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- PDB-8asc: Ku70/80 binds to the Ku-binding motif of PAXX -

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基本情報

登録情報
データベース: PDB / ID: 8asc
タイトルKu70/80 binds to the Ku-binding motif of PAXX
要素
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
  • DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
  • Protein PAXX
キーワードDNA BINDING PROTEIN / NHEJ / DNA repair
機能・相同性
機能・相同性情報


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / cellular hyperosmotic salinity response / 2-LTR circle formation / hematopoietic stem cell proliferation / telomeric DNA binding / positive regulation of protein kinase activity / 付加脱離酵素（リアーゼ）; 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / DNA polymerase binding / neurogenesis / activation of innate immune response / DNA helicase activity / telomere maintenance / cyclin binding / cellular response to leukemia inhibitory factor / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / double-strand break repair via nonhomologous end joining / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / double-strand break repair / site of double-strand break / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / molecular adaptor activity / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor, type A domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / Protein PAXX
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
DNA molecule (その他)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.95 Å
データ登録者Seif El Dahan, M. / Ropars, V. / Charbonnier, J.B.
資金援助 フランス, 1件
組織認可番号国
French Alternative Energies and Atomic Energy Commission (CEA)ANR Break Dance フランス
引用ジャーナル: Sci Adv / 年: 2023
タイトル: PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
著者: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / ...著者: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / Madeleine Bossaert / Arun Prasad Pandurangan / Katheryn Meek / Tom L Blundell / Virginie Ropars / Patrick Calsou / Jean-Baptiste Charbonnier / Amanda K Chaplin /
要旨: Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX ...Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryo-electron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells.
履歴
登録2022年8月19日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年6月21日Provider: repository / タイプ: Initial release
改定 1.12024年2月7日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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 1.22024年10月16日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
C: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
D: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
E: X-ray repair cross-complementing protein 6
F: X-ray repair cross-complementing protein 5
G: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
H: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
J: Protein PAXX
K: X-ray repair cross-complementing protein 6
L: X-ray repair cross-complementing protein 5
M: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
N: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
O: X-ray repair cross-complementing protein 6
P: X-ray repair cross-complementing protein 5
Q: DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')
R: DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')
T: Protein PAXX
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)573,91122
ポリマ－573,52618
非ポリマー3844
水36020
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, isothermal titration calorimetry
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)85.024, 428.570, 96.065
Angle α, β, γ (deg.)90.000, 90.010, 90.000
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詳細
11(chain A and (resid 33 through 223 or resid 233 through 534))
21(chain E and (resid 33 through 223 or resid 233 through 534))
31(chain K and (resid 33 through 223 or resid 233 through 534))
41(chain O and (resid 33 through 223 or resid 233 through 534))
12(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))
22(chain F and (resid 6 through 169 or resid 173...
32(chain L and (resid 6 through 169 or resid 180 through 543))
42(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))
13chain C
23(chain G and resid 0 through 18)
33chain M
43(chain Q and resid 0 through 18)
14chain D
24(chain H and resid 16 through 29)
34chain N
44(chain R and resid 16 through 29)
15chain J
25chain T

