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- PDB-7z4d: Crystal structure of SpCas9 bound to a 10 nucleotide complementar... -

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基本情報

登録情報
データベース: PDB / ID: 7z4d
タイトルCrystal structure of SpCas9 bound to a 10 nucleotide complementary DNA substrate
要素
  • CRISPR-associated endonuclease Cas9/Csn1
  • Non-target strand of 10 nucleotide complementary DNA substrate
  • Target strand of 10 nucleotide complementary DNA substrate
  • sgRNA
キーワードHYDROLASE / CRISPR / Cas9 / R-loop / substrate binding / off-target
機能・相同性
機能・相同性情報


maintenance of CRISPR repeat elements / 3'-5' exonuclease activity / DNA endonuclease activity / defense response to virus / 加水分解酵素; エステル加水分解酵素 / DNA binding / RNA binding / metal ion binding
類似検索 - 分子機能
CRISPR-associated endonuclease Cas9, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 ...CRISPR-associated endonuclease Cas9, bridge helix / Bridge helix of CRISPR-associated endonuclease Cas9 / CRISPR-associated endonuclease Cas9, PAM-interacting domain / CRISPR-associated endonuclease Cas9, REC lobe / REC lobe of CRISPR-associated endonuclease Cas9 / PAM-interacting domain of CRISPR-associated endonuclease Cas9 / : / Cas9 RuvC domain / HNH endonuclease / CRISPR-associated endonuclease Cas9 / Cas9-type HNH domain / Cas9-type HNH domain profile. / HNH nuclease / Ribonuclease H superfamily
類似検索 - ドメイン・相同性
: / DNA / DNA (> 10) / RNA / RNA (> 10) / CRISPR-associated endonuclease Cas9/Csn1
類似検索 - 構成要素
生物種Streptococcus pyogenes (化膿レンサ球菌)
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: 3.1 Å
データ登録者Pacesa, M. / Jinek, M.
資金援助 スイス, 1件
組織認可番号国
Swiss National Science Foundation31003A_182567 スイス
引用ジャーナル: Nature / 年: 2022
タイトル: R-loop formation and conformational activation mechanisms of Cas9.
著者: Martin Pacesa / Luuk Loeff / Irma Querques / Lena M Muckenfuss / Marta Sawicka / Martin Jinek /
要旨: Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage. The programmable activity of Cas9 has been widely utilized for genome editing applications, yet its precise ...Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage. The programmable activity of Cas9 has been widely utilized for genome editing applications, yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-electron microscopy structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide-target hybridization past the seed region induces rearrangements of the REC2 and REC3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide-target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide-target heteroduplex, and complementary REC2 and REC3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
履歴
登録2022年3月3日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年8月31日Provider: repository / タイプ: Initial release
改定 1.12022年9月7日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
改定 1.22022年9月14日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: Target strand of 10 nucleotide complementary DNA substrate
D: Non-target strand of 10 nucleotide complementary DNA substrate
E: CRISPR-associated endonuclease Cas9/Csn1
F: sgRNA
G: Target strand of 10 nucleotide complementary DNA substrate
H: Non-target strand of 10 nucleotide complementary DNA substrate
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)409,03124
ポリマ－408,4068
非ポリマー62616
水1,58588
1
A: sgRNA
B: CRISPR-associated endonuclease Cas9/Csn1
C: Target strand of 10 nucleotide complementary DNA substrate
D: Non-target strand of 10 nucleotide complementary DNA substrate
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)204,59414
ポリマ－204,2034
非ポリマー39110
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
2
E: CRISPR-associated endonuclease Cas9/Csn1
F: sgRNA
G: Target strand of 10 nucleotide complementary DNA substrate
H: Non-target strand of 10 nucleotide complementary DNA substrate
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)204,43810
ポリマ－204,2034
非ポリマー2356
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)88.636, 95.509, 169.797
Angle α, β, γ (deg.)80.830, 78.040, 62.340
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 10 through 72 or resid 78 through 82))
d_2ens_1(chain "F" and (resid 10 through 72 or resid 78 through 82))
d_1ens_2(chain "B" and (resid 5 through 232 or resid 234...
d_2ens_2(chain "E" and (resid 5 through 179 or resid 181...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1AAA
d_21ens_1AAF
d_11ens_2TYRGLUB4 - 230
d_12ens_2LYSPHEB232 - 516
d_13ens_2LEUILEB589 - 665
d_14ens_2ARGHISB689 - 696
d_15ens_2SERLEUB716 - 717
d_16ens_2GLUASNB719 - 776
d_17ens_2LYSLYSB798
d_18ens_2SERSERB800
d_19ens_2GLYGLYB806
d_110ens_2VALVALB813 - 866
d_111ens_2GLUGLYB868 - 902
d_112ens_2TYRASPB904 - 908
d_113ens_2LYSLYSB911
d_114ens_2PHESERB928 - 931
d_115ens_2ILEALAB933 - 944
d_116ens_2GLYGLYB946 - 961
d_117ens_2ILELYSB963 - 1014
d_118ens_2ASPTYRB1016 - 1133
d_119ens_2LEUGLYB1136 - 1258
d_21ens_2TYRSERE4 - 178
d_22ens_2VALGLUE180 - 231
d_23ens_2LYSPHEE233 - 517
d_24ens_2LEUILEE549 - 625
d_25ens_2ARGHISE645 - 652
d_26ens_2SERLEUE654 - 655
d_27ens_2GLUSERE657 - 716
d_28ens_2GLYGLYE722
d_29ens_2VALVALE729 - 782
d_210ens_2GLUGLYE784 - 818
d_211ens_2TYRASPE820 - 824
d_212ens_2LYSLYSE828
d_213ens_2PHESERE835 - 838
d_214ens_2ILEALAE840 - 851
d_215ens_2GLYGLYE853 - 868
d_216ens_2ILELYSE870 - 921
d_217ens_2ASPTYRE923 - 1040
d_218ens_2LEUGLYE1043 - 1165

