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- PDB-7lzp: LC/A-JPU-B9-JPU-A11-JPU-G11 -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 7lzp
タイトルLC/A-JPU-B9-JPU-A11-JPU-G11
要素
  • Botulinum neurotoxin A light chain
  • JPU-A11
  • JPU-B9
  • JPU-G11
キーワードANTITOXIN (抗毒素) / Single domain antibody (ナノボディ) / VHH / protease inhibitor (プロテアーゼ阻害剤)
機能・相同性
機能・相同性情報


Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / ボツリヌストキシン / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane ...Toxicity of botulinum toxin type A (botA) / ganglioside GT1b binding / ボツリヌストキシン / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / タンパク質分解 / zinc ion binding / extracellular region / 生体膜
類似検索 - 分子機能
Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily ...Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
類似検索 - ドメイン・相同性
Botulinum neurotoxin type A
類似検索 - 構成要素
生物種Clostridium botulinum (ボツリヌス菌)
Vicugna pacos (アルパカ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.86 Å
データ登録者Lam, K. / Jin, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 米国
引用ジャーナル: Plos Pathog. / 年: 2022
タイトル: Probing the structure and function of the protease domain of botulinum neurotoxins using single-domain antibodies.
著者: Lam, K.H. / Tremblay, J.M. / Perry, K. / Ichtchenko, K. / Shoemaker, C.B. / Jin, R.
履歴
登録2021年3月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年12月22日Provider: repository / タイプ: Initial release
改定 1.12022年1月19日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year
改定 1.22023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
A: Botulinum neurotoxin A light chain
C: JPU-G11
D: Botulinum neurotoxin A light chain
E: JPU-A11
G: JPU-B9
F: JPU-G11
B: JPU-A11
H: JPU-B9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)183,36812
ポリマ－183,1078
非ポリマー2624
水362
1
A: Botulinum neurotoxin A light chain
C: JPU-G11
G: JPU-B9
B: JPU-A11
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,6846
ポリマ－91,5534
非ポリマー1312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
D: Botulinum neurotoxin A light chain
E: JPU-A11
F: JPU-G11
H: JPU-B9
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)91,6846
ポリマ－91,5534
非ポリマー1312
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)132.604, 132.604, 413.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21
12
22
13
23
14
24

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
111PROPROASNASN(chain 'A' and (resid 2 through 64 or resid 66...AA2 - 269 - 33
121METMETPROPRO(chain 'A' and (resid 2 through 64 or resid 66...AA30 - 6337 - 70
131LYSLYSPHEPHE(chain 'A' and (resid 2 through 64 or resid 66...AA66 - 19473 - 201
141GLUGLUGLUGLU(chain 'A' and (resid 2 through 64 or resid 66...AA197 - 201204 - 208
151PHEPHEASNASN(chain 'A' and (resid 2 through 64 or resid 66...AA213 - 246220 - 253
161LEULEUASNASN(chain 'A' and (resid 2 through 64 or resid 66...AA256 - 410263 - 417
171ASNASNLYSLYS(chain 'A' and (resid 2 through 64 or resid 66...AA412 - 438419 - 445
281PROPROASNASN(chain 'D' and (resid 2 through 6 or (resid 7...DC2 - 269 - 33
291METMETPROPRO(chain 'D' and (resid 2 through 6 or (resid 7...DC30 - 6337 - 70
2101LYSLYSPHEPHE(chain 'D' and (resid 2 through 6 or (resid 7...DC66 - 19473 - 201
2111GLUGLUGLUGLU(chain 'D' and (resid 2 through 6 or (resid 7...DC197 - 201204 - 208
2121PHEPHEASNASN(chain 'D' and (resid 2 through 6 or (resid 7...DC213 - 246220 - 253
2131LEULEUASNASN(chain 'D' and (resid 2 through 6 or (resid 7...DC256 - 410263 - 417
2141ASNASNLYSLYS(chain 'D' and (resid 2 through 6 or (resid 7...DC412 - 438419 - 445
1152GLNGLNTHRTHR(chain 'B' and ((resid 1 and (name N or name...BG1 - 256 - 30
1162THRTHRVALVAL(chain 'B' and ((resid 1 and (name N or name...BG28 - 12833 - 133
2172GLNGLNTHRTHR(chain 'E' and (resid 1 through 12 or (resid 13...ED1 - 256 - 30
2182THRTHRVALVAL(chain 'E' and (resid 1 through 12 or (resid 13...ED28 - 12833 - 133
1193GLNGLNVALVAL(chain 'C' and (resid 3 through 10 or (resid 11...CB3 - 128 - 17
1203PROPROVALVAL(chain 'C' and (resid 3 through 10 or (resid 11...CB14 - 11519 - 120
2213GLNGLNVALVALchain 'F'FF3 - 128 - 17
2223PROPROVALVALchain 'F'FF14 - 11519 - 120
1234VALVALGLNGLN(chain 'G' and (resid 2 through 38 or (resid 39...GE2 - 397 - 44
1244GLNGLNSERSER(chain 'G' and (resid 2 through 38 or (resid 39...GE44 - 11049 - 115
2254VALVALGLNGLNchain 'H'HH2 - 397 - 44
2264GLNGLNSERSERchain 'H'HH44 - 11049 - 115

