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- PDB-6sb4: Crystal structure of murine perforin-2 P2 domain crystal form 2 -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6sb4
タイトルCrystal structure of murine perforin-2 P2 domain crystal form 2
要素Macrophage-expressed gene 1 protein
キーワードTOXIN / pore-forming protein / P2 domain / membrane binding / beta-hairpin
機能・相同性
機能・相同性情報


dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane ...dendritic cell antigen processing and presentation / antigen processing and presentation of exogenous peptide antigen / phagolysosome membrane / endolysosome / pore-forming activity / antibacterial innate immune response / wide pore channel activity / antigen processing and presentation of exogenous peptide antigen via MHC class I / phagocytic vesicle / phagocytic vesicle membrane / cytoplasmic vesicle / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium
類似検索 - 分子機能
Macrophage-expressed gene 1 protein / membrane-attack complex / perforin / MAC/Perforin domain / Membrane attack complex/perforin (MACPF) domain profile. / Membrane attack complex component/perforin (MACPF) domain
類似検索 - ドメイン・相同性
Macrophage-expressed gene 1 protein
類似検索 - 構成要素
生物種Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.17 Å
データ登録者Ni, T. / Yu, X. / Ginger, L. / Gilbert, R.J.C.
資金援助 英国, 1件
組織認可番号国
Medical Research Council (United Kingdom)MR/N000331/1 英国
引用ジャーナル: Sci Adv / 年: 2020
タイトル: Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity.
著者: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor ...著者: Tao Ni / Fang Jiao / Xiulian Yu / Saša Aden / Lucy Ginger / Sophie I Williams / Fangfang Bai / Vojtěch Pražák / Dimple Karia / Phillip Stansfeld / Peijun Zhang / George Munson / Gregor Anderluh / Simon Scheuring / Robert J C Gilbert /
要旨: Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual ...Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins.
履歴
登録2019年7月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年2月5日Provider: repository / タイプ: Initial release
改定 1.12020年2月26日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22024年11月13日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Macrophage-expressed gene 1 protein
B: Macrophage-expressed gene 1 protein
C: Macrophage-expressed gene 1 protein
D: Macrophage-expressed gene 1 protein
E: Macrophage-expressed gene 1 protein
F: Macrophage-expressed gene 1 protein
G: Macrophage-expressed gene 1 protein
H: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)258,3658
ポリマ－258,3658
非ポリマー00
水00
1
A: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
8
H: Macrophage-expressed gene 1 protein


分子量 (理論値)分子数
合計 (水以外)32,2961
ポリマ－32,2961
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)70.230, 70.050, 128.140
Angle α, β, γ (deg.)78.500, 79.050, 85.010
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
11
21
31
41
51
61
71
81

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))AA377 - 46432 - 119
12GLYGLYVALVAL(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))AA473 - 538128 - 193
13SERSERILEILE(chain 'A' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))AA550 - 579205 - 234
24THRTHRALAALA(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))BB377 - 46432 - 119
25GLYGLYVALVAL(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))BB473 - 538128 - 193
26SERSERILEILE(chain 'B' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))BB550 - 579205 - 234
37THRTHRALAALA(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))CC377 - 46432 - 119
38GLYGLYVALVAL(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))CC473 - 538128 - 193
39SERSERILEILE(chain 'C' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))CC550 - 579205 - 234
410THRTHRALAALA(chain 'D' and (resid 377 through 465 or resid 473 through 580))DD377 - 46432 - 119
411GLYGLYVALVAL(chain 'D' and (resid 377 through 465 or resid 473 through 580))DD473 - 538128 - 193
412SERSERILEILE(chain 'D' and (resid 377 through 465 or resid 473 through 580))DD550 - 579205 - 234
513THRTHRALAALA(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))EE377 - 46432 - 119
514GLYGLYVALVAL(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))EE473 - 538128 - 193
515SERSERILEILE(chain 'E' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))EE550 - 579205 - 234
616THRTHRALAALA(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))FF377 - 46432 - 119
617GLYGLYVALVAL(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))FF473 - 538128 - 193
618SERSERILEILE(chain 'F' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))FF550 - 579205 - 234
719THRTHRALAALA(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))GG377 - 46432 - 119
720GLYGLYVALVAL(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))GG473 - 538128 - 193
721SERSERILEILE(chain 'G' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))GG550 - 579205 - 234
822THRTHRALAALA(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))HH377 - 46432 - 119
823GLYGLYVALVAL(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))HH473 - 538128 - 193
824SERSERILEILE(chain 'H' and (resid 377 through 465 or resid 473 through 539 or resid 550 through 580))HH550 - 579205 - 234