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
111SERSERILEILE(chain A and (resid 33 through 223 or resid 233 through 534))AA33 - 22333 - 223
121PHEPHETYRTYR(chain A and (resid 33 through 223 or resid 233 through 534))AA233 - 534233 - 534
211SERSERILEILE(chain E and (resid 33 through 223 or resid 233 through 534))EE33 - 22333 - 223
221PHEPHETYRTYR(chain E and (resid 33 through 223 or resid 233 through 534))EE233 - 534233 - 534
311SERSERILEILE(chain K and (resid 33 through 223 or resid 233 through 534))KJ33 - 22333 - 223
321PHEPHETYRTYR(chain K and (resid 33 through 223 or resid 233 through 534))KJ233 - 534233 - 534
411SERSERILEILE(chain O and (resid 33 through 223 or resid 233 through 534))ON33 - 22333 - 223
421PHEPHETYRTYR(chain O and (resid 33 through 223 or resid 233 through 534))ON233 - 534233 - 534
112ASNASNLEULEU(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB6 - 16923 - 186
122ASPASPGLYGLY(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB173 - 174190 - 191
132PROPROLYSLYS(chain B and (resid 6 through 169 or resid 173 through 174 or resid 182 through 543))BB182 - 543199 - 560
212ASNASNLEULEU(chain F and (resid 6 through 169 or resid 173...FF6 - 16923 - 186
222ASPASPGLYGLY(chain F and (resid 6 through 169 or resid 173...FF173 - 174190 - 191
232PROPROLYSLYS(chain F and (resid 6 through 169 or resid 173...FF182 - 466199 - 483
242LYSLYSLYSLYS(chain F and (resid 6 through 169 or resid 173...FF469 - 543486 - 560
312ASNASNLEULEU(chain L and (resid 6 through 169 or resid 180 through 543))LK6 - 16923 - 186
322ASPASPLYSLYS(chain L and (resid 6 through 169 or resid 180 through 543))LK180 - 543197 - 560
412ASNASNLEULEU(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO6 - 16923 - 186
422ASPASPLYSLYS(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO180 - 466197 - 483
432LYSLYSLYSLYS(chain P and (resid 6 through 169 or resid 180 through 466 or resid 469 through 543))PO469 - 543486 - 560
113DCDCDTDTchain CCC0 - 181 - 19
213DCDCDTDT(chain G and resid 0 through 18)GG0 - 181 - 19
313DCDCDTDTchain MML0 - 181 - 19
413DCDCDTDT(chain Q and resid 0 through 18)QP0 - 181 - 19
114DGDGDGDGchain DDD16 - 292 - 15
214DGDGDGDG(chain H and resid 16 through 29)HH16 - 292 - 15
314DGDGDGDGchain NNM16 - 292 - 15
414DGDGDGDG(chain R and resid 16 through 29)RQ16 - 292 - 15
115ARGARGTHRTHRchain JJI177 - 2041 - 28
215ARGARGTHRTHRchain TTR177 - 2041 - 28

NCSアンサンブル:
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixベクター
1given(0.0288791695735, -0.0068562391336, -0.999559395709), (-0.202863536474, -0.979206645021, 0.000855521395743), (-0.97878106803, 0.202749447182, -0.0296695556666)56.677011888, -107.642787276, 71.06102645
2given(-0.99999750509, -0.00123564310169, 0.00186091375217), (0.00122911159569, -0.99999309544, -0.00350690135369), (0.00186523418184, -0.00350460533362, 0.99999211929)42.3572816682, -216.110114103, 47.6357517707
3given(-0.0270274566348, 0.00673742444461, 0.999611986573), (0.200830965542, 0.979625208005, -0.001172655617), (-0.979253000949, 0.200721346532, -0.0278298612841)-14.1771317148, -108.44650006, 118.83945631
4given(0.0916578636257, -0.119131041712, -0.988638776771), (-0.163140331448, -0.981200087795, 0.103109747191), (-0.982336026159, 0.151836038579, -0.109369781467)47.3389229362, -111.632204397, 69.4031911546
5given(-0.999999571199, -0.000914838684214, -0.000143776824327), (0.000914898373918, -0.999999495102, -0.00041563926798), (-0.000143396508853, -0.000415770630936, 0.999999903286)42.5908198637, -216.154028163, 48.0922187027
6given(-0.093173558402, 0.113060096009, 0.98920983755), (0.16201038144, 0.982012199051, -0.0969777150696), (-0.982380437672, 0.151226504306, -0.10981448026)-5.24162956212, -104.531238547, 117.404405388
7given(-0.79789895127, 0.27435536446, -0.536736804732), (-0.00199986119563, -0.891619005366, -0.452782011376), (-0.602787909731, -0.360200892923, 0.711970541961)67.9922474948, -80.7889703579, 3.89831162687
8given(-0.998154011977, 0.00758007702557, -0.0602586990137), (-0.00899575302725, -0.999689049544, 0.0232568409321), (-0.0600636728981, 0.0237559814563, 0.997911824032)44.7584422336, -216.830787339, 50.2084088981
9given(0.788370929199, -0.279354601665, 0.548117035425), (0.00784473820566, 0.895449658602, 0.445093663167), (-0.615150175223, -0.346599070162, 0.70813794312)-26.2977935628, -134.825291793, 53.0388206897
10given(-0.400520005668, 0.155761543492, -0.902951862852), (-0.0635807334128, -0.987794579537, -0.142194792366), (-0.914079436044, 0.000458482632003, 0.405534923768)68.7640660142, -100.854646525, 42.4720578107
11given(-0.999535758611, -0.0289124488095, -0.00960924351004), (0.0290640562536, -0.999448992184, -0.0160309905146), (-0.00914045354914, -0.0163028318593, 0.999825319635)40.2942543608, -215.676724326, 46.8182204795
12given(0.366994924216, -0.134579877077, 0.920436299961), (0.0747451056707, 0.990546107138, 0.115028599971), (-0.927215128639, 0.0265831961748, 0.373584580655)-25.0443842097, -114.218078386, 93.5620415636
13given(-0.998261435298, -0.0397030283321, 0.0435634748066), (0.0412858376978, -0.998496595148, 0.0360559160632), (0.0420664522102, 0.0377917850706, 0.998399816997)40.7715854003, -219.086135572, 46.9252300838