NCSアンサンブル:
ID
1
2
3
4

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要素

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タンパク質 , 1種, 2分子 AD

#1: タンパク質 Botulinum neurotoxin A light chain / LC


分子量: 50894.594 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Clostridium botulinum (ボツリヌス菌)
遺伝子: botA, atx, bonT / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DPI0, ボツリヌストキシン

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抗体 , 3種, 6分子 CFEBGH

#2: 抗体 JPU-G11


分子量: 13515.010 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#3: 抗体 JPU-A11


分子量: 14714.107 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)
#4: 抗体 JPU-B9


分子量: 12429.715 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Vicugna pacos (アルパカ) / 発現宿主: Escherichia coli (大腸菌)

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非ポリマー , 2種, 6分子

#5: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn
#6: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 2 / 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: 2.86 Å3/Da / 溶媒含有率: 57.03 %
結晶化温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: 0.1 M sodium cacodylate pH 6.5, 15 % ethylene glycol, 25 % PEG 4000

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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: APS / ビームライン: 24-ID-E / 波長: 0.97918 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019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: 0.97918 Å / 相対比: 1
反射解像度: 2.86→137.68 Å / Num. obs: 50539 / % possible obs: 99.6 % / 冗長度: 9.7 % / Biso Wilson estimate: 79.1 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.088 / Net I/σ(I): 12.2
反射 シェル解像度: 2.86→2.96 Å / Num. unique obs: 4409 / CC1/2: 0.405 / Rpim(I) all: 0.893

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解析

ソフトウェア
名称バージョン分類
PHENIX1.14_3260精密化
PHASER位相決定
MOSFLMデータ削減
Aimlessデータスケーリング
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 3V0A

