_restr0.076840
X-RAY DIFFRACTIONf_plane_restr0.012948
X-RAY DIFFRACTIONf_dihedral_angle_d18.2323538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A2116X-RAY DIFFRACTION13.758TORSIONAL
12B2116X-RAY DIFFRACTION13.758TORSIONAL
13C2116X-RAY DIFFRACTION13.758TORSIONAL
14D2116X-RAY DIFFRACTION13.758TORSIONAL
15E2116X-RAY DIFFRACTION13.758TORSIONAL
16F2116X-RAY DIFFRACTION13.758TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8732-3.02440.32361440.25832690283495
3.0244-3.21330.27711440.23842652279695
3.2133-3.46060.2731410.22152666280795
3.4606-3.80740.24841640.18662643280794
3.8074-4.35490.21311440.1652711285595
4.3549-5.47360.21111420.1622729287195
5.4736-22.51260.1911410.16852827296895
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)
11.1565-0.47581.02620.5994-0.5750.83360.0463-0.13220.11230.1784-0.1148-0.11160.1628-0.22090.04840.22630.0023-0.07270.14380.02690.1793129.105934.1578126.0307
22.0880.47270.23181.7488-0.72782.70060.021-0.3979-0.4438-0.2422-0.1687-0.3575-0.28680.1522-0.03010.307-0.08910.00270.19790.0190.09123.866318.5951132.7831
31.3132-0.35140.30580.2572-0.05210.97930.13270.08750.1220.00240.00250.0545-0.19260.25670.08650.21360.02430.03750.14650.03150.1423130.231436.8637121.1921
40.1024-0.0905-0.02730.10520.0410.01590.1578-0.37240.29190.36470.18750.2607-0.0099-0.34410.1040.74890.1260.07530.5230.02780.3935125.4462-14.0435171.8645
51.2905-0.62930.35582.14020.10630.14740.2629-0.3456-0.47010.29710.01790.0420.1206-0.2689-0.08830.3229-0.06090.00120.42450.15380.2466122.46220.2617163.7517
60.2757-0.10190.28710.3914-0.00780.3197-0.0481-0.0646-0.00680.1757-0.21910.0635-0.0022-0.2268-0.3626-0.1314-0.03970.55630.32120.1513-0.0781123.376920.78153.7128
70.94740.27761.4272.47571.07162.32310.22010.17580.0549-0.42510.0344-0.1297-0.13550.56020.28080.3019-0.19690.22610.1960.1482-0.1224128.625712.4385148.988
81.0288-0.039-0.12871.10590.74221.06930.040.016-0.238-0.0463-0.1929-0.03950.42780.0522-0.16490.55520.1520.07510.05950.13870.667133.92292.8888149.4528
92.3303-2.89891.4854.2643-1.05451.9305-0.243-0.1193-0.1046-0.1578-0.28910.08520.0747-0.1467-0.00280.3430.00880.11930.15690.09530.3463125.95881.3131154.8414
101.51710.5097-0.1770.7313-0.24270.894-0.1001-0.1612-0.0263-0.0963-0.07620.11470.0001-0.1301-0.17150.39160.2308-0.40230.65720.01340.671116.645112.1791146.8602
110.66610.32950.62633.33520.39950.9574-0.09640.3362-0.26610.0865-0.17050.43870.2554-0.23010.0110.8647-0.0111-0.22990.6058-0.02370.5051108.037910.2781145.7635
123.67981.3082-0.69461.6893-0.89880.51680.15410.1013-0.3263-0.18390.0820.40650.22210.0171-0.03460.33950.0073-0.07520.44740.20840.4293111.00196.2158153.2143
13-0.0044-0.0088-0.01620.00390.1321.62830.09630.1510.31240.1558-0.25890.03890.4483-0.136-0.04440.17570.0699-0.14390.23530.06060.36128.8457-0.5015163.3881
141.41820.00520.22592.9892-0.76121.3808-0.10670.15270.0656-0.0394-0.1219-0.30030.31650.20390.05040.1901-0.0177-0.06350.20840.06160.2875133.120716.8825154.4439
150.0584-0.04710.01230.05-0.05590.16770.0578-0.13740.03070.1257-0.06830.02870.02090.12-0.03220.6529-0.07320.27590.9616-0.42250.270298.476452.7048170.9656
160.8807-0.8566-0.94231.08220.64410.967-0.04910.1315-0.22040.0478-0.09270.1813-0.1676-0.14210.03870.1536-0.0066-0.01870.2211-0.030.1038117.303639.6959153.139
171.83170.6160.37712.2064-0.20441.605-0.31260.26890.079-0.5301-0.21650.0158-0.42070.1861-0.26750.1303-0.01420.06610.3213-0.08460.1325119.032746.1463149.8898
