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- PDB-6vme: Human ESCRT-I heterotetramer headpiece -

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基本情報

登録情報
データベース: PDB / ID: 6vme
タイトルHuman ESCRT-I heterotetramer headpiece
要素
  • Multivesicular body subunit 12Aエンドソーム
  • Tumor susceptibility gene 101 proteinTSG101
  • Vacuolar protein sorting-associated protein 28 homolog液胞
  • Vacuolar protein sorting-associated protein 37B液胞
キーワードPROTEIN TRANSPORT / Endosomal transport / HIV release / macroautophagy (オートファジー)
機能・相同性
機能・相同性情報


virus maturation / : / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / regulation of epidermal growth factor receptor signaling pathway / intracellular transport of virus / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly ...virus maturation / : / positive regulation of viral budding via host ESCRT complex / positive regulation of ubiquitin-dependent endocytosis / extracellular transport / regulation of epidermal growth factor receptor signaling pathway / intracellular transport of virus / ESCRT I complex / negative regulation of epidermal growth factor-activated receptor activity / regulation of extracellular exosome assembly / ウイルス排出 / regulation of MAP kinase activity / exosomal secretion / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / receptor catabolic process / protein targeting to vacuole / membrane fission / positive regulation of exosomal secretion / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / endosome to lysosome transport via multivesicular body sorting pathway / multivesicular body assembly / 宿主 / Flemming body / protein targeting to membrane / virion binding / endosomal transport / endosome to lysosome transport / negative regulation of epidermal growth factor receptor signaling pathway / viral budding via host ESCRT complex / autophagosome maturation / viral release from host cell / keratinocyte differentiation / negative regulation of protein ubiquitination / ウイルスのライフサイクル / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / エンドソーム / HCMV Late Events / ubiquitin binding / regulation of cell growth / オートファジー / Late endosomal microautophagy / protein modification process / Budding and maturation of HIV virion / SH3 domain binding / calcium-dependent protein binding / positive regulation of protein catabolic process / transcription corepressor activity / late endosome / protein transport / late endosome membrane / midbody / early endosome membrane / vesicle / エンドソーム / endosome membrane / regulation of cell cycle / エンドソーム / 細胞周期 / 細胞分裂 / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / 中心体 / lipid binding / ubiquitin protein ligase binding / protein-containing complex binding / 核小体 / ゴルジ体 / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / extracellular exosome / 核質 / 細胞膜 / 細胞質基質 / 細胞質
類似検索 - 分子機能
Multivesicular body subunit 12A / Multivesicular body subunit 12 / Multivesicular body subunit 12 / Helix Hairpins - #820 / Modifier of rudimentary, Modr / UMA domain / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / UMA domain profile. / MABP domain ...Multivesicular body subunit 12A / Multivesicular body subunit 12 / Multivesicular body subunit 12 / Helix Hairpins - #820 / Modifier of rudimentary, Modr / UMA domain / Modifier of rudimentary (Mod(r)) protein / VPS37 C-terminal domain profile. / UMA domain profile. / MABP domain / MABP domain profile. / Vacuolar protein sorting-associated Vps28 / Vacuolar protein sorting-associated, VPS28, N-terminal / Vacuolar protein sorting-associated, VPS28, C-terminal / VPS28, C-terminal domain superfamily / VPS28, N-terminal domain superfamily / VPS28 protein / VPS28 C-terminal domain profile. / VPS28 N-terminal domain profile. / Steadiness box (SB) domain / Vps23 core domain / Steadiness box (SB) domain profile. / Ubiquitin E2 variant, N-terminal / UEV domain / UEV domain profile. / ESCRT assembly domain / Helix hairpin bin domain superfamily / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Helix Hairpins / Ubiquitin-conjugating enzyme/RWD-like / Helix non-globular / Special
