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- PDB-7s81: Structure of human PARP1 domains (Zn1, Zn3, WGR, HD) bound to a D... -

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基本情報

登録情報
データベース: PDB / ID: 7s81
タイトルStructure of human PARP1 domains (Zn1, Zn3, WGR, HD) bound to a DNA double strand break.
要素
  • (Poly [ADP-ribose] polymerase ...) x 3
  • DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
キーワードDNA BINDING PROTEIN / PARP / ADP-ribose transferase / DNA break detection / zinc finger
機能・相同性
機能・相同性情報


NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep ...NAD+-histone H2BS6 serine ADP-ribosyltransferase activity / NAD+-histone H3S10 serine ADP-ribosyltransferase activity / NAD+-histone H2BE35 glutamate ADP-ribosyltransferase activity / positive regulation of myofibroblast differentiation / negative regulation of ATP biosynthetic process / NAD+-protein-tyrosine ADP-ribosyltransferase activity / NAD+-protein-histidine ADP-ribosyltransferase activity / regulation of base-excision repair / positive regulation of single strand break repair / regulation of circadian sleep/wake cycle, non-REM sleep / vRNA Synthesis / carbohydrate biosynthetic process / NAD+-protein-serine ADP-ribosyltransferase activity / negative regulation of adipose tissue development / NAD DNA ADP-ribosyltransferase activity / DNA ADP-ribosylation / mitochondrial DNA metabolic process / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / replication fork reversal / ATP generation from poly-ADP-D-ribose / positive regulation of necroptotic process / transcription regulator activator activity / response to aldosterone / HDR through MMEJ (alt-NHEJ) / positive regulation of DNA-templated transcription, elongation / signal transduction involved in regulation of gene expression / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / mitochondrial DNA repair / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / positive regulation of intracellular estrogen receptor signaling pathway / negative regulation of cGAS/STING signaling pathway / positive regulation of cardiac muscle hypertrophy / NAD+-protein-glutamate ADP-ribosyltransferase activity / positive regulation of mitochondrial depolarization / cellular response to zinc ion / NAD+-protein mono-ADP-ribosyltransferase activity / nuclear replication fork / R-SMAD binding / decidualization / protein autoprocessing / site of DNA damage / NAD+ poly-ADP-ribosyltransferase activity / negative regulation of transcription elongation by RNA polymerase II / macrophage differentiation / 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの / positive regulation of SMAD protein signal transduction / POLB-Dependent Long Patch Base Excision Repair / SUMOylation of DNA damage response and repair proteins / positive regulation of double-strand break repair via homologous recombination / nucleosome binding / protein localization to chromatin / nucleotidyltransferase activity / telomere maintenance / transforming growth factor beta receptor signaling pathway / negative regulation of innate immune response / Downregulation of SMAD2/3:SMAD4 transcriptional activity / nuclear estrogen receptor binding / response to gamma radiation / DNA Damage Recognition in GG-NER / mitochondrion organization / enzyme activator activity / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / protein-DNA complex / cellular response to nerve growth factor stimulus / protein modification process / positive regulation of protein localization to nucleus / histone deacetylase binding / cellular response to insulin stimulus / NAD binding / cellular response to amyloid-beta / cellular response to UV / nuclear envelope / site of double-strand break / double-strand break repair / regulation of protein localization / cellular response to oxidative stress / transcription regulator complex / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / chromosome, telomeric region / positive regulation of canonical NF-kappaB signal transduction / nuclear body / innate immune response / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / apoptotic process / DNA damage response / chromatin binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
類似検索 - 分子機能
Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily ...Poly [ADP-ribose] polymerase / PADR1 domain / PADR1 domain superfamily / : / PADR1 domain, zinc ribbon fold / PADR1, N-terminal helical domain / PADR1 domain profile. / PADR1 / Zinc finger poly(ADP-ribose) polymerase (PARP)-type signature. / Zinc finger, PARP-type superfamily / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger poly(ADP-ribose) polymerase (PARP)-type profile. / Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region / Zinc finger, PARP-type / : / Poly(ADP-ribose) polymerase, regulatory domain / WGR domain / WGR domain superfamily / WGR domain / WGR domain profile. / Proposed nucleic acid binding domain / Poly(ADP-ribose) polymerase, regulatory domain superfamily / Poly(ADP-ribose) polymerase, regulatory domain / PARP alpha-helical domain profile. / BRCA1 C Terminus (BRCT) domain / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily
類似検索 - ドメイン・相同性
DNA / DNA (> 10) / Poly [ADP-ribose] polymerase 1
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: 3.6 Å
データ登録者Rouleau-Turcotte, E. / Pascal, J.M.
資金援助 カナダ, 1件
組織認可番号国
Canadian Institutes of Health Research (CIHR)PJT173370 カナダ
引用ジャーナル: Mol.Cell / 年: 2022
タイトル: Captured snapshots of PARP1 in the active state reveal the mechanics of PARP1 allostery.
著者: Rouleau-Turcotte, E. / Krastev, D.B. / Pettitt, S.J. / Lord, C.J. / Pascal, J.M.
履歴
登録2021年9月17日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年6月29日Provider: repository / タイプ: Initial release
改定 1.12022年7月20日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22022年8月31日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月18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