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(-0.999999237799, -0.00115128836583, -0.000446023112474), (-0.00115053335501, 0.999997911206, -0.00168933613424), (0.000447967093861, -0.00168882168216, -0.999998473602)-46.4371441371, 0.0476650436215, 13.3329021029
2given(-0.999992227836, -0.00287751842639, -0.00269520970147), (-0.00287790301423, 0.999995849192, 0.000138825685249), (0.00269479904071, 0.000146581158396, -0.999996358279)-46.4327120008, 0.0139315297274, 13.4966428317

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要素

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DNA鎖 , 2種, 4分子 CGDH

#3: DNA鎖 Target strand of 10 nucleotide complementary DNA substrate


分子量: 9149.889 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#4: DNA鎖 Non-target strand of 10 nucleotide complementary DNA substrate


分子量: 9221.965 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)

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RNA鎖 / タンパク質 , 2種, 4分子 AFBE

#1: RNA鎖 sgRNA


分子量: 27242.301 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物)
#2: タンパク質 CRISPR-associated endonuclease Cas9/Csn1 / SpCas9 / SpyCas9


分子量: 158588.781 Da / 分子数: 2 / Mutation: D10A, H840A / 由来タイプ: 組換発現
由来: (組換発現) Streptococcus pyogenes (化膿レンサ球菌)
遺伝子: cas9, csn1, SPy_1046 / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: Q99ZW2, 加水分解酵素; エステル加水分解酵素

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非ポリマー , 2種, 104分子

#5: 化合物
ChemComp-K / POTASSIUM ION


分子量: 39.098 Da / 分子数: 16 / 由来タイプ: 合成 / 式: K
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 88 / 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: 3.04 Å3/Da / 溶媒含有率: 59.54 %
結晶化温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 0.1 M sodium cacodylate pH 6.5, 0.8-1.2M ammonium formate, 12-14% PEG4000

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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: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 2M-F / 検出器: PIXEL / 日付: 2017年3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 Å / 相対比: 1
反射解像度: 3.1→66.49 Å / Num. obs: 85696 / % possible obs: 89.18 % / 冗長度: 10.2 % / Biso Wilson estimate: 52.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.3403 / Net I/σ(I): 7.62
反射 シェル解像度: 3.1→3.211 Å / 冗長度: 10.1 % / Rmerge(I) obs: 2.176 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 4963 / CC1/2: 0.446 / % possible all: 56.74

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XDSデータ削減
XSCALE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: 5FQ5