類似検索 - ドメイン・相同性
Multivesicular body subunit 12A / Tumor susceptibility gene 101 protein / Vacuolar protein sorting-associated protein 37B / Vacuolar protein sorting-associated protein 28 homolog
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.19 Å
データ登録者Flower, T.G. / Hurley, J.H. / Tjahjono, N.
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)R37 AI112442 米国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2020
タイトル: A helical assembly of human ESCRT-I scaffolds reverse-topology membrane scission.
著者: Flower, T.G. / Takahashi, Y. / Hudait, A. / Rose, K. / Tjahjono, N. / Pak, A.J. / Yokom, A.L. / Liang, X. / Wang, H.G. / Bouamr, F. / Voth, G.A. / Hurley, J.H.
履歴
登録2020年1月27日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年5月20日Provider: repository / タイプ: Initial release
改定 1.12020年6月3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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22020年6月24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_author.identifier_ORCID
改定 1.32023年10月11日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
B: Tumor susceptibility gene 101 protein
C: Vacuolar protein sorting-associated protein 37B
D: Multivesicular body subunit 12A
E: Vacuolar protein sorting-associated protein 28 homolog
F: Tumor susceptibility gene 101 protein
G: Tumor susceptibility gene 101 protein
H: Tumor susceptibility gene 101 protein
I: Tumor susceptibility gene 101 protein
J: Tumor susceptibility gene 101 protein
K: Vacuolar protein sorting-associated protein 37B
L: Vacuolar protein sorting-associated protein 37B
M: Vacuolar protein sorting-associated protein 37B
N: Vacuolar protein sorting-associated protein 37B
O: Vacuolar protein sorting-associated protein 37B
P: Multivesicular body subunit 12A
Q: Multivesicular body subunit 12A
R: Multivesicular body subunit 12A
A: Multivesicular body subunit 12A
T: Multivesicular body subunit 12A
U: Vacuolar protein sorting-associated protein 28 homolog
V: Vacuolar protein sorting-associated protein 28 homolog
W: Vacuolar protein sorting-associated protein 28 homolog
X: Vacuolar protein sorting-associated protein 28 homolog
Y: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)204,22224
ポリマ－204,22224
非ポリマー00
水5,549308
1
B: Tumor susceptibility gene 101 protein
C: Vacuolar protein sorting-associated protein 37B
D: Multivesicular body subunit 12A
E: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint-52 kcal/mol
Surface area13360 Å2
手法PISA
2
F: Tumor susceptibility gene 101 protein
K: Vacuolar protein sorting-associated protein 37B
P: Multivesicular body subunit 12A
U: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-53 kcal/mol
Surface area13430 Å2
手法PISA
3
G: Tumor susceptibility gene 101 protein
L: Vacuolar protein sorting-associated protein 37B
Q: Multivesicular body subunit 12A
V: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-51 kcal/mol
Surface area13050 Å2
手法PISA
4
H: Tumor susceptibility gene 101 protein
M: Vacuolar protein sorting-associated protein 37B
R: Multivesicular body subunit 12A
W: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-56 kcal/mol
Surface area13510 Å2
手法PISA
5
I: Tumor susceptibility gene 101 protein
N: Vacuolar protein sorting-associated protein 37B
A: Multivesicular body subunit 12A
X: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-52 kcal/mol
Surface area13240 Å2
手法PISA
6
J: Tumor susceptibility gene 101 protein
O: Vacuolar protein sorting-associated protein 37B
T: Multivesicular body subunit 12A
Y: Vacuolar protein sorting-associated protein 28 homolog