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要素

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X-ray repair cross-complementing protein ... , 2種, 8分子 AEKOBFLP

#1: タンパク質
X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


分子量: 62629.629 Da / 分子数: 4 / 由来タイプ: 組換発現 / 詳細: A C-terminal truncated version of Ku70 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: XRCC6, G22P1 / プラスミド: pFL / Cell (発現宿主): Sf21
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P12956, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与, 付加脱離酵素（リアーゼ）; 炭素- ...参照: UniProt: P12956, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与, 付加脱離酵素（リアーゼ）; 炭素-酸素リアーゼ類; その他の炭素-酸素リアーゼ
#2: タンパク質
X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


分子量: 65356.836 Da / 分子数: 4 / 由来タイプ: 組換発現
詳細: A C-terminal truncated version of Ku80 with a 10 histidines tag in N-terminal and a TEV-cleavage site
由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: XRCC5, G22P2 / プラスミド: pFL / Cell (発現宿主): Sf21
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P13010, 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与

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DNA鎖 , 2種, 8分子 CGMQDHNR

#3: DNA鎖
DNA (5'-D(P*CP*GP*GP*AP*TP*CP*GP*AP*GP*GP*GP*CP*CP*CP*GP*AP*TP*AP*T)-3')


分子量: 9313.990 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) DNA molecule (その他)
#4: DNA鎖
DNA (5'-D(P*GP*GP*GP*CP*CP*CP*TP*CP*GP*AP*TP*CP*CP*G)-3')


分子量: 4546.936 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) DNA molecule (その他)

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タンパク質・ペプチド , 1種, 2分子 JT

#5: タンパク質・ペプチド Protein PAXX / Paralog of XRCC4 and XLF / XRCC4-like small protein


分子量: 3068.467 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: synthesized peptide / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: Q9BUH6

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非ポリマー , 2種, 24分子

#6: 化合物
ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 4 / 由来タイプ: 合成 / 式: SO4
#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 20 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
Has protein modificationY

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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: 3.3 Å3/Da / 溶媒含有率: 62.78 %
結晶化温度: 290 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 12% PEG- 3350; 0.1 M Bis-Tris Propane pH 8.5; 0.3 M Ammonium Sulfate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.978565 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2022年1月29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: 0.978565 Å / 相対比: 1
反射解像度: 2.95→47.734 Å / Num. obs: 34200 / % possible obs: 86.7 % / 冗長度: 7.8 % / Biso Wilson estimate: 67.64 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.098 / Rrim(I) all: 0.273 / Net I/σ(I): 6
反射 シェル解像度: 2.973→3.588 Å / 冗長度: 6.6 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1710 / CC1/2: 0.402 / Rpim(I) all: 0.695 / Rrim(I) all: 1.806 / % possible all: 53.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
XDSデータ削減
STARANISO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: 1JEY

