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- PDB-6uri: HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 ... -

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基本情報

登録情報
データベース: PDB / ID: 6uri
タイトルHIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex
要素
  • (AP-2 complex subunit ...) x 4
  • Protein Nef
  • cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4
キーワードVIRAL PROTEIN / CD4
機能・相同性
機能・相同性情報


virus-mediated perturbation of host defense response => GO:0019049 / Nef mediated downregulation of CD28 cell surface expression / perturbation by virus of host immune response / negative regulation of CD4 production / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / low-density lipoprotein particle receptor catabolic process / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation ...virus-mediated perturbation of host defense response => GO:0019049 / Nef mediated downregulation of CD28 cell surface expression / perturbation by virus of host immune response / negative regulation of CD4 production / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / low-density lipoprotein particle receptor catabolic process / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation / protein trimerization / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / low-density lipoprotein particle clearance / MHC class II antigen presentation / AP-2 adaptor complex / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / symbiont-mediated suppression of host apoptosis / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / maintenance of protein location in cell / peptidase activator activity / T cell selection / clathrin coat assembly / Retrograde neurotrophin signalling / Formation of annular gap junctions / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / Clathrin-mediated endocytosis / clathrin adaptor activity / suppression by virus of host autophagy / vesicle budding from membrane / MHC class II protein binding / membrane coat / clathrin-dependent endocytosis / membrane organization / coronary vasculature development / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / CD4 receptor binding / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / thioesterase binding / Alpha-defensins / positive regulation of kinase activity / aorta development / negative regulation of protein localization to plasma membrane / Wnt signaling pathway, planar cell polarity pathway / regulation of T cell activation / ventricular septum development / Neutrophil degranulation / T cell receptor complex / extracellular matrix structural constituent / Other interleukin signaling / low-density lipoprotein particle receptor binding / clathrin binding / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / host cell Golgi membrane / MHC class I protein binding / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / regulation of calcium ion transport / positive regulation of receptor internalization / macrophage differentiation / regulation of endocytosis / Generation of second messenger molecules / synaptic vesicle endocytosis / T cell differentiation / EPH-ephrin mediated repulsion of cells / PD-1 signaling / ephrin receptor signaling pathway / positive regulation of protein kinase activity / Binding and entry of HIV virion / coreceptor activity / positive regulation of calcium-mediated signaling / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / regulation of calcium-mediated signaling / cell surface receptor protein tyrosine kinase signaling pathway / viral life cycle / T cell activation / MHC class II antigen presentation / positive regulation of interleukin-2 production
類似検索 - 分子機能
AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / HIV-1 Nef protein, anchor domain superfamily / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain ...AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / HIV-1 Nef protein, anchor domain superfamily / Adaptor protein complex, sigma subunit / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / CD4, extracellular / T cell CD4 receptor C-terminal region / AP complex subunit beta / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Immunoglobulin C2-set / Immunoglobulin C2-set domain / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Armadillo-like helical / Immunoglobulin subtype / Immunoglobulin / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
類似検索 - ドメイン・相同性
cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 / T-cell surface glycoprotein CD4 / Protein Nef / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit alpha / Protein Nef / AP-2 complex subunit mu
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
Homo sapiens (ヒト)
Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å
データ登録者Jia, X. / Kwon, Y.
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2020
タイトル: Structural basis of CD4 downregulation by HIV-1 Nef.
著者: Kwon, Y. / Kaake, R.M. / Echeverria, I. / Suarez, M. / Karimian Shamsabadi, M. / Stoneham, C. / Ramirez, P.W. / Kress, J. / Singh, R. / Sali, A. / Krogan, N. / Guatelli, J. / Jia, X.
履歴
登録2019年10月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02020年7月29日Provider: repository / タイプ: Initial release
改定 1.12020年8月12日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
改定 1.22020年9月23日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.32023年10月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
A: AP-2 complex subunit alpha
S: AP-2 complex subunit sigma
N: Protein Nef
B: AP-2 complex subunit beta
M: AP-2 complex subunit mu
D: cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4


分子量 (理論値)分子数
合計 (水以外)202,0436
ポリマ－202,0436
非ポリマー00
水362
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: gel filtration
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area18590 Å2
ΔGint-74 kcal/mol
Surface area65210 Å2
手法PISA
単位格子
Length a, b, c (Å)109.154, 109.154, 178.915
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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要素