分子量 (理論値)分子数
合計 (水以外)34,0374
ポリマ－34,0374
非ポリマー00
水543
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-53 kcal/mol
Surface area12660 Å2
手法PISA
単位格子
Length a, b, c (Å)162.584, 162.584, 139.715
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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要素

#1: タンパク質
Tumor susceptibility gene 101 protein / TSG101 / ESCRT-I complex subunit TSG101


分子量: 9343.720 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TSG101 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q99816
#2: タンパク質
Vacuolar protein sorting-associated protein 37B / 液胞 / hVps37B / ESCRT-I complex subunit VPS37B


分子量: 8061.243 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VPS37B / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q9H9H4
#3: タンパク質・ペプチド
Multivesicular body subunit 12A / エンドソーム / CIN85/CD2AP family-binding protein / ESCRT-I complex subunit MVB12A / Protein FAM125A


分子量: 2655.937 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MVB12A, CFBP, FAM125A / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q96EY5
#4: タンパク質
Vacuolar protein sorting-associated protein 28 homolog / 液胞 / H-Vps28 / ESCRT-I complex subunit VPS28


分子量: 13976.124 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VPS28 / 発現宿主: Escherichia coli BL21 (大腸菌) / 参照: UniProt: Q9UK41
#5: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 308 / 由来タイプ: 天然 / 式: H2O

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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: 2.61 Å3/Da / 溶媒含有率: 52.88 %
結晶化温度: 291.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5
詳細: 2 % w/v gamma-Polyglutamic acid (gamma-PGA), 100 mM sodium formate, 100 mM sodium acetate pH 5.0

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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: 1.11583 Å
検出器タイプ: DECTRIS PILATUS3 S 6M / 検出器: PIXEL / 日付: 2018年10月1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: 1.11583 Å / 相対比: 1
反射解像度: 2.19→99.18 Å / Num. obs: 107460 / % possible obs: 99.46 % / 冗長度: 20 % / Biso Wilson estimate: 48.48 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.04189 / Net I/σ(I): 17.22
反射 シェル解像度: 2.19→2.269 Å / Num. unique obs: 10167 / CC1/2: 0.281 / % possible all: 95.09

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解析

ソフトウェア
名称バージョン分類
Blu-Iceデータ収集
PHENIX1.17_3644精密化
XDSデータ削減
PHASER位相決定
Aimlessデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 2F66