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要素

#1: タンパク質
Macrophage-expressed gene 1 protein / Mpg-1 / Perforin-2 / P-2 / Protein MPS1


分子量: 32295.625 Da / 分子数: 8 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Mpeg1 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: A1L314
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: 3.53 Å3/Da / 溶媒含有率: 65.18 %
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: 0.1M MES pH6.0 10% PEG6000, 40mM potassium sodium tartrate

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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: Diamond / ビームライン: I24 / 波長: 0.9686 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2017年3月14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: 0.9686 Å / 相対比: 1
反射解像度: 3.17→56.09 Å / Num. obs: 37940 / % possible obs: 95.3 % / 冗長度: 10.7 % / Biso Wilson estimate: 73.77 Å2 / Net I/σ(I): 10.41
反射 シェル解像度: 3.17→3.28 Å / Num. unique obs: 2362

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解析

ソフトウェア
名称バージョン分類
PHENIXdev_3488精密化
PHENIXdev_3488精密化
xia2データ削減
xia2データスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 3.17→56.09 Å / SU ML: 0.3529 / 交差検証法: FREE R-VALUE / σ(F): 1.97 / 位相誤差: 24.2192
Rfactor反射数%反射
Rfree0.2246 1975 5.21 %
Rwork0.1887 --
obs0.1906 37940 95.32 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 90.03 Å2
精密化ステップサイクル: LAST / 解像度: 3.17→56.09 Å
タンパク質核酸リガンド溶媒全体
原子数11992 0 0 0 11992
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002912282
X-RAY DIFFRACTIONf_angle_d0.763516606
X-RAY DIFFRACTIONf_chiral_restr0.04811824
X-RAY DIFFRACTIONf_plane_restr0.00532138
X-RAY DIFFRACTIONf_dihedral_angle_d3.16557225
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.17-3.250.2923860.28021595X-RAY DIFFRACTION59.69
3.25-3.340.30861260.27642064X-RAY DIFFRACTION76.02
3.34-3.440.29421320.2392669X-RAY DIFFRACTION99.79
3.44-3.550.30641470.23482707X-RAY DIFFRACTION99.89
3.55-3.670.23931520.21822712X-RAY DIFFRACTION99.97
3.67-3.820.25111290.20192684X-RAY DIFFRACTION100
3.82-3.990.22491490.18942698X-RAY DIFFRACTION99.93
3.99-4.20.20821560.1872667X-RAY DIFFRACTION99.89
4.2-4.470.21931620.16582700X-RAY DIFFRACTION99.86
4.47-4.810.16481490.14382669X-RAY DIFFRACTION100
4.81-5.30.19531710.1582697X-RAY DIFFRACTION100
5.3-6.060.23221300.18162720X-RAY DIFFRACTION100
6.06-7.630.20491330.19262706X-RAY DIFFRACTION100
7.63-56.090.22421530.17992677X-RAY DIFFRACTION99.4
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)
13.53859653787-5.03557741171.997884659136.78027737502-2.225004600951.988436795030.4737993787090.206788007594-0.741280431632-0.177760503241-0.4107390172270.7781949192510.5887715398130.414273423367-0.1229524267920.6359812419310.01417445682170.03213713190290.536585873913-0.03839058170030.60603083913989.891387670342.294132243-17.2333636738
27.78479080323-0.4386476242510.08223443305794.49125812872-0.2819651146339.312976403910.1310652571940.2152201268570.102318817773-0.00595490580286-0.3800599764510.516269053192-0.652894822006-1.133918221510.2755707551480.4301778824870.1463621123820.03642035136260.437279916444-0.03216298051370.43960999826473.470898207662.2648870262-17.2274331397
39.07807119327-0.390468755001-1.16000207422.260558932074.47701851988.857481514820.4248047438660.6105552677610.5363959976070.206337499159-0.497708282387-0.0493028362515-0.440927864396-0.526504328978-0.04263949515620.5524754000950.0306810331527-0.01626269956970.4117706993470.1616862843610.42679310946598.655290927364.4473879008-8.42177740728
46.94845294461-2.675411853230.1996918492330.9851849314470.2039415934610.779024967465-0.256054958698-0.8245115251321.6356739755-1.012613850830.719090101346-1.03566666765-0.724898630732-0.0719897154307-0.3057960793460.99131555356-0.1258908372910.06409341170080.633871685521-0.0469126492240.75446364222994.938989506176.6116441226-1.15165405088