1jey


解像度: 2.95→45.32 Å / SU ML: 0.6 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 38.74 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2981 1995 5.84 %
Rwork0.252 32169 -
obs0.2547 34164 23.91 %
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: 287.95 Å2 / Biso mean: 101.0598 Å2 / Biso min: 0.04 Å2
精密化ステップサイクル: final / 解像度: 2.95→45.32 Å
タンパク質核酸リガンド溶媒全体
原子数33555 2788 20 20 36383
Biso mean--87.76 35.52 -
残基数----4317
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A10120X-RAY DIFFRACTION10.711TORSIONAL
12E10120X-RAY DIFFRACTION10.711TORSIONAL
13K10120X-RAY DIFFRACTION10.711TORSIONAL
14O10120X-RAY DIFFRACTION10.711TORSIONAL
21B10583X-RAY DIFFRACTION10.711TORSIONAL
22F10583X-RAY DIFFRACTION10.711TORSIONAL
23L10583X-RAY DIFFRACTION10.711TORSIONAL
24P10583X-RAY DIFFRACTION10.711TORSIONAL
31C748X-RAY DIFFRACTION10.711TORSIONAL
32G748X-RAY DIFFRACTION10.711TORSIONAL
33M748X-RAY DIFFRACTION10.711TORSIONAL
34Q748X-RAY DIFFRACTION10.711TORSIONAL
41D548X-RAY DIFFRACTION10.711TORSIONAL
42H548X-RAY DIFFRACTION10.711TORSIONAL
43N548X-RAY DIFFRACTION10.711TORSIONAL
44R548X-RAY DIFFRACTION10.711TORSIONAL
51J272X-RAY DIFFRACTION10.711TORSIONAL
52T272X-RAY DIFFRACTION10.711TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.95-3.030.848310.34641920
3.03-3.110.498650.405762671
3.11-3.20.454570.37661391461
3.2-3.30.373170.3582362533
3.31-3.420.3379210.36993463674
3.42-3.560.4087440.35056416857
3.56-3.720.3718510.31338999509
3.72-3.920.304760.30431231130713
3.92-4.160.33751010.27711685178617
4.16-4.480.30861490.25942302245124
4.48-4.940.30061910.24223100329132
4.94-5.650.31552680.25834289455745
5.65-7.110.3574760.28567628810479
7.11-45.320.25155880.223495921018099
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)
10.1410.0999-0.04050.2632-0.15830.1289-0.0101-0.07-0.27270.2809-0.0433-0.40690.0952-0.0181-0.11450.2203-0.0942-0.08940.09020.29080.23468.6729-103.344319.9075
20.07050.0030.06940.13410.06780.2878-0.03040.1054-0.23330.1229-0.0643-0.19670.3101-0.30190.060.1282-0.0923-0.69980.10520.060.2156-0.37-70.36259.5571
3-0.00940.01030.0041-0.00030.0046-0.00640.0250.05030.10560.0240.0123-0.0575-0.01230.024400.8691-0.2712-0.17840.8789-0.1750.91365.8956-72.217333.6837
40.0011-0.00190.00660.0022-0.00450.00090.00290.02230.02060.04590.0477-0.0177-0.0328-0.085201.5278-0.0103-0.19861.3772-0.01131.46860.066-81.510229.7696
50.0986-0.1808-0.0230.0969-0.01290.24180.3728-0.1371-0.17680.0648-0.02730.1762-0.2912-0.28920.34450.15230.0838-0.57690.1950.1481-0.136437.6679-8.013840.7439
60.14760.02550.12630.0476-0.07840.1086-0.1458-0.22430.12870.37160.1898-0.1966-0.02310.14090.01910.0522-0.2108-0.61970.13520.01340.170946.454-41.364457.9906
70.00350.01040.0115-0.0005-0.00180.001-0.09330.04340.00590.08410.03390.02-0.0579-0.0219-00.9882-0.1711-0.15930.787-0.15830.943324.701-32.79749.9443
80.00290.0028-0.00920.00040.00260.00330.097-0.08570.0295-0.04940.10560.02730.0662-0.000101.1606-0.04310.18190.964-0.04911.192828.7513-25.751154.1458