2f66


解像度: 2.19→99.18 Å / SU ML: 0.2757 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.3667
Rfactor反射数%反射
Rfree0.2396 1998 1.87 %
Rwork0.1934 --
obs0.1943 106911 99.17 %
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: 61.12 Å2
精密化ステップサイクル: LAST / 解像度: 2.19→99.18 Å
タンパク質核酸リガンド溶媒全体
原子数12478 0 0 308 12786
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00812642
X-RAY DIFFRACTIONf_angle_d0.885116991
X-RAY DIFFRACTIONf_chiral_restr0.04511955
X-RAY DIFFRACTIONf_plane_restr0.00562165
X-RAY DIFFRACTIONf_dihedral_angle_d9.89821716
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.240.34361300.29866728X-RAY DIFFRACTION89.47
2.24-2.30.3121390.28257477X-RAY DIFFRACTION99.36
2.3-2.370.33121390.27367516X-RAY DIFFRACTION99.84
2.37-2.450.31621470.25487548X-RAY DIFFRACTION99.94
2.45-2.540.29661400.24137536X-RAY DIFFRACTION99.97
2.54-2.640.29691440.22797520X-RAY DIFFRACTION99.96
2.64-2.760.27531460.21227584X-RAY DIFFRACTION99.96
2.76-2.90.25031430.20027538X-RAY DIFFRACTION100
2.9-3.080.26261380.18777515X-RAY DIFFRACTION100
3.08-3.320.25091430.1897553X-RAY DIFFRACTION99.97
3.32-3.660.22181440.16597563X-RAY DIFFRACTION99.97
3.66-4.190.21621470.16477581X-RAY DIFFRACTION99.97
4.19-5.270.19081460.16577580X-RAY DIFFRACTION99.99
5.27-99.180.23721520.20267674X-RAY DIFFRACTION99.91
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.471015818462-0.1332788381050.9426419775930.07687034464070.2075949116190.147959396135-0.181564173603-0.2084759015450.0470232648188-0.01852461175460.1296836396870.207692788528-0.0561068349767-0.213311344629.1658517776E-50.426404892817-0.0532722653796-0.01900014205830.3846933935160.006516678134080.38100618821333.8750775394-35.211458904424.1693073293
20.3520455701620.106938284210.4742312168430.924354220561-0.1417093719430.609302821244-0.257153975993-0.5909008328860.603609123053-0.05599066730630.04524596426430.216167634065-0.1177408660340.01887434938060.0002389508477610.441945825251-0.0268454805122-0.04736533997810.3761403967350.03072420429030.47319991977924.6384643109-29.012752981222.1049242688
30.04610996433350.00473943962581-0.1476893096150.331478803132-0.1563006469190.364449438148-0.30467389407-0.1383241356070.0170391508654-0.8642489474970.335070850287-0.27473815129-0.1488091985830.161775154138-0.0004830015486250.480548059634-0.06821203506950.04328966825290.4755296893590.03804427646840.45819744819341.8727322969-34.09063707114.5883616822
40.2754293949880.1020282402770.06829084363220.03955156805740.07298899288030.09169685358810.8860873744971.17458837096-1.574322049450.328924114584-0.3816022195540.4386439206970.8695775569650.0447319014139-0.008729391026370.529998113046-0.0355959241184-0.04812273235480.550681016056-0.04720015229920.56564706404435.723911424-42.197142769117.002866882
50.277403066079-0.1751783752620.02033866964510.11236542761-0.0176864912922-0.0468117002813-0.06770535949540.198456043538-0.06871899012670.113824350547-0.1932397175440.6456517977370.02928760939450.3444730927730.0006136089374820.537293551087-0.0360325316867-0.09991123041980.5129441068790.02607719057040.38305327885523.6606269002-30.101132246412.9498541313
60.2013309164250.134119610922-0.5311114273350.101106787116-0.3627480111551.31957366071.843744471-0.5019115384460.1609952837860.861328391263-0.000125670446846-0.3990470582520.195634435037-1.211691635180.0637171418140.812845977801-0.030241257038-0.3341406212310.6359260447890.1759610842351.7590437760782.5820554569-13.21465774997.98132116356
70.5987463098730.837215458099-1.39023688711.15404808496-1.870818296383.18403517834-0.8835668993260.2104607971990.448924414503-0.8487369872511.0364279301-0.4826951580650.6461599100320.1940195131530.1091443126290.328168804760.1884579044430.005196292416080.562395148424-0.2700202286330.87272884636669.6671207029-12.79957222641.41108396535