5fq5


解像度: 3.1→66.49 Å / SU ML: 0.4114 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 28.9541
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2757 3882 4.98 %
Rwork0.2465 74025 -
obs0.2479 77907 89.2 %
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 mean: 68.11 Å2
精密化ステップサイクル: LAST / 解像度: 3.1→66.49 Å
タンパク質核酸リガンド溶媒全体
原子数19796 5182 16 88 25082
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002525950
X-RAY DIFFRACTIONf_angle_d0.547336063
X-RAY DIFFRACTIONf_chiral_restr0.03744125
X-RAY DIFFRACTIONf_plane_restr0.00463699
X-RAY DIFFRACTIONf_dihedral_angle_d20.03910494
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.263549808838
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.899332626795
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.140.3425740.33111432X-RAY DIFFRACTION48.55
3.14-3.180.3222950.31191774X-RAY DIFFRACTION58.85
3.18-3.220.31871000.30171895X-RAY DIFFRACTION64.73
3.22-3.260.37611100.29582051X-RAY DIFFRACTION68.56
3.26-3.310.30591090.27122187X-RAY DIFFRACTION73.68
3.31-3.360.30671200.28292317X-RAY DIFFRACTION78.84
3.36-3.410.30871400.28352515X-RAY DIFFRACTION83.2
3.41-3.470.34931240.29562475X-RAY DIFFRACTION86.2
3.47-3.530.32061430.27812829X-RAY DIFFRACTION92.7
3.53-3.590.30141440.25882807X-RAY DIFFRACTION96.5
3.59-3.660.29451250.27752417X-RAY DIFFRACTION85.62
3.67-3.740.29161230.25892373X-RAY DIFFRACTION91.9
3.74-3.820.29761610.24933024X-RAY DIFFRACTION99.97
3.82-3.910.3231290.26832439X-RAY DIFFRACTION84.45
3.91-40.25861580.25172990X-RAY DIFFRACTION99.75
4-4.110.26711540.22582957X-RAY DIFFRACTION100
4.11-4.230.24031590.22562989X-RAY DIFFRACTION100
4.23-4.370.23431560.21022965X-RAY DIFFRACTION100
4.37-4.530.25691540.21942935X-RAY DIFFRACTION100
4.53-4.710.25771560.21372958X-RAY DIFFRACTION100
4.71-4.920.23061570.21432982X-RAY DIFFRACTION100
4.92-5.180.24521550.20442954X-RAY DIFFRACTION99.97
5.18-5.50.24661570.22122959X-RAY DIFFRACTION100
5.5-5.930.26211570.24432986X-RAY DIFFRACTION99.94
5.93-6.520.29931540.25332924X-RAY DIFFRACTION100
6.53-7.470.31091570.2592979X-RAY DIFFRACTION100
7.47-9.40.27911550.24292971X-RAY DIFFRACTION100
9.41-66.490.23461560.24952941X-RAY DIFFRACTION99.52
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)
11.512282242770.555394659464-0.32819401152.56175084912-0.2742094524830.132759616435-0.179792137146-0.7670790249140.08925804733010.826147909991-0.1263429390150.249025001714-0.2224965601340.1573563162540.1566689735210.4341129664510.375159865464-0.02846334235060.3677654599190.0485513190810.186633470802-13.8863921083-2.0558560488337.7963583968
20.643179804280.358672375186-0.2731144619260.785601101544-0.4931990138960.260238436944-0.06007104456170.0649638968558-0.304649006717-0.0855428954711-0.0961956633876-0.450560135297-0.1951613100350.3037657755410.1065227514670.3759467473890.0293344878583-0.03907425581460.321645827136-0.1124199414660.4326270608522.1765539622116.470979797417.3777057363
31.55273989351-1.699123658270.5745669517142.00211403667-0.6787055358170.7559565710440.08406201860870.105197802659-0.367132333188-0.1135119650760.1153898501940.7792619803970.398428541591-0.121861731704-0.06298724922910.3649027614490.0972676654846-0.01915203090040.341550013266-0.02972171203080.521910320802-19.8374392874-23.135957249926.1443177093
40.00125453177501-0.002731894195720.002228412381990.0002050929936780.0009439386928690.0009192432361870.0133204888809-0.157198193243-0.29462611290.2083270165230.05973022394610.00689893791670.3705542001180.097418820786-0.01686979801471.682648942710.18807969504-0.0636614068221.593084554430.06346085657031.76879739805-24.0046554727-41.161996105523.3369281104
55.828570178273.34158626114-1.719385016765.574210746171.340861780626.61533389849-0.591726642634-0.898540364836-0.19389931120.7795517328780.7373679427090.944587741611-0.496521982783-0.890144139394-0.02238470444240.8573177490810.321731288360.08077109985790.866066727520.1402386714260.778553417707-10.7888908729-52.290693287731.2079180093