55.39358909931-1.334552624090.3544484039611.76801723041-2.144465480643.48090221425-0.02862782009080.2349234081220.4612816726040.0359506778072-0.0362674252009-0.245406666753-0.2935349505020.5664465492080.2607374123540.460824417533-0.03196574418760.03375032487820.4837079962910.001658649762990.381009835111104.27916728870.989192855-5.78435554561
67.4704146268-2.12866433642-0.01219164203754.732867379390.8506664817459.123249691680.0823239416017-0.0153814606917-0.835192641940.1125805975710.142929151861-0.3200488293681.129472691580.883138625878-0.08492866943430.633486707020.230693842245-0.07125804959920.522911440414-0.0730271141120.509845357886111.54539936453.9342568721-0.586997295992
78.696664588930.04299901712711.070519084243.066486509541.370779506036.640606507570.0714095688239-0.7421374830710.06753089316460.1871619268590.537982811940.2577088169910.774554403408-0.332771556464-0.6466197848060.5872619174540.03689643499420.0879511779090.4929566255170.2165746194220.478449551526105.18141313763.232202274124.2416938024
86.12170070601-0.06059710276643.277020861396.37692094781-1.467805167792.166270236451.148653786361.097426465030.953456907162-2.04643906787-0.6069283206570.513773838805-0.251081928649-1.36607080772-0.6635241961770.9329604341290.4125287719720.003295628226261.14842033190.2970905986590.89225063409698.594818732579.007395225823.3201318848
96.613488319621.66371328869-1.012634540175.332763377412.13709805196.07728741194-0.45502831720.628411985771-0.448528939221-0.03206627903490.2497451248460.0195337155310.342165124733-0.2836743591690.1703808115520.6112570663580.1399375388180.04126794980750.738429687236-0.06759880961930.468036705583102.9310065261.227358230117.9506576087
105.5703119652-6.18602540857-1.111105299987.95047758746-0.1019975571261.547847604790.26522150874-0.06467991700881.02131704474-0.8232706781510.187961433763-0.559967920722-0.623389960056-0.255684904719-0.3993527692070.8241037040550.05231515069510.02431473739710.5739230728690.03514742235990.66236701000496.286823219785.089146895726.9721377378
117.520132417882.676185715210.5782875185986.74509827934-0.07344948468459.2419890963-0.246979697760.232683410062-0.13024152787-0.0562483513530.305903696059-0.4348574641380.2214117660561.53242432941-0.06281297911550.4140233260250.1599100010970.1088028554070.6926947454670.08178882566790.36174471773117.4518533164.880402066421.0320740032
124.20414392859-0.337770712389-0.1747978553572.476805330323.138570313467.005686318210.301046333292-0.0977299719991-0.5966192991230.505619765659-0.150113834336-0.4877701283981.2698611871.19355861873-0.06594052765480.6263233206470.3238894952770.005967599707830.5820418406380.04299249576130.572932947861117.48217550158.74543412129.2473229517
134.1687428153-1.35241654713-1.413962589244.741057636371.844150970294.051109795730.2064639823520.4884671643670.8729545291440.581559050631-0.406110871260.0206258975868-0.5246817912920.1726943500960.2595143136140.606163035292-0.0403151415534-0.01425585997610.3642561636030.09789132106340.594469532574110.74628005182.299891969950.0652314503
146.66154584185-5.356514352220.8112248468129.33624961822-0.9764920064852.652230154470.344869161324-0.02635089088911.71768124148-0.513938438092-0.382264594632-0.567436995152-0.45640357621-0.712420556641-0.05738651593260.9307556936180.0153202272011-0.02851402393540.6284611027930.01523056742121.12091392204103.034721823100.19091370652.1828344827
158.22090146367-1.27296864809-0.9523026519067.595045224312.894546622783.997550675380.1449941060140.1266337555190.2906612612950.7380199453440.136758542037-1.391738835040.5767993973371.38234842225-0.2337664249570.5293902870630.0773216786386-0.1693335987070.706279215463-0.05655876855530.804494316873126.68036055571.994283568450.5889621026