90.0067-0.01050.00210.00360.00020.00110.009-0.07120.02760.01070.02850.01440.00620.02100.65780.03390.0450.78720.00510.644546.3439-6.620834.1242
100.1415-0.0053-0.05630.1280.14490.22790.1952-0.09450.28250.2791-0.31530.3835-0.01930.0547-0.09540.4592-0.03460.15030.087-0.15160.566233.7997-112.535467.7947
11-0.02560.0039-0.04970.1086-0.05290.14740.08950.09050.01410.3301-0.00550.3798-0.33710.16510.08170.12560.01390.69140.215-0.11740.052943.019-145.547257.6839
12-0.00530.0087-0.0015-0.0001-0.0034-0.00780.0339-0.0198-0.0478-0.00350.01830.0221-0.0732-0.0736-00.9668-0.15470.12810.92580.13981.119336.3813-143.647781.7583
13-0.00090.0030.0015-0.00270.001-0.0001-0.00360.0273-0.05260.03380.0610.02490.01250.065801.3624-0.13210.09751.21710.18111.232942.2827-134.383677.9155
140.0532-0.1460.13650.1158-0.04010.27120.3087-0.09880.05570.0801-0.02170.06530.31580.34440.21070.279-0.12330.23620.27680.00780.00014.8045-207.899288.7295
150.10660.0096-0.04130.03470.06460.17840.00080.0876-0.13170.29460.130.09850.1505-0.0412-0.01860.1504-0.05830.66860.277-0.11180.0534-3.6986-174.5643105.9453
160.00310.0037-0.02-0.0026-0.0015-0.001-0.0570.0912-0.00970.06890.0669-0.03680.03910.0798-01.041-0.27030.04460.68510.23661.011317.709-183.036697.8577
170.0046-0.00460.00580.0038-0.00170.00450.0325-0.0385-0.0436-0.01080.042-0.0117-0.0044-0.02501.254-0.0687-0.02951.0502-0.0441.306313.7949-190.081102.0324
18-0.0045-0.00060.0009-0.0001-0.0009-0-0.0206-0.0769-0.02390.007-0.00110.01010.0064-0.0073-00.82690.014-0.14330.9209-0.07310.7357-3.7667-208.899982.5596
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 33 through 534)A33 - 534
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 544)B6 - 544
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 18)C0 - 18
4X-RAY DIFFRACTION4(chain 'D' and resid 16 through 29)D16 - 29
5X-RAY DIFFRACTION5(chain 'E' and resid 33 through 535)E33 - 535
6X-RAY DIFFRACTION6(chain 'F' and resid 4 through 543)F4 - 543
7X-RAY DIFFRACTION7(chain 'G' and resid 0 through 19)G0 - 19
8X-RAY DIFFRACTION8(chain 'H' and resid 15 through 29)H15 - 29
9X-RAY DIFFRACTION9(chain 'J' and resid 177 through 204)J177 - 204
10X-RAY DIFFRACTION10(chain 'K' and resid 33 through 535)K33 - 535
11X-RAY DIFFRACTION11(chain 'L' and resid 5 through 543)L5 - 543
12X-RAY DIFFRACTION12(chain 'M' and resid 0 through 18)M0 - 18
13X-RAY DIFFRACTION13(chain 'N' and resid 16 through 29)N16 - 29
14X-RAY DIFFRACTION14(chain 'O' and resid 33 through 535)O33 - 535
15X-RAY DIFFRACTION15(chain 'P' and resid 4 through 543)P4 - 543
16X-RAY DIFFRACTION16(chain 'Q' and resid 0 through 19)Q0 - 19
17X-RAY DIFFRACTION17(chain 'R' and resid 15 through 29)R15 - 29
18X-RAY DIFFRACTION18(chain 'T' and resid 177 through 204)T177 - 204

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万見について

-
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