61.1168300728-0.07318959015810.1255101614931.17529613739-0.5069911462820.888584816074-0.16980628195-0.2561020763180.1556768187340.4723594429740.155301757920.048604145266-0.290724513405-0.122896166537-0.03391378529710.2096252011080.416603948755-0.003877181700060.0161634919573-0.1142186917310.14749845311-15.6908282366-0.97942309013335.3063107127
71.07614536589-0.08425227132520.4973858922121.24143846202-0.0654634351232.11857106707-0.0402798436108-0.506671845593-0.1819305031240.641724547273-0.0201474920123-0.226906798064-0.06601122764540.2297128148330.0342763707251.442667380480.2947382866380.07408016945721.15280107598-0.1188317803720.35846834269-20.974720857712.38254147962.8638919622
81.00946045557-0.0757160265151-0.223251660521.4138903178-0.3473076814341.58432258598-0.113685897132-0.466642426946-0.2180207331590.3737172382750.0303997800205-0.00776137165421-0.3741572454770.07157087117210.07135864376750.3656718293310.283556573826-0.02271207097270.3373998969420.02929846906610.283262665041-16.10198522378.3544184930138.1064559338
91.7103844847-0.123587075041-0.5873303686770.735915435291-0.1188652319680.9905818986050.0637049743338-0.6408158067780.2245405143310.2600097620470.01425559527460.223243339822-0.0797862965562-0.430959412112-0.02393369988090.6482923002090.07561686595490.06521467527090.907722793286-0.02186024022180.537007780014-35.1265514824-27.430035741565.3946904164
101.645645028170.1927308146770.5115771902121.165134676790.5186856652632.17425056220.101611929646-1.08625951869-0.01770609845910.922782961775-0.1458166559040.2196721918940.2073966024460.0621883731750.02076296213820.7322909015840.1759757366740.01179018245810.8678842530830.04942151781390.411500117202-4.50836886892-40.27975158666.3316959531
111.72787749827-0.149827961061-0.304217269392.42936229072-0.381988834070.7192402866920.426834831071-0.4028814555340.02729979793670.295786687975-0.636003463318-0.471971358474-0.09729980794831.290549126920.101773191722-0.1032510485790.66465812662-0.009885321502850.163400748485-0.08718009314940.3631159178969.02528777394-31.142008811536.5122045127
120.4485628759030.1533739493470.6238739617520.7431157886580.8006487486368.200337390550.0524374846860.18867122746-0.30895488153-0.1615691827720.108351967740.07731894812320.531574527561-0.140145886805-0.1530511982390.6845213757660.208310655820.1717094727690.7534501274630.03426488553120.55095361558518.5852915731-18.806924141415.8798016977
130.368764453150.8525273540540.5561213386842.612268206850.2517838166982.51784267071-0.07732294285050.0322935590013-0.137940464202-0.1120710913720.0809521233481-0.3943521781710.1674745180030.545271430382-0.01889374048560.3036040728860.05105164849190.08471345370280.2424563496820.05398729489870.47454534791711.8626640017-9.3914103295329.308585131
146.02011712186-3.98759770823-6.858877404012.629520513854.54145068127.78714059957-0.159283522213-0.1196987403580.07478725361880.1787496454370.239523844499-0.0493391402941-0.04719503509550.0542967199131-0.06028182467660.5076258625510.2115791351470.07770831774170.3444048206080.1242352679940.37377096142-9.70799795877-2.0565966975641.1091886869
151.840179425511.31633247751-0.4023555835819.23053759499-2.587747380881.65127099127-0.195812250426-0.36284926937-0.4247021639820.4994516805190.2394950416060.09067131646430.331596470931-0.0299159320444-0.067856416950.5462233804470.768559560830.1680011588940.3635713980810.3847631006260.523590753506-24.7880803323-9.8585878475551.6956568482
161.11490962099-0.0255075315771-1.571196808710.0009366490754330.03557884242912.21765812878-0.112262232305-1.21929519982-0.6964714164981.026006346240.0791093761551-0.4042301383580.4738245097480.6124612964090.109050515841.206699792090.468244232216-0.1664533546211.329995172260.4626691239291.05374186162-18.2374029374-24.881627161863.8561009758
175.283224223050.775442607231-2.531745867153.83194884189-1.600782151751.620959231150.00748849614395-0.7172470724410.2657223450540.715202247396-0.0633679494678-0.151311288827-0.1985055705430.199029476094-0.009039317336441.07705188819-0.01978200918470.02918174116071.101441715720.2184216644321.00276470667-28.2665236794-36.721998632572.1049824205