3v0a


解像度: 2.86→67.06 Å / SU ML: 0.4983 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.0495 / 立体化学のターゲット値: CDL v1.2
Rfactor反射数%反射
Rfree0.2727 2533 5.03 %
Rwork0.2346 47847 -
obs0.2365 50380 99.69 %
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: 81.97 Å2
精密化ステップサイクル: LAST / 解像度: 2.86→67.06 Å
タンパク質核酸リガンド溶媒全体
原子数12106 0 4 2 12112
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002812418
X-RAY DIFFRACTIONf_angle_d0.583916870
X-RAY DIFFRACTIONf_chiral_restr0.04451867
X-RAY DIFFRACTIONf_plane_restr0.00382163
X-RAY DIFFRACTIONf_dihedral_angle_d12.62864412
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.86-2.920.39211490.34282465X-RAY DIFFRACTION95.23
2.92-2.980.33471330.31762620X-RAY DIFFRACTION100
2.98-3.040.36291390.34772596X-RAY DIFFRACTION100
3.04-3.110.36031410.33972616X-RAY DIFFRACTION100
3.11-3.190.3541460.32392618X-RAY DIFFRACTION99.89
3.19-3.280.38181350.30522609X-RAY DIFFRACTION100
3.28-3.370.34121350.28532621X-RAY DIFFRACTION99.96
3.37-3.480.31871430.29112630X-RAY DIFFRACTION99.93
3.48-3.610.34531440.28852616X-RAY DIFFRACTION100
3.61-3.750.31571200.26832647X-RAY DIFFRACTION100
3.75-3.920.26911380.23982660X-RAY DIFFRACTION99.93
3.92-4.130.27211250.22232684X-RAY DIFFRACTION100
4.13-4.390.24381430.19862641X-RAY DIFFRACTION99.96
4.39-4.730.21281400.17932683X-RAY DIFFRACTION99.93
4.73-5.20.23891420.18192689X-RAY DIFFRACTION100
5.2-5.960.271400.20492734X-RAY DIFFRACTION99.97
5.96-7.50.28051550.21362755X-RAY DIFFRACTION99.86
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)
11.312835425630.0368974995328-0.2040832920241.10537988716-1.421219359752.042674158680.0712733126816-0.257632901123-0.04901906942340.0679956204701-0.172519226942-0.5908036344260.1800198409660.09391909038860.0001843339200680.2767552216770.0635571094444-0.04797112366770.9160281252580.003930452318490.55839411557170.8500949705-79.1993958082-1.45279489238
22.52500801250.599356915173-0.3664221152220.262634995728-0.207421285881.505284921670.252941792826-0.3480074070020.055741965680.164148584878-0.100071323047-0.0222937404645-0.1276319374810.05018772732021.83325043154E-80.4332815096310.0529560449163-0.0542164067910.809375143723-0.125847997630.54485277568761.4521672118-76.05970498870.265270254282
30.2564856164650.01713671435850.1626135744021.61994639285-0.390577056830.3173024313430.188484041008-0.3478768469880.366642604082-0.181321516645-0.0447299010947-0.2452895801150.01523072644950.4402012175970.0068545431520.4160173946920.01681597696870.01066625913320.905070170827-0.1399621650440.58078886882262.3389137258-69.1244908239-2.41342121025
43.0579164010.0623094579951-0.3949524566741.305289930350.6375330299670.7194930770280.603238818529-0.881400304805-1.059777190.0341021375591-0.4702781090950.4923966853080.474192714272-0.07610272679490.1336752634260.445011131542-0.0614220657372-0.1361035590050.939599177841-0.1963263743620.55480000219749.8231452956-85.23824147978.88233131546
52.019301771460.0997966152299-0.2920557139592.41525752231-0.8685940136252.515978929230.1819605021610.1510251263220.227474872259-0.255193873331-0.01010114975830.08673159524040.00775533724994-0.00406449255001-2.07528946375E-70.3532254024770.0879330597083-0.1181507760580.67978950608-0.150572563460.54919409847547.1311315647-71.6266933383-11.3476229261
62.009471262920.5809381826780.1858902714511.18676530681-1.022988795551.17911070709-0.0573061463276-0.353452705407-0.5103066697660.09454256794370.02993431484880.4215768909760.2384444702630.0966715260413-0.0001565595680380.4694328493940.0497380127437-0.07048091847830.83589555161-0.01312380671980.57279988807447.6552978354-88.271604093110.2236570892
70.253666064234-0.25749632843-0.05898867846020.277953029505-0.0390261768690.262812896144-0.6136539293460.244733711701-0.1187007645730.1745078049080.313798991994-0.2345501821940.6908323569820.299625325761-0.007378523573621.15058985393-0.337906194399-0.1837692182950.966049628526-0.2114562779470.6835541404543.3230073692-105.940851557-27.0217922096
80.5977568765360.2542716661190.02248968051790.9349747694640.3163995412630.1166944277860.0973925105556-0.0518960453078-0.880478598993-0.0516250256345-0.4549571279440.577036064589-0.167753328278-0.0902370314906-0.05586152091040.988534809129-0.466562400618-0.2407071591551.00693010188-0.02377255687660.71203257276837.6097813728-103.690231404-26.7270896252