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AP-2 complex subunit ... , 4種, 4分子 ASBM

#1: タンパク質 AP-2 complex subunit alpha


分子量: 72069.844 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 遺伝子: Ap2a2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q66HM2, UniProt: P18484*PLUS
#2: タンパク質 AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / HA2 17 kDa subunit / Plasma membrane adaptor AP-2 17 kDa protein / Sigma2-adaptin


分子量: 17066.701 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AP2S1, AP17, CLAPS2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P53680
#4: タンパク質 AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


分子量: 69473.812 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AP2B1, ADTB2, CLAPB1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P63010
#5: タンパク質 AP-2 complex subunit mu / AP-2 mu chain / Adaptin-mu2 / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein ...AP-2 mu chain / Adaptin-mu2 / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit mu / Clathrin assembly protein complex 2 mu medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50 / HA2 50 kDa subunit / Plasma membrane adaptor AP-2 50 kDa protein


分子量: 15518.836 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: AP2M1, CLAPM1, KIAA0109 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96CW1

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タンパク質 , 2種, 2分子 ND

#3: タンパク質 Protein Nef / 3'ORF / Negative factor / F-protein


分子量: 21032.518 Da / 分子数: 1 / 由来タイプ: 組換発現
由来: (組換発現) Human immunodeficiency virus 1 (ヒト免疫不全ウイルス)
遺伝子: nef / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q90VU7, UniProt: P03406*PLUS
#6: タンパク質 cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4 / cDNA / FLJ79360 / highly similar to T-cell surface glycoprotein CD4 / FLJ79361


分子量: 6881.758 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: B4DT49, UniProt: P01730*PLUS

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非ポリマー , 1種, 2分子

#7: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2 / 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: 3 Å3/Da / 溶媒含有率: 58.94 % / 解説: Rods
結晶化温度: 298 K / 手法: マイクロバッチ法 / pH: 6.9
詳細: 15% Peg 4000, 0.2M potassium chloride, ~10% 1,6-hexanediol, 0.1M HEPES

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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: NSLS-II / ビームライン: 17-ID-2 / 波長: 0.9793 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年5月8日
放射モノクロメーター: Si 111 double crystal monochromator
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: 0.9793 Å / 相対比: 1
反射解像度: 3→50 Å / Num. obs: 41865 / % possible obs: 100 % / 冗長度: 16 % / Biso Wilson estimate: 90.23 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.287 / Rpim(I) all: 0.074 / Rrim(I) all: 0.296 / Χ2: 1.01 / Net I/σ(I): 11.8
反射 シェル解像度: 3→3.11 Å / 冗長度: 15.9 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4189 / CC1/2: 0.366 / Rpim(I) all: 0.021 / Rrim(I) all: 0.084 / Χ2: 0.999 / % possible all: 100

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解析

ソフトウェア
名称バージョン分類
PHENIX1.15.2_3472精密化
HKL-2000データ削減
HKL-2000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: 2XA7, 4EMZ