80.8741810897430.1115107755710.6694207437580.638465336809-0.7078102036991.141904092590.168924186714-0.0239773795257-0.2909263884560.0536721158453-0.09483955701060.075322597340.133808136946-0.1324625566583.51019886717E-50.4192680120480.0353677789086-0.01160315497460.416711536037-0.02861939804990.38514369761649.5663856111-3.414264054595.22432001317
91.142736673361.34267543850.2988162175741.516667627470.7204076442060.522683050107-0.1119904463280.1209884882210.13719862215-0.097801328528-0.0124906912620.8625752319960.1526386854880.05147802411216.41108891119E-60.4721792585650.000920679832161-0.08940472671810.525639228863-0.1061210396340.49473755026138.82974538121.177175267665.02543097684
100.08987254181-0.0207098946485-0.02694901408380.0337525039119-0.1042049527910.281134667517-0.739123427337-0.705797173801-1.100808057031.14201280326-0.2094397286940.4271260499450.8227581395081.41957742754-0.00127142225740.633515902137-0.0732719777487-0.02803373184530.5526757384570.1336025526960.58043188246449.8632681151-14.808747243214.4171311182
112.945545433751.897145386720.7886315797751.299951013010.5288974431460.238664574835-0.71456017846-2.211222670460.4398662059060.931212843617-0.1799159300650.1744374413642.139514574070.853371193908-0.1146436734560.712665251387-0.01109572189670.034814737750.6938266317580.0139862989380.3545199540852.364902042-6.1975208293916.1101207881
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580.642585264594-1.530766236630.6376891811520.3119263165350.2290402317550.4951971259970.971657550729-1.11810507507-0.6788879934841.08960580271-0.72326347866-0.0487257576976-0.0886692755565-0.2008051097650.1631013600310.705499106217-0.116557060635-0.3231048814670.5506951673860.3533765279080.81943156382822.4074096985-62.217174577877.7400661071
590.167065952723-0.101839211949-0.1265760759950.06990962702850.1125864745480.130160223968-1.037009837871.17799777221-0.537265989428-0.4840150072560.565827000134-0.2995213760250.2747079063760.645743901953-0.001636254034130.495220902403-0.06606191937190.02744357959920.577472974221-0.09416828633430.51908785584360.4938387454-29.472770242131.9886597834
600.323867096353-0.8833453702270.05938080439783.10127198998-0.5672268555710.1217444228030.435535399715-0.1967119179140.677793734386-0.869313984643-0.278791060792-0.1724180067080.5853216899120.5716795044560.1831597896790.242622479981-0.0842724293028-0.1298633218890.844755249436-0.01596278501870.58469808055974.4179964323-33.790350206642.1624219249
614.95948323678-2.719954813510.8801116609072.001425597241.616370755066.98593654906-0.3711538721820.2037881582270.6923409037040.681978781585-2.422956286490.00945112485181-0.218571412496-1.03509438258-1.693748194350.3502152179030.324665483625-0.2889420777480.818574627725-0.3828446025390.57177763595338.470036553-55.166195235520.2535351305
620.545945643937-0.175470952429-0.2085381185620.2096380729940.04331510023840.184719649926-0.5318605084060.974319218334-0.914296173069-0.199951906324-0.222202088362-0.3857145036950.427070881756-0.2006653259820.00999889413220.4623370736210.0945377226332-0.008948874342340.7019183186650.0404579866610.85259460130746.8929025819-65.280838547427.0932120041
630.0617494941630.008418516773630.03426070305610.191759893610.144295057850.229693213123-0.507445448122-0.8333978065610.0614146866050.299119034430.4993726293840.06548199450660.650438876213-0.0338528850541-0.01272954420780.4928636657760.07126291433910.005967762331830.744980287007-0.01532113892560.47117309056567.18763013655.2269965991913.995015244
641.96334814620.901455142766-0.4625826476431.351081281270.7570864608051.120736235930.1296863198160.19412138083-0.002349833836870.7266891491771.5223724038-0.6281233771081.00184090967-0.05496545611830.3136248135930.4597777110160.103916294111-0.08171920469670.7491512598260.2590474117631.0668828774582.72724619144.590648978467.6112981391
650.126088399049-0.0144561380343-0.08276664652390.0007018237122570.007859564666080.0378279653339-0.1026164390321.178040563910.3088649012430.4638908359450.0922884858847-0.311128072142-0.1348484691640.6856680165230.00164231091560.613081603505-0.0941788822201-0.01757317035070.666282867547-0.009373507784770.62740801268555.0063398936-36.2869935276.2419691019