90.796410593690.0307462777245-1.222697663940.8595639697380.6895974622892.52404882957-0.0207729295246-0.4171782215160.1943425310470.403772632891-0.4300242820860.4466996465181.04977291684-0.0382853697093-0.9561774303340.631449369111-0.0766434886331-0.07576417273781.19327554561-0.3726112781540.44006530534542.8820931449-90.8750272041-15.1469012899
100.2353365539910.250949203623-0.01559797051570.2455960941260.006851148711330.002832185706820.08588297383890.5283838348070.425868400189-0.66101912667-0.370977689238-0.1268654405640.19465700648-0.268880593601-2.6165565903E-60.8187289836150.0359737000326-0.08324159982420.849254181202-0.07465027736960.67896809753847.0369670101-96.1854606893-32.9346616975
110.0203201594745-0.03608403265860.01366712166650.0530109718828-0.009537025831920.0277905286248-0.348419090844-0.259394603414-0.03403308814840.2282065305890.535460519937-0.0631463818305-0.148079703481-0.0239949919278-3.10155271472E-50.807100398605-0.12738098192-0.1565592363051.08676803821-0.03018332598260.56712441678536.4778707409-87.810121372-29.4198830546
120.03537718116560.0326639319030.09548973617370.207157106990.0306986791170.1171271977160.210648421875-0.1998988092380.0210200254304-0.961803878633-0.06644452123330.1204926924380.253868057541-0.228172014687-6.77600564689E-70.9265686465230.00813703515103-0.146088151630.911138821935-0.1033735689370.60070292344136.2230051381-95.3597064522-29.8399033451
130.1700534002150.2261318069780.05624173004720.1714636879180.03843133818510.0167262783264-0.4372610652570.3949859857950.0775892430481-0.791465739695-0.1561999901230.423897226386-0.00212628072708-0.156760632166-5.49865691614E-80.738420917459-0.118065211771-0.07132467358060.935579100684-0.1756192262480.58916920836541.7603272076-100.268464345-32.1882691413
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60-0.0037567747925-0.0104409569247-0.01313115685060.01120221178270.01792212061450.0220626217642-0.155733796747-0.264114816683-0.06647143532830.0274619942383-0.1056583693610.08008814108970.12359998541-0.0917093888448-0.06124716360560.8112835323770.727245312377-0.04418969078541.92773062777-0.5925926134351.008171786479.9070711504-50.36972410720.4901618728
610.246787743017-0.001155997399090.1915222468150.493249988784-0.1578467146990.1931934045030.1716287739580.0445031982431-0.223308080440.09290018623690.1428363302490.1848337127390.3027602186750.4497799167420.3097437844690.7678332997530.407478229361-0.2358171222841.70173246295-0.719045372331.1949558210173.493755621-43.831413983327.9985165411
620.01532039691340.0140701970823-0.009233855086640.00942461248416-0.006711352192260.00454057873312-0.257882698963-0.2175286996020.13965928213-0.156926432923-0.121879954597-0.01352358402760.2723331305040.2014347301423.58395662526E-51.832832480840.779695545154-0.123934922172.27947035393-0.2485795731651.044008262583.2962289092-54.501494839528.6162665625
630.175672314065-0.0125637033432-0.8155934724771.167311951890.5872737161154.00629965174-0.0961673912541-0.4812327548140.2770449172090.163352798168-0.3080864107060.3070380884650.6852062170940.640839231475-2.19552702290.7635387994140.118907885764-0.1391251199032.10402326427-1.213973190060.90321129993782.9335312155-38.770913096925.3896661859
640.3413308458680.6739092993620.2403631345971.321705591130.463060185670.513423172736-0.183763337406-0.155349153371-0.2836330582620.330350170349-0.160901404306-0.1035629574390.02399072818630.0960848069446-0.003302517377611.641688611891.12080870318-0.307489177562.60236407459-0.492039068821.847531957393.2954224473-53.364001390325.5684137884
651.30939837475-1.032081980440.03398221574991.24329616406-0.1723298523480.397044862335-0.19970144153-0.5219779375840.5289138449880.0283958440867-0.3168509353090.2245420060120.09315282950630.581694483037-0.9147230202530.08578457689210.415795471775-0.2129757330242.28459549711-0.9853914065311.4172843976681.9083936858-44.647200557712.553583205