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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
M: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
C: Poly [ADP-ribose] polymerase 1
K: Poly [ADP-ribose] polymerase 1
E: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
N: Poly [ADP-ribose] polymerase 1
I: Poly [ADP-ribose] polymerase 1
A: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
P: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
O: Poly [ADP-ribose] polymerase 1
J: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)260,41224
ポリマ－259,88916
非ポリマー5238
水1267
1
M: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
L: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
K: Poly [ADP-ribose] polymerase 1
N: Poly [ADP-ribose] polymerase 1
I: Poly [ADP-ribose] polymerase 1
P: Poly [ADP-ribose] polymerase 1
O: Poly [ADP-ribose] polymerase 1
J: Poly [ADP-ribose] polymerase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,20612
ポリマ－129,9448
非ポリマー2624
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Poly [ADP-ribose] polymerase 1
E: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
D: DNA (5'-D(*AP*TP*GP*CP*GP*GP*CP*CP*GP*CP*AP*T)-3')
A: Poly [ADP-ribose] polymerase 1
G: Poly [ADP-ribose] polymerase 1
H: Poly [ADP-ribose] polymerase 1
F: Poly [ADP-ribose] polymerase 1
B: Poly [ADP-ribose] polymerase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)130,20612
ポリマ－129,9448
非ポリマー2624
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)104.759, 128.552, 227.379
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))
21(chain F and (resid 7 through 9 or resid 11 through 200))
31(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))
41(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))
12(chain B and (resid 229 through 232 or resid 234 through 400))
22(chain G and (resid 229 through 232 or resid 234 through 400))
32(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))
42(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))
13(chain C and (resid 532 through 577 or resid 581...
23(chain H and (resid 532 through 577 or resid 581...
33(chain K and (resid 532 through 577 or resid 581...
43(chain P and (resid 532 through 577 or resid 581...
14chain D
24chain E
34chain L
44chain M