180.716647433201-0.12460758803-0.2049927828750.36977795839-0.4941764044881.001775499860.153139136346-0.486515192890.2385380810260.03982407571440.02312367610780.0296689825668-0.2683294638160.542507578291-0.1603942983430.8794073130620.08500116789320.1122913068731.30317293588-0.1904706612580.99017056-21.0604719957-25.828399944262.7254903398
195.366142819620.425835765157-0.1222705367955.61928443611-2.665765435382.890799853830.284386177113-0.0978382938490.3901871893170.1484207842450.327236517249-0.8139930227-0.3866582776441.05612773501-0.427992654675-0.160078760140.2190106310530.3048594641150.45259947231-0.02089808888760.85893933983712.908438397-13.836499171624.4232663818
201.0995190243-0.2460836451270.2198459842751.252511454420.4757303428331.11611910706-0.1768883161550.242181068160.245457285481-0.3634441216860.230626222448-0.0615189726766-0.434261027637-0.0533161402735-0.04851282817170.0999470092332-0.6464196052290.0937997002098-0.2066183568970.0991575606740.0667240260534-30.788341916-0.807870347666-21.9577968475
210.02444537269890.3318242570310.00483700382930.8926364504180.5897134192461.28907310752-0.002533460295570.423324825229-0.0495628065989-0.5580842166580.104817151237-0.285243369783-0.2625852760260.255052103281-0.02471169185520.607209447071-0.1768180768450.06825122869340.651400708229-0.01655105225170.5218143902-22.0510002098-4.1913667598-39.8751741124
221.78918542370.1035666840330.04919797434762.428492214140.5365411793251.183595056760.003220795465330.509461638393-0.206907767153-0.195603212143-0.2050477731510.4010338682740.231939592458-0.4952237491230.1757058475770.266600345733-0.317015937842-0.02065170431880.529929697642-0.02481244283740.357050753199-51.4743266154-34.1828289373-29.7869895059
230.882727430068-1.64019798557-1.723947105543.032412742673.212887084683.36244590012-0.1219821238681.465128510580.26774663186-1.26969215864-0.04161647867920.197881734118-2.37618020107-0.0695177718140.3930624420941.32357979724-0.4832089911740.1714015904360.962449230372-0.01178700392860.474239330414-28.0708532032-14.273642342-41.3404822396
240.3845238548510.603213960442-0.04054972300690.9810941385120.1988535101490.662597771126-0.08025774674280.172357305360.0903529384640.03920048554690.0416184091532-0.0900949859565-0.0131779871718-0.1626615193340.007002843751540.314397252368-0.0999558245401-0.05888516680430.2813231888790.0397165978680.246881816578-38.46739545172.19471040289-9.59298017508
250.580071995697-0.6306755810060.8541359873070.686088946717-0.9324469639081.26103775625-0.00260788347004-0.11002396373-0.187231814462-0.2653345027810.158918565494-0.536884779110.06725691245940.51331559438-0.1362321919720.94020287662-0.396868430696-0.3165356758131.01157599769-0.1589942283930.997273495331-24.6555781838-44.0300438284-7.10953292154
262.49377925685-0.28598568914-1.547524668633.48805015816-1.44597628111.7304437995-0.5925725358380.7860779352970.0903289185897-0.6572591740090.73195369876-0.823329683147-0.6351237858560.651066459378-0.01212652338811.01000815127-0.2312373598920.01905077725981.02903406333-0.04089748454480.779196118261-31.978138302-49.1212740893-16.8925883352
271.141559179430.463693676135-2.467910709471.32028059346-0.1675649817545.95267002807-0.138701860239-0.342348482106-0.4909436635290.3274678453250.0810291785850.1250681300720.6419475733710.05000198230690.08973873467160.688781299871-0.1895612224320.1030602596320.90245895352-0.1517568950410.428727847336-65.048898178-18.7898948443-2.6443892722
280.8739183118590.200187174223-1.689991737191.56973538915-0.5966402331013.277016424590.05636957125070.0182501270580.05796314786920.1898324051390.07344705732680.453696117294-0.00108344891951-0.36140012599-0.1539424139160.215910070626-0.001225648877120.00728023054250.57662784594-0.05953292601630.387048809829-58.3957659677-9.3765763488-16.0637089964