660.4800713597780.1528087658620.1304249775290.05500060234680.05313432512640.0536867424312-0.2000383687260.05360357853530.1728267801330.0904509331249-0.02824587094950.3120143644870.126367074564-0.0148790255035-0.1100804010311.236657159580.711941812295-0.2790701314342.12067559677-0.7473655560981.4462879131596.2241014614-50.052533362517.887840696
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 138 )
3X-RAY DIFFRACTION3chain 'A' and (resid 139 through 182 )
4X-RAY DIFFRACTION4chain 'A' and (resid 183 through 216 )
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 358 )
6X-RAY DIFFRACTION6chain 'A' and (resid 359 through 438 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'C' and (resid 17 through 23 )
9X-RAY DIFFRACTION9chain 'C' and (resid 24 through 31 )
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 51 )
11X-RAY DIFFRACTION11chain 'C' and (resid 52 through 59 )
12X-RAY DIFFRACTION12chain 'C' and (resid 60 through 76 )
13X-RAY DIFFRACTION13chain 'C' and (resid 77 through 99 )
14X-RAY DIFFRACTION14chain 'C' and (resid 100 through 116 )
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 53 )
16X-RAY DIFFRACTION16chain 'D' and (resid 54 through 100 )
17X-RAY DIFFRACTION17chain 'D' and (resid 101 through 138 )
18X-RAY DIFFRACTION18chain 'D' and (resid 139 through 182 )
19X-RAY DIFFRACTION19chain 'D' and (resid 183 through 256 )
20X-RAY DIFFRACTION20chain 'D' and (resid 257 through 298 )
21X-RAY DIFFRACTION21chain 'D' and (resid 299 through 390 )
22X-RAY DIFFRACTION22chain 'D' and (resid 391 through 438 )
23X-RAY DIFFRACTION23chain 'E' and (resid 1 through 39 )
24X-RAY DIFFRACTION24chain 'E' and (resid 40 through 51 )
25X-RAY DIFFRACTION25chain 'E' and (resid 52 through 61 )
26X-RAY DIFFRACTION26chain 'E' and (resid 62 through 73 )
27X-RAY DIFFRACTION27chain 'E' and (resid 74 through 91 )
28X-RAY DIFFRACTION28chain 'E' and (resid 92 through 113 )
29X-RAY DIFFRACTION29chain 'E' and (resid 114 through 130 )
30X-RAY DIFFRACTION30chain 'G' and (resid 1 through 7 )
31X-RAY DIFFRACTION31chain 'G' and (resid 8 through 24 )
32X-RAY DIFFRACTION32chain 'G' and (resid 25 through 32 )
33X-RAY DIFFRACTION33chain 'G' and (resid 33 through 52 )
34X-RAY DIFFRACTION34chain 'G' and (resid 53 through 66 )
35X-RAY DIFFRACTION35chain 'G' and (resid 67 through 76 )
36X-RAY DIFFRACTION36chain 'G' and (resid 77 through 96 )
37X-RAY DIFFRACTION37chain 'G' and (resid 97 through 110 )
38X-RAY DIFFRACTION38chain 'F' and (resid 3 through 16 )
39X-RAY DIFFRACTION39chain 'F' and (resid 17 through 23 )
40X-RAY DIFFRACTION40chain 'F' and (resid 24 through 31 )
41X-RAY DIFFRACTION41chain 'F' and (resid 32 through 39 )
42X-RAY DIFFRACTION42chain 'F' and (resid 40 through 51 )
43X-RAY DIFFRACTION43chain 'F' and (resid 52 through 59 )
44X-RAY DIFFRACTION44chain 'F' and (resid 60 through 66 )
45X-RAY DIFFRACTION45chain 'F' and (resid 67 through 76 )
46X-RAY DIFFRACTION46chain 'F' and (resid 77 through 83 )
47X-RAY DIFFRACTION47chain 'F' and (resid 84 through 90 )
48X-RAY DIFFRACTION48chain 'F' and (resid 91 through 99 )
49X-RAY DIFFRACTION49chain 'F' and (resid 100 through 110 )
50X-RAY DIFFRACTION50chain 'F' and (resid 111 through 115 )
51X-RAY DIFFRACTION51chain 'B' and (resid 0 through 7 )
52X-RAY DIFFRACTION52chain 'B' and (resid 8 through 51 )
53X-RAY DIFFRACTION53chain 'B' and (resid 52 through 60 )
54X-RAY DIFFRACTION54chain 'B' and (resid 61 through 73 )
55X-RAY DIFFRACTION55chain 'B' and (resid 74 through 83 )
56X-RAY DIFFRACTION56chain 'B' and (resid 84 through 110 )
57X-RAY DIFFRACTION57chain 'B' and (resid 111 through 128 )
58X-RAY DIFFRACTION58chain 'H' and (resid 2 through 17 )
59X-RAY DIFFRACTION59chain 'H' and (resid 18 through 39 )
60X-RAY DIFFRACTION60chain 'H' and (resid 40 through 52 )
61X-RAY DIFFRACTION61chain 'H' and (resid 53 through 59 )
62X-RAY DIFFRACTION62chain 'H' and (resid 60 through 66 )
63X-RAY DIFFRACTION63chain 'H' and (resid 67 through 82 )
64X-RAY DIFFRACTION64chain 'H' and (resid 83 through 90 )
65X-RAY DIFFRACTION65chain 'H' and (resid 91 through 104 )
66X-RAY DIFFRACTION66chain 'H' and (resid 105 through 110 )

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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