181.84010.452-0.65750.7081-0.45071.3832-0.04690.08640.1048-0.0190.0564-0.0435-0.01110.1250.03450.7384-0.0560.45010.65740.14570.4276129.448355.4967144.8376
190.7278-0.3548-0.50410.41950.36250.62880.03910.12570.1205-0.0705-0.05260.0867-0.03090.01610.00080.21450.00180.01830.18150.02790.1503116.044843.9336157.4025
200.5818-0.0545-0.85971.88760.8691.5406-0.1621-0.0560.13930.13690.1917-0.24720.3502-0.1633-0.03980.4888-0.04260.18970.3387-0.03420.2443116.043317.0323116.7381
214.1019-1.72870.70822.83790.40380.3580.037-0.2742-0.22960.17370.10270.5099-0.098-0.179-0.07010.5055-0.16390.41440.6343-0.16740.940591.278530.028119.0483
223.56412.2645-1.56762.69390.36022.14750.0861-0.0189-0.32480.4509-0.1094-0.22250.17410.47680.1590.8885-0.25760.36890.5185-0.01710.761494.855620.7063130.8688
230.1510.202-0.12232.3310.0940.2905-0.1088-0.04780.16780.32620.11990.36380.34380.0053-0.0310.5571-0.08290.10260.3884-0.00290.4256103.758415.9742127.0568
243.31090.8002-0.13682.0379-0.38611.8967-0.164-0.2450.11980.0568-0.39280.30440.1748-0.65350.13280.34880.13050.01590.5574-0.17730.3555104.742838.4829130.0839
250.38460.05720.14131.38090.46620.85510.1414-0.0558-0.1334-0.0206-0.19310.02550.1521-0.43720.05890.2726-0.11210.03910.2550.00640.308105.932820.8216120.0954
260.06740.39970.05712.42580.82664.4386-0.04240.1417-0.12-0.2869-0.05920.07980.1782-0.26630.18240.62970.07070.04841.0168-0.25470.2806100.500723.4833110.1664
274.7072-0.3196-0.12742.0910.18172.10080.06380.0086-0.07730.0060.1335-0.22610.1623-0.2915-0.02240.6327-0.09070.00710.24670.03250.2646116.099218.0705106.9287
280.6163-0.541-0.16943.00311.81641.1405-0.01710.2707-0.58160.05780.099-0.33020.6250.67540.07271.07680.17530.55570.7207-0.12110.8879134.63244.2589105.6245
292.1271-1.16374.13050.6611-2.21868.0662-0.08190.20030.1912-0.16140.2092-0.0718-0.04460.42790.02841.1594-0.06110.10740.55130.08370.9902127.06643.753597.6563
304.3893-2.1976-2.52732.70961.6671.66330.4390.4412-0.1355-0.6203-0.0086-0.0038-0.0115-0.0293-0.11030.7078-0.0305-0.02930.4625-0.04280.8174116.32464.484394.4902
310.30420.25070.01171.0039-0.13140.93230.01420.32860.014-0.5492-0.0742-0.2796-0.324-0.010.16170.6495-0.21080.24920.3768-0.17920.5728126.413313.693796.8936
320.568-0.0424-0.20330.4792-0.22540.2114-0.04560.06260.11590.0264-0.0776-0.0010.41990.3670.04350.4583-0.1020.1140.5275-0.12740.4532132.89223.414196.8411
331.40310.20980.29161.6452-0.5891.8328-0.01570.0212-0.53280.0301-0.2832-0.1650.12740.05060.09980.5372-0.15510.00840.2874-0.00480.386115.083510.1071106.2823
341.568-0.0315-0.53510.14350.28121.98080.50140.1114-0.10270.00110.34310.2418-0.1241-0.235-0.10260.34510.0893-0.06360.78760.1050.5867106.27863.1137165.345
350.1487-0.19640.79270.2503-1.02684.18620.0017-0.2648-0.20990.2461-0.10150.04770.1487-0.0572-0.07481.1275-0.1210.36420.98490.34960.7821105.5621-25.0522161.4699
362.11730.25710.18641.0892-0.41510.7047-0.06290.005-0.1589-0.1844-0.1029-0.17430.13150.04090.07740.6732-0.38140.39291.2624-0.10280.985899.3711-17.3209150.9423
370.16270.1990.01480.57040.26820.1837-0.0433-0.17220.11980.2127-0.02391.0527-0.2982-0.70240.16920.5489-0.09710.0491.13760.1410.894698.5541-7.1144154.5145
380.0729-0.09430.02190.85880.72960.7634-0.17050.1501-0.283-0.22940.1431-0.15280.6624-0.3140.02870.4742-0.092-0.00750.7376-0.0450.7173118.5502-15.4038153.0707