660.376478049383-0.184928317787-0.2682776803221.16930433260.05970240838260.1689073586110.7536829805980.436445841827-1.40412116038-0.57593224599-0.1931326554460.175248413840.1292549067850.1678858569550.02578491067920.4156905792620.0350158609174-0.02665935979130.5711553294580.05060314233060.60286509212164.3365549313-43.061581860384.7386061826
670.3965599415990.145523442768-0.070303878760.1190286728550.002623586066670.0663730919455-0.7533452125220.843134677111-0.536529156114-0.4868885186970.642905484909-0.1811135656460.0879401165792-0.7027523074130.002226658436810.520298084095-0.0811612099507-0.03484004495170.5502114577590.1749212344430.69560435620829.2575473254-57.829936755263.9021673038
680.794457007311-1.0147633731-0.4344188102361.438251915230.4786652567330.3296649697260.2147771919070.202961485793-0.52663120483-0.25186991467-0.264859184447-0.9620652236930.07318860163140.09414271353610.0819979391690.801466751297-0.241149358839-0.2947159572320.4843292554290.06808057613481.2665608432135.0721842659-68.731237518769.2632708488
690.026496917924-0.1536799172380.08454982229960.284047715289-0.0356972108208-0.06563190497320.345570451083-0.4595566792820.3209311799380.3652893772980.1522640064-0.435752154232-0.2024513242980.1635444967860.001399908524630.48170661564-0.008463812289270.001351331259150.488197962278-0.113297695570.69550819935470.2283873442-13.620029701542.0366387093
700.3272660200060.5456874326171.04852900759-0.1783752634450.3217939001380.68966127381-0.1182510405380.04141641327010.2677466583860.0249031971110.08397637501690.321640310983-0.225554164796-0.0372083267815-0.001148186553750.409089248028-0.0448624005124-0.01547851504510.332508918065-0.01948851218080.43997645582944.9104376058-14.981593251935.6297774427
711.38345258169-0.973856154650.809422203621.283299152050.003857500831890.911324650296-0.383535238335-0.6626328751660.104152185532-0.1770402965380.006543039114050.220600624458-0.04893162075830.01312373884070.0001512874102620.4005613745140.0189009943953-0.03500466474980.322475063573-0.02955347117350.40814784039540.8821463094-8.448746459732.1550175878
720.2121333890690.02278698823380.4366224472690.238931010316-0.06286105405881.07313852665-0.1693439015990.292010848178-0.378776957002-0.2666340843630.1095657357110.1538383563610.1272752972120.117338393374-4.20076393247E-50.511152187381-0.00870305361321-0.05190079894050.427324028682-0.05340345063810.39044562953143.4569767382-14.682703875525.4890576418
730.66540494110.554060433391-0.1813811337560.558131603582-0.04131660485280.2177089123291.20715979691-0.147934032936-0.627493719016-0.6549651647520.0530847827484-0.6781550367850.2303105619671.331060025560.01782869860550.7445112995310.296852009762-0.06747507934310.6378497624560.03201499184050.88711641108158.7594278343-56.302310613729.645171523
740.1263673877740.0464292799505-0.09609605143610.1679455950660.1736280990460.2777215012130.2089944561220.175195980872-0.250350341148-0.213515851918-0.2032662551970.265860275142-0.393137896812-0.018595802991-0.0006168580872030.531776577608-0.0632160916904-0.09520439917580.43941062894-0.02759350478470.65190906719151.6174506638-43.016005696132.3304571969
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'V' and (resid 30 through 57 )
2X-RAY DIFFRACTION2chain 'V' and (resid 58 through 84 )
3X-RAY DIFFRACTION3chain 'V' and (resid 85 through 98 )
4X-RAY DIFFRACTION4chain 'V' and (resid 99 through 103 )
5X-RAY DIFFRACTION5chain 'V' and (resid 104 through 118 )
6X-RAY DIFFRACTION6chain 'W' and (resid 14 through 20 )
7X-RAY DIFFRACTION7chain 'W' and (resid 21 through 29 )
8X-RAY DIFFRACTION8chain 'W' and (resid 30 through 57 )
9X-RAY DIFFRACTION9chain 'W' and (resid 58 through 84 )
10X-RAY DIFFRACTION10chain 'W' and (resid 85 through 91 )