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
111LYSLYSTYRTYR(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AI7 - 927 - 29
121VALVALGLUGLU(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AI11 - 9031 - 110
131ZNZNZNZN(chain A and (resid 7 through 9 or resid 11 through 90 or resid 200))AS200
211LYSLYSTYRTYR(chain F and (resid 7 through 9 or resid 11 through 200))FO7 - 927 - 29
221VALVALZNZN(chain F and (resid 7 through 9 or resid 11 through 200))FO - W11 - 20031
311LYSLYSTYRTYR(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IH7 - 927 - 29
321VALVALGLUGLU(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IH11 - 9031 - 110
331ZNZNZNZN(chain I and (resid 7 through 9 or resid 11 through 90 or resid 200))IR200
411LYSLYSTYRTYR(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NG7 - 927 - 29
421VALVALGLUGLU(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NG11 - 9031 - 110
431ZNZNZNZN(chain N and (resid 7 through 9 or resid 11 through 90 or resid 200))NQ200
112ASPASPSERSER(chain B and (resid 229 through 232 or resid 234 through 400))BP229 - 23215 - 18
122LEULEUZNZN(chain B and (resid 229 through 232 or resid 234 through 400))BP - X234 - 40020
212ASPASPSERSER(chain G and (resid 229 through 232 or resid 234 through 400))GJ229 - 23215 - 18
222LEULEUZNZN(chain G and (resid 229 through 232 or resid 234 through 400))GJ - T234 - 40020
312ASPASPSERSER(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JN229 - 23215 - 18
322LEULEUPROPRO(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JN234 - 35820 - 144
332ZNZNZNZN(chain J and (resid 229 through 232 or resid 234 through 358 or resid 400))JV400
412ASPASPSERSER(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OM229 - 23215 - 18
422LEULEUPROPRO(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OM234 - 35820 - 144
432ZNZNZNZN(chain O and (resid 229 through 232 or resid 234 through 358 or resid 400))OU400
113ALAALAASPASP(chain C and (resid 532 through 577 or resid 581...CC532 - 57726 - 71
123ASNASNILEILE(chain C and (resid 532 through 577 or resid 581...CC581 - 64375 - 137
133LYSLYSSERSER(chain C and (resid 532 through 577 or resid 581...CC695 - 702175 - 182
143ARGARGTYRTYR(chain C and (resid 532 through 577 or resid 581...CC704 - 775184 - 255
213ALAALAASPASP(chain H and (resid 532 through 577 or resid 581...HL532 - 57726 - 71
223ASNASNILEILE(chain H and (resid 532 through 577 or resid 581...HL581 - 64375 - 137
233LYSLYSSERSER(chain H and (resid 532 through 577 or resid 581...HL695 - 702175 - 182
243ARGARGTYRTYR(chain H and (resid 532 through 577 or resid 581...HL704 - 775184 - 255
313ALAALAASPASP(chain K and (resid 532 through 577 or resid 581...KD532 - 57726 - 71
323ASNASNILEILE(chain K and (resid 532 through 577 or resid 581...KD581 - 64375 - 137
333LYSLYSSERSER(chain K and (resid 532 through 577 or resid 581...KD695 - 702175 - 182
343ARGARGTYRTYR(chain K and (resid 532 through 577 or resid 581...KD704 - 775184 - 255
413ALAALAASPASP(chain P and (resid 532 through 577 or resid 581...PK532 - 57726 - 71
423ASNASNILEILE(chain P and (resid 532 through 577 or resid 581...PK581 - 64375 - 137
433LYSLYSSERSER(chain P and (resid 532 through 577 or resid 581...PK695 - 702175 - 182
443ARGARGTYRTYR(chain P and (resid 532 through 577 or resid 581...PK704 - 775184 - 255
114DADADTDTchain DDF1 - 121 - 12
214DADADTDTchain EEE15 - 261 - 12
314DADADTDTchain LLB15 - 261 - 12
414DADADTDTchain MMA1 - 121 - 12

NCSアンサンブル:
ID
1
2
3
4

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要素

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DNA鎖 , 1種, 4分子 MLED

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


分子量: 3663.392 Da / 分子数: 4 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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Poly [ADP-ribose] polymerase ... , 3種, 12分子 CKPHNIAFGOJB

#2: タンパク質
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


分子量: 29813.668 Da / 分子数: 4 / Fragment: WGR domain and helical domain (HD) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PARP1, ADPRT, PPOL / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P09874, NAD+ ADP-ribosyltransferase, 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの
#3: タンパク質
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


分子量: 13101.821 Da / 分子数: 4 / Fragment: first zinc finger (Zn1) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PARP1, ADPRT, PPOL / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P09874, NAD+ ADP-ribosyltransferase, 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの
#4: タンパク質
Poly [ADP-ribose] polymerase 1 / PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 ...PARP-1 / ADP-ribosyltransferase diphtheria toxin-like 1 / ARTD1 / DNA ADP-ribosyltransferase PARP1 / NAD(+) ADP-ribosyltransferase 1 / ADPRT 1 / Poly[ADP-ribose] synthase 1 / Protein poly-ADP-ribosyltransferase PARP1


分子量: 18393.297 Da / 分子数: 4 / Fragment: third zinc finger (Zn3) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PARP1, ADPRT, PPOL / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P09874, NAD+ ADP-ribosyltransferase, 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの

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非ポリマー , 2種, 15分子

#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 7 / 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

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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: 2.95 Å3/Da / 溶媒含有率: 58.37 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: Tert-butanol, Tris pH 8.5

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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: ALS / ビームライン: 8.3.1 / 波長: 0.98 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2019年12月6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: 0.98 Å / 相対比: 1
反射解像度: 3.6→49.35 Å / Num. obs: 36391 / % possible obs: 100 % / 冗長度: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.029 / Rrim(I) all: 0.098 / Net I/σ(I): 13.8 / Num. measured all: 414757
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.6-3.7611.91.2935200443860.8070.3911.3522100
12.47-49.3510.10.04399089830.9990.0140.04556.698.6

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解析

ソフトウェア
名称バージョン分類
Aimless0.7.4データスケーリング
PHENIX1.18.2_3874精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4DQY

4dqy


解像度: 3.6→49.35 Å / SU ML: 0.86 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 41.41 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3122 1824 5.1 %
Rwork0.2516 33955 -
obs0.2547 35779 98.48 %
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: 457.51 Å2 / Biso mean: 219.3711 Å2 / Biso min: 82.64 Å2
精密化ステップサイクル: final / 解像度: 3.6→49.35 Å
タンパク質核酸リガンド溶媒全体
原子数13492 972 8 7 14479
Biso mean--203.08 83.97 -
残基数----1754
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A681X-RAY DIFFRACTIONPOSITIONAL0.01
12F681X-RAY DIFFRACTIONPOSITIONAL0.01
13I681X-RAY DIFFRACTIONPOSITIONAL0.006
14N681X-RAY DIFFRACTIONPOSITIONAL0.007
21B984X-RAY DIFFRACTIONPOSITIONAL0.006
22G984X-RAY DIFFRACTIONPOSITIONAL0.006
23J984X-RAY DIFFRACTIONPOSITIONAL0.006
24O984X-RAY DIFFRACTIONPOSITIONAL0.007
31C1507X-RAY DIFFRACTIONPOSITIONAL0.124
32H1507X-RAY DIFFRACTIONPOSITIONAL0.124
33K1507X-RAY DIFFRACTIONPOSITIONAL0.113
34P1507X-RAY DIFFRACTIONPOSITIONAL0.127
41D243X-RAY DIFFRACTIONPOSITIONAL0.014
42E243X-RAY DIFFRACTIONPOSITIONAL0.014
43L243X-RAY DIFFRACTIONPOSITIONAL0.01
44M243X-RAY DIFFRACTIONPOSITIONAL0.007
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6-3.70.54861380.49492444258294
3.7-3.810.59731100.47032269237987
3.81-3.930.40511180.339626182736100
3.93-4.070.40021410.300126202761100
4.07-4.230.34771380.264326322770100
4.23-4.420.33841300.252626272757100
4.42-4.660.33651570.238826122769100
4.66-4.950.35491330.219626502783100
4.95-5.330.27581660.207826342800100
5.33-5.870.34141410.231226542795100
5.87-6.710.35991310.252926842815100
6.71-8.450.29791550.247226972852100
8.45-49.350.2411660.210228142980100
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)
1-0.50430.8041.2503-0.12261.11481.2711-0.4239-0.1029-0.3099-0.24991.6341-0.13780.9793-1.94010.01581.40880.01210.19981.3936-0.05661.376431.732117.9903-15.3152
20.59490.48041.61480.19080.88441.1832-0.1173-0.6696-0.12520.1460.47180.7107-1.33970.434801.49460.32270.16561.3572-0.04581.617831.260616.4316-15.4796
32.64060.1697-5.59271.58831.83714.9965-0.3152-0.61310.2404-0.1062-0.00480.07680.77330.01-0.00531.4874-0.221-0.01521.8661-0.06051.417-23.620426.9815-36.5917