391.7440.8374-0.29140.7623-0.74641.8529-0.04270.6521-0.0823-0.24170.0236-0.13710.3636-0.75550.03080.1865-0.087-0.00481.06560.1960.605699.3705-7.1833163.0954
401.4479-0.2623-0.79310.6726-0.09080.51330.1198-0.1247-0.03050.5899-0.10310.2367-0.1441-0.191-0.02090.2916-0.0065-0.03360.4848-0.09420.2487125.011536.364140.2651
410.4539-0.0569-0.01551.21310.52080.23040.04180.37070.0594-0.02080.0078-0.10050.11920.0293-0.01410.51520.12130.00910.4020.07460.1645120.423738.8372141.4239
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 98 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 127 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 160 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 48 through 52 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 61 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 62 through 71 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 78 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 91 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 92 through 98 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 99 through 105 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 106 through 115 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 116 through 127 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 128 through 150 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 151 through 160 )B0
15X-RAY DIFFRACTION15chain 'C' and (resid 48 through 52 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 53 through 91 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 92 through 105 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 106 through 114 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 115 through 160 )C0
20X-RAY DIFFRACTION20chain 'D' and (resid 48 through 61 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 62 through 72 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 73 through 82 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 83 through 98 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 99 through 117 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 118 through 158 )D0
26X-RAY DIFFRACTION26chain 'E' and (resid 48 through 52 )E0
27X-RAY DIFFRACTION27chain 'E' and (resid 53 through 61 )E0
28X-RAY DIFFRACTION28chain 'E' and (resid 62 through 71 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 72 through 78 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 79 through 91 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 92 through 106 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 107 through 127 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 128 through 157 )E0
34X-RAY DIFFRACTION34chain 'F' and (resid 48 through 61 )F0
35X-RAY DIFFRACTION35chain 'F' and (resid 62 through 71 )F0
36X-RAY DIFFRACTION36chain 'F' and (resid 72 through 81 )F0
37X-RAY DIFFRACTION37chain 'F' and (resid 82 through 98 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 99 through 127 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 128 through 159 )F0
40X-RAY DIFFRACTION40chain 'H' and (resid -1 through 4 )H0
41X-RAY DIFFRACTION41chain 'I' and (resid 0 through 5 )I0

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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

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