11X-RAY DIFFRACTION11chain 'W' and (resid 92 through 98 )
12X-RAY DIFFRACTION12chain 'W' and (resid 99 through 103 )
13X-RAY DIFFRACTION13chain 'W' and (resid 104 through 118 )
14X-RAY DIFFRACTION14chain 'X' and (resid 18 through 29 )
15X-RAY DIFFRACTION15chain 'X' and (resid 30 through 57 )
16X-RAY DIFFRACTION16chain 'X' and (resid 58 through 84 )
17X-RAY DIFFRACTION17chain 'X' and (resid 85 through 103 )
18X-RAY DIFFRACTION18chain 'X' and (resid 104 through 112 )
19X-RAY DIFFRACTION19chain 'X' and (resid 113 through 118 )
20X-RAY DIFFRACTION20chain 'Y' and (resid 19 through 29 )
21X-RAY DIFFRACTION21chain 'Y' and (resid 30 through 57 )
22X-RAY DIFFRACTION22chain 'Y' and (resid 58 through 84 )
23X-RAY DIFFRACTION23chain 'Y' and (resid 85 through 98 )
24X-RAY DIFFRACTION24chain 'Y' and (resid 99 through 118 )
25X-RAY DIFFRACTION25chain 'B' and (resid 313 through 322 )
26X-RAY DIFFRACTION26chain 'B' and (resid 323 through 355 )
27X-RAY DIFFRACTION27chain 'B' and (resid 356 through 383 )
28X-RAY DIFFRACTION28chain 'B' and (resid 384 through 388 )
29X-RAY DIFFRACTION29chain 'C' and (resid 99 through 134 )
30X-RAY DIFFRACTION30chain 'C' and (resid 135 through 165 )
31X-RAY DIFFRACTION31chain 'D' and (resid 205 through 215 )
32X-RAY DIFFRACTION32chain 'D' and (resid 216 through 223 )
33X-RAY DIFFRACTION33chain 'E' and (resid 16 through 29 )
34X-RAY DIFFRACTION34chain 'E' and (resid 30 through 62 )
35X-RAY DIFFRACTION35chain 'E' and (resid 63 through 91 )
36X-RAY DIFFRACTION36chain 'E' and (resid 92 through 117 )
37X-RAY DIFFRACTION37chain 'F' and (resid 312 through 355 )
38X-RAY DIFFRACTION38chain 'F' and (resid 356 through 388 )
39X-RAY DIFFRACTION39chain 'G' and (resid 314 through 350 )
40X-RAY DIFFRACTION40chain 'G' and (resid 351 through 388 )
41X-RAY DIFFRACTION41chain 'H' and (resid 312 through 317 )
42X-RAY DIFFRACTION42chain 'H' and (resid 318 through 350 )
43X-RAY DIFFRACTION43chain 'H' and (resid 351 through 355 )
44X-RAY DIFFRACTION44chain 'H' and (resid 356 through 387 )
45X-RAY DIFFRACTION45chain 'I' and (resid 313 through 355 )
46X-RAY DIFFRACTION46chain 'I' and (resid 356 through 387 )
47X-RAY DIFFRACTION47chain 'J' and (resid 312 through 355 )
48X-RAY DIFFRACTION48chain 'J' and (resid 356 through 387 )
49X-RAY DIFFRACTION49chain 'K' and (resid 102 through 129 )
50X-RAY DIFFRACTION50chain 'K' and (resid 130 through 166 )
51X-RAY DIFFRACTION51chain 'L' and (resid 102 through 129 )
52X-RAY DIFFRACTION52chain 'L' and (resid 130 through 166 )
53X-RAY DIFFRACTION53chain 'M' and (resid 101 through 129 )
54X-RAY DIFFRACTION54chain 'M' and (resid 130 through 165 )
55X-RAY DIFFRACTION55chain 'N' and (resid 99 through 129 )
56X-RAY DIFFRACTION56chain 'N' and (resid 130 through 165 )
57X-RAY DIFFRACTION57chain 'O' and (resid 103 through 129 )
58X-RAY DIFFRACTION58chain 'O' and (resid 130 through 164 )
59X-RAY DIFFRACTION59chain 'P' and (resid 206 through 215 )
60X-RAY DIFFRACTION60chain 'P' and (resid 216 through 225 )
61X-RAY DIFFRACTION61chain 'Q' and (resid 206 through 215 )
62X-RAY DIFFRACTION62chain 'Q' and (resid 216 through 223 )
63X-RAY DIFFRACTION63chain 'R' and (resid 204 through 215 )
64X-RAY DIFFRACTION64chain 'R' and (resid 216 through 224 )
65X-RAY DIFFRACTION65chain 'A' and (resid 204 through 211 )
66X-RAY DIFFRACTION66chain 'A' and (resid 212 through 223 )
67X-RAY DIFFRACTION67chain 'T' and (resid 205 through 211 )
68X-RAY DIFFRACTION68chain 'T' and (resid 212 through 222 )
69X-RAY DIFFRACTION69chain 'U' and (resid 17 through 29 )
70X-RAY DIFFRACTION70chain 'U' and (resid 30 through 62 )
71X-RAY DIFFRACTION71chain 'U' and (resid 63 through 91 )
72X-RAY DIFFRACTION72chain 'U' and (resid 92 through 118 )
73X-RAY DIFFRACTION73chain 'V' and (resid 15 through 21 )
74X-RAY DIFFRACTION74chain 'V' and (resid 22 through 29 )

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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