166.782701403894.26057754317-2.844697449272.73058369232-1.749265201951.400984479920.461567721682-0.647146403142-0.560766165329-0.09832447707180.190125300893-0.1887063116840.1699356285110.947068644444-0.5670601720430.8422467134370.0144901814404-0.3860854431650.760235721488-0.02681218540050.812990590411131.07726841276.129355171456.9140392427
178.6089428173-1.403706189611.399364286050.225578117107-0.3379984470949.81404270869-0.1369042497830.0140055633323-0.309452256089-0.3747928991960.145259845467-0.3549566970790.6168885189970.4404724583620.00996857370170.636748516322-0.0860538488960.1029402929490.315514762309-0.0850908819030.591892485709105.08173347973.102223231569.8985977035
185.76301914069-5.016443181092.290213423757.22869703827-2.766127516171.7978859466-0.109455062593-0.830767617315-1.048477561560.2692595134930.2792781189130.4317994367710.352331008958-0.0578937069475-0.2425431951690.931694401-0.0748261382690.07831510013190.6379600698290.2123366754550.773448574764114.87369608357.415315767483.3261146425
196.880693685011.010698878021.530199416333.496077094551.322521833145.68864101934-0.306309094308-0.454659732080.6988813801860.0939394346086-0.14803536650.367672142203-0.910692806523-1.184554878120.432238904860.5919940424750.103845084214-0.008797133651530.524097623677-0.07434267220370.45837299639294.293057775182.63108505976.5794777318
208.55251967852-4.971434755921.320742193475.061975068610.3367012033473.775378144240.5648408230010.636563103839-1.13024374825-0.904019809324-0.3691309576780.06622875329091.02796521395-0.382552488442-0.2435879782161.1538559639-0.2464009663050.1017611167550.505230423791-0.2049361255060.82295539376195.468905697860.076525101444.7395999234
212.72258493817-3.132259954440.8591667078889.308701729480.07006258162350.09070368852980.145913128028-0.0912214446798-0.3238878094940.5856531914040.0909547561509-0.707665005430.3249033699250.18479962539-0.2478082493960.980985778876-0.1308763413460.07268213082060.662403304858-0.1039102352240.822260156057106.17847580247.846833208854.4157738005
225.9830322783-0.407037002203-0.9466530139688.68699080123-2.099823237713.793013238240.0005484720979030.0125215205409-0.535065321198-0.711086086988-0.03291003115031.236278740991.31649529858-1.311537303130.02835189774430.667762604307-0.3220274202180.07315320065731.04404434304-0.2290056624380.63142787536383.168069346565.763813789851.1701180554
237.60944430117-0.9224166202322.582302855236.66726716335-0.5730695767488.2826355768-0.2569598830690.1985556233210.0849998204957-0.403253577380.03892046484110.407900689242-0.481790374491-1.190363332130.2691027120210.554653196452-0.009803303814980.08928259569310.683738895637-0.1218916485170.38027490190887.086747044575.414203043850.635147098
244.93839089291-0.906713024941.024054269658.1921616384-5.531400155574.496687867460.06424632014830.43913719832-1.083788863750.220478548823-0.3305039023260.168711876151.116287153051.055760664130.201730170590.8533476105940.1979390169710.09690989922160.479631598963-0.09629419160460.63403340895986.210422651751.31165364425.66596835074
252.92774548282-5.175426090710.2227008785897.34174310762-0.4464647757661.06121066749-0.456744630651-0.192995795675-0.7628363676781.119557511790.5436578489520.423978892780.5445658674040.08016674088510.03224808246351.177083196330.1133268315170.05940290927330.5692559887560.08758733831680.89453153834591.596290402632.926824362513.3178066797
268.24987819665-1.542382618111.961444420793.542356921160.2751028066088.77477863846-0.441240494416-0.669823493313-0.3498865231290.8561296243340.2163255236720.606445506192-0.562474584563-0.7998951906070.2347910097190.6862020316460.1998004403150.310359100990.5314047271480.070845696990.68004049291972.638130821558.92008857711.2879489992