47.288-1.2259-2.18282.62570.22012.39340.39751.29711.2877-0.9159-0.88-0.1229-0.49680.8473-0.00471.6603-0.2669-0.10631.40250.07961.688839.421130.8615-43.9901
50.93221.45840.82430.89960.39920.0726-0.4021-0.06211.0041-0.705-0.6603-0.296-2.1761-4.6885-0.00033.33260.7427-0.20373.2662-0.21871.888-8.014426.136-66.3781
60.1738-0.3212-0.22050.77990.89810.6725-0.1002-0.03560.8418-2.80431.1015-1.0182-1.60661.7355-0.11442.51230.2146-0.00682.3022-0.05032.0299-9.465426.4442-66.8795
77.18830.0299-2.67392.3523-1.91652.6658-0.1912-0.20150.69140.0745-0.0111-0.53030.56080.545301.71540.0069-0.051.3573-0.24071.544339.932834.61076.9525
88.99680.9867-0.8943.5168-3.5072.3210.57990.5356-0.5326-0.04270.05070.03031.0156-0.0226-0.00021.86490.094-0.04671.1161-0.07741.810733.0402-3.6603-35.2818
94.6214-0.0678-3.52242.8928-0.18161.72980.10870.4880.00880.1489-1.2649-0.3277-0.1491-0.54730.00021.2342-0.02680.08541.91230.01911.708810.01413.7277-47.5144
10-0.3641.26473.3917-2.1130.30320.77321.0914-1.56080.3299-0.2573-0.94980.3837-0.7123-0.2548-0.01732.6914-0.1813-0.26832.5973-0.79762.4833-25.35944.5785-84.2305
114.267-2.17551.92293.67961.4058.5835-0.3144-0.5398-1.43710.3158-0.14850.70340.6878-0.72440.00012.1786-0.34470.29942.1588-0.18351.737827.35521.052411.7416
120.3242-0.81731.98626.71263.78678.12160.49080.38160.4797-1.94740.1444-0.65-1.40340.51310.00022.44790.03620.05281.79730.00381.93558.238724.8464-92.4559
130.20670.48822.5717-1.05120.4624.25620.25940.04840.0284-0.1504-0.38680.1592-0.13540.0077-0.00011.2166-0.14910.12151.8867-0.20681.468258.817522.80441.2527
142.91111.5031-1.99834.54911.95942.6520.82330.0938-0.29260.4644-0.0554-0.41870.98130.4856-0.00021.95670.1481-0.15051.5891-0.19331.520753.8052-1.9455-26.2133
151.55810.517-1.13590.1891-0.3422-0.0648-0.5121-1.37340.32070.20390.3950.6179-2.20540.06420.00252.30360.5279-0.33142.36970.22282.4315-27.923926.8911-89.4498
164.6336-0.85650.12173.5381-1.5793.73910.29240.8613-0.7581-1.1535-0.07670.7988-0.7033-0.0780.00011.5579-0.2960.05191.2558-0.16041.9411-4.0607-2.0817-58.0914
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 1 through 12)M1 - 12
2X-RAY DIFFRACTION2(chain 'L' and resid 15 through 26)L15 - 26
3X-RAY DIFFRACTION3(chain 'C' and resid 531 through 776)C531 - 776
4X-RAY DIFFRACTION4(chain 'K' and resid 531 through 776)K531 - 776
5X-RAY DIFFRACTION5(chain 'E' and resid 15 through 26)E15 - 26
6X-RAY DIFFRACTION6(chain 'D' and resid 1 through 12)D1 - 12
7X-RAY DIFFRACTION7(chain 'N' and resid 6 through 94)N6 - 94
8X-RAY DIFFRACTION8(chain 'I' and resid 5 through 91)I5 - 91
9X-RAY DIFFRACTION9(chain 'A' and resid 5 through 95)A5 - 95
10X-RAY DIFFRACTION10(chain 'G' and resid 224 through 358)G224 - 358
11X-RAY DIFFRACTION11(chain 'P' and resid 532 through 775)P532 - 775
12X-RAY DIFFRACTION12(chain 'H' and resid 531 through 776)H531 - 776
13X-RAY DIFFRACTION13(chain 'O' and resid 222 through 359)O222 - 359
14X-RAY DIFFRACTION14(chain 'J' and resid 223 through 361)J223 - 361
15X-RAY DIFFRACTION15(chain 'F' and resid 6 through 90)F6 - 90
16X-RAY DIFFRACTION16(chain 'B' and resid 229 through 358)B229 - 358

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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