291.45787150301-0.474002141422-0.5968836770261.916055411860.05756367629880.562708800277-0.2209037964990.163484518402-0.172027403097-0.4162648852610.0568210561944-0.13864632188-0.0828886795999-0.1300673906230.01834217042440.532991244117-1.02501934740.1381721773580.258895813337-0.3246254858860.241658391662-29.3521059011-5.86193851887-33.0037660721
301.728772886360.520687374781-0.3081209448242.849652885110.1215010504471.780583673050.02657043652850.804952501455-0.434080531778-1.01913992961-0.1745911620430.761878760476-0.0309055621537-0.5152252512780.1616267008480.988960900882-0.226037419506-0.1492456447491.03733795084-0.2066747364190.787042543279-29.9694852498-22.2546166943-47.3312417731
313.837191172930.0276758157818-3.322398478680.00082799863714-0.02316923819622.87668676357-0.01601389385850.0640476966015-0.0850885321364-0.08100563553990.1186156733630.07290440025760.07345128549750.0106180300427-0.1047789209141.56331749717-0.0782084455110.2390777442431.42855784331-0.1172341388651.39180148974-15.8121420458-41.407137863-55.0812059548
320.001368793348820.0001552475187470.0001143583664880.0005566051592840.000376173634948-0.000696619830248-0.07094808738110.08356527581870.0115688301186-0.191907284352-0.0361202812821-0.358962860582-0.09667074002080.272688815580.04583999938421.26559681395-0.4644504009070.1666595575711.24805773715-0.04212871019941.46492352157-19.6771478936-33.4665322624-51.1255371586
338.0380185926-0.565348318028-6.6920829530.04928204140230.4794869251415.553833226680.5346845255061.390866564130.852351295586-0.79833263387-0.033394248246-0.723291597443-0.5906029356660.0965993398767-0.5627345596540.518705551673-0.215867120490.1292110598830.8086798299220.09866310423220.695846018846-46.0332243614-16.7823484894-29.6180615773
342.28209368833-1.12231545834-1.593921322221.769001870810.3661114993352.700645451120.0144757739437-0.06542532718020.08011778826530.1140126194820.2761447237650.57573382383-0.116929160252-0.693720777517-0.1502262222320.207717885706-0.2185921648810.2796781708120.500556655228-0.005876046002140.805583416239-61.7273403585-12.9943625408-6.5730167038
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 27 )AA8 - 27
22chain 'A' and (resid 28 through 52 )AA28 - 52
33chain 'A' and (resid 53 through 72 )AA53 - 72
44chain 'A' and (resid 73 through 77 )AA73 - 77
55chain 'A' and (resid 78 through 82 )AA78 - 82
66chain 'B' and (resid 2 through 207 )BB2 - 2071 - 205
77chain 'B' and (resid 208 through 315 )BB208 - 315206 - 313
88chain 'B' and (resid 316 through 512 )BB316 - 512314 - 510
99chain 'B' and (resid 513 through 870 )BB513 - 870511 - 780
1010chain 'B' and (resid 871 through 1036 )BB871 - 1036781 - 927
1111chain 'B' and (resid 1037 through 1368 )BB1037 - 1368928 - 1259
1212chain 'C' and (resid -9 through -5 )CC-9 - -5
1313chain 'C' and (resid -4 through 0 )CC-4 - 0
1414chain 'C' and (resid 1 through 5 )CC1 - 5
1515chain 'C' and (resid 6 through 10 )CC6 - 10
1616chain 'C' and (resid 11 through 15 )CC11 - 15
1717chain 'C' and (resid 16 through 20 )CC16 - 20
1818chain 'D' and (resid -20 through -3 )DD-20 - -3
1919chain 'D' and (resid -2 through 9 )DD-2 - 9
2020chain 'E' and (resid 2 through 207 )EE2 - 2071 - 206
2121chain 'E' and (resid 208 through 910 )EE208 - 910207 - 717
2222chain 'E' and (resid 911 through 1368 )EE911 - 1368718 - 1166
2323chain 'F' and (resid 6 through 15 )FF6 - 15
2424chain 'F' and (resid 16 through 70 )FF16 - 70
2525chain 'F' and (resid 71 through 75 )FF71 - 75
2626chain 'F' and (resid 76 through 82 )FF76 - 82
2727chain 'G' and (resid -9 through -5 )GG-9 - -5
2828chain 'G' and (resid -4 through 0 )GG-4 - 0
2929chain 'G' and (resid 1 through 10 )GG1 - 10
3030chain 'G' and (resid 11 through 18 )GG11 - 18
3131chain 'G' and (resid 19 through 20 )GG19 - 20
3232chain 'H' and (resid -20 through -16 )HH-20 - -16
3333chain 'H' and (resid -15 through 0 )HH-15 - 0
3434chain 'H' and (resid 1 through 9 )HH1 - 9

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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