275.128060677850.2452497146571.555112639179.34662859032-1.900668787199.75367246910.144412168654-0.6272450276510.498756065778-0.799138555594-0.1130392189530.004604972610610.434927320368-1.56711596895-0.1747930569050.761861311280.2519544504420.2140150692861.087914486030.1665308434830.5873433179869.9761545757.511491695919.6736481155
288.33649381455-3.92088075046-0.2873320564062.573702842841.546220948065.468471418510.6824924462062.636905954980.887907834311-1.2564223374-0.6786834147610.329392777912-0.6826599769820.03926432155160.11144033120.799867224708-0.0326401565797-0.03194508889661.152481536190.3468949597230.7057004653298.664242348368.6763844593-38.7248963918
294.13358647136-4.91347462113-1.221081570299.376973573941.610192692480.7959394746910.0235469247633-0.002415150771010.88445581290.215776361302-0.0947746115579-0.520948311284-0.3412080462590.1364338455490.06622235216640.713900101997-0.171418738306-0.02932722296060.696832306339-0.04754240661170.69820203540591.815065875384.0749684913-26.7842174467
301.73844444227-1.095504141062.526394109350.685190022147-1.585384561673.670318497310.5503299596791.10835258517-2.03469230319-1.190845798190.570180550156-1.224180205550.00871734380278-0.530839554938-0.1685806044840.661066115728-0.105272916090.2684109993891.82267792326-0.6950629633541.38833171892107.18832199951.0377547621-46.8840439116
317.00281497097-1.53288269016-1.449170322656.293720274330.3096567267866.39624565442-0.2523239604551.308658141310.169415289566-0.4920507619130.192846674391-0.8880378235060.4262925178271.212703254510.1077255716750.4609049817260.06076319587620.01679738249451.23254317223-0.09507734522870.561097280792111.92369632260.0754390678-32.1019735091
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 377 through 463 )
2X-RAY DIFFRACTION2chain 'A' and (resid 464 through 581 )
3X-RAY DIFFRACTION3chain 'B' and (resid 376 through 412 )
4X-RAY DIFFRACTION4chain 'B' and (resid 413 through 435 )
5X-RAY DIFFRACTION5chain 'B' and (resid 436 through 511 )
6X-RAY DIFFRACTION6chain 'B' and (resid 512 through 579 )
7X-RAY DIFFRACTION7chain 'C' and (resid 376 through 387 )
8X-RAY DIFFRACTION8chain 'C' and (resid 388 through 397 )
9X-RAY DIFFRACTION9chain 'C' and (resid 398 through 412 )
10X-RAY DIFFRACTION10chain 'C' and (resid 413 through 464 )
11X-RAY DIFFRACTION11chain 'C' and (resid 465 through 511 )
12X-RAY DIFFRACTION12chain 'C' and (resid 512 through 579 )
13X-RAY DIFFRACTION13chain 'D' and (resid 376 through 434 )
14X-RAY DIFFRACTION14chain 'D' and (resid 435 through 464 )
15X-RAY DIFFRACTION15chain 'D' and (resid 465 through 566 )
16X-RAY DIFFRACTION16chain 'D' and (resid 567 through 580 )
17X-RAY DIFFRACTION17chain 'E' and (resid 376 through 413 )
18X-RAY DIFFRACTION18chain 'E' and (resid 414 through 463 )
19X-RAY DIFFRACTION19chain 'E' and (resid 464 through 579 )
20X-RAY DIFFRACTION20chain 'F' and (resid 376 through 412 )
21X-RAY DIFFRACTION21chain 'F' and (resid 413 through 464 )
22X-RAY DIFFRACTION22chain 'F' and (resid 465 through 511 )
23X-RAY DIFFRACTION23chain 'F' and (resid 512 through 579 )
24X-RAY DIFFRACTION24chain 'G' and (resid 377 through 412 )
25X-RAY DIFFRACTION25chain 'G' and (resid 413 through 464 )
26X-RAY DIFFRACTION26chain 'G' and (resid 465 through 566 )
27X-RAY DIFFRACTION27chain 'G' and (resid 567 through 581 )
28X-RAY DIFFRACTION28chain 'H' and (resid 377 through 412 )
29X-RAY DIFFRACTION29chain 'H' and (resid 413 through 464 )
30X-RAY DIFFRACTION30chain 'H' and (resid 465 through 474 )
31X-RAY DIFFRACTION31chain 'H' and (resid 475 through 579 )

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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