2xa7

4emz


解像度: 3→48.82 Å / SU ML: 0.3956 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.5837
Rfactor反射数%反射
Rfree0.2768 1018 2.43 %
Rwork0.241 --
obs0.2419 41859 99.98 %
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: 118.3 Å2
精密化ステップサイクル: LAST / 解像度: 3→48.82 Å
タンパク質核酸リガンド溶媒全体
原子数12261 0 0 2 12263
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.004712488
X-RAY DIFFRACTIONf_angle_d0.875416921
X-RAY DIFFRACTIONf_chiral_restr0.05031957
X-RAY DIFFRACTIONf_plane_restr0.00562164
X-RAY DIFFRACTIONf_dihedral_angle_d4.06447634
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.160.33841470.31485806X-RAY DIFFRACTION99.97
3.16-3.360.32631450.30655842X-RAY DIFFRACTION100
3.36-3.620.28251340.26045812X-RAY DIFFRACTION100
3.62-3.980.25931500.23645819X-RAY DIFFRACTION100
3.98-4.550.24281440.21185847X-RAY DIFFRACTION100
4.55-5.740.26471490.23095830X-RAY DIFFRACTION100
5.74-48.820.28781490.23535885X-RAY DIFFRACTION99.88
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)
11.907670864640.0535619606010.9817012224941.875486648730.6973038004594.08531217673-0.07806291126860.297394703843-0.6049505844580.06553101819380.483758811548-0.5167650305270.8652613447661.12762575358-0.336858440980.7729278458520.2381722995310.1454047176620.975499345212-0.2537411041880.71824524361150.0230199156-25.0641292765-3.3266586192
24.870803734213.31605073558-2.862594350884.27058336941-1.821333726434.721231092050.5746886358610.4748070838060.4450201013620.256788610931-0.134583974270.107625352887-0.919698915796-0.939690244166-0.3581066798970.9350563029930.28145267530.1059922817850.546720875206-0.02812784778970.49485519927247.271658651411.3436054737-41.0925620413
33.35078275118-1.19481048052-4.780294934927.915127541414.267020531738.29015600056-0.5374479758520.6310695775880.289658680823-0.4805103883480.403080833739-1.158934464890.2201995922531.495845486070.1003977163920.4754888917520.05732295247820.08024190467691.13876010275-0.1543653812250.66610905184749.6387465026-10.4816873783-0.479235097963
42.07453592943-2.823237229322.481679516943.71389884232-0.04187379023723.947351193390.4965129607840.7701570496210.726080568081-0.147125121552-0.42267126914-0.0384183976717-0.08076722473660.295983107972-0.0507044635870.9566295966330.01765508975410.2456468161720.887922677283-0.1895561198830.56413251058644.1049684535-2.93871415693-5.08217895448
58.419018683120.876942086032-9.284756573094.66722125512-3.559554111422.01309670839-0.2311244028182.18842673988-0.530985199683-0.9080086216870.932362052439-2.618376846770.3778163459131.17095376762-0.8806854872780.9314349524790.07084776022810.1956300211221.83762065578-0.2885518193391.1018186195545.6212155412-7.02014842814-13.2781135428
63.18158283291-5.65729486225-2.574234554882.069431382056.320905618335.99968836569-0.305702544587-0.606168692337-0.195663631284-0.3626069030780.6028143546240.448290961839-0.1504662122631.25724840354-0.2499592766290.6089788148110.0676236472970.1609566634240.798220159713-0.1607653886410.55163341520540.0016637193-10.9110460265-3.70388230413
78.526742573788.05486675052-3.248647542729.85031473014-5.159347030393.15550241963-0.5715429631642.09963042285-0.700184471127-2.890079139820.626854605675-0.9670339112831.25199846120.938063972133-0.1496301565771.13197498179-0.08199749770510.2388149064161.48149710912-0.4864414637320.58661391769946.0737358164-17.4328441586-15.6925149286
84.970051277340.5202913657362.044057529975.555295042692.536852813937.07261653017-0.520766928103-0.79224823731-0.5190963797540.6056188061590.2858159741060.02998731213150.7528949782360.4765082715150.2554558449690.6583743882270.2216756564070.1056117290010.793426284925-0.09125429019990.42381581278540.871994409-19.40849194516.44057873666
99.597433305612.919163237066.01566427068.41529953953-1.647002223525.199361674420.770699605776-0.514946660407-1.215970454470.588003452499-0.502399691283-0.03975060170690.7265163219810.376118144221-0.2347295133270.9587174825520.2829053557670.2124554575980.789884927691-0.1446667558170.66322947242345.3306701567-29.694650496.23850102816
102.017014033165.48525299649-7.049499981981.995946410951.913233762031.98316868530.0732336033739-0.9954478431380.761119588309-0.8480179025181.334628434790.553239843626-1.248798295212.57501083168-1.412176732262.43422899211-0.11591811232-0.4929482581222.0510489886-0.1363118201151.56546392086.78900331387-34.8517832239-15.7796015493
117.353382103033.480279123925.568426350227.00049565264-1.868630984366.579900378030.187704512984-0.559695940132-0.432694170478-0.04166090348650.067083086925-0.07799019282590.6804567910190.0144255494657-0.3896010874760.6249404472880.02840494833950.1340385203610.836690664159-0.02854370687180.6501716976548.77905449495-24.59058090321.84825232368
128.740793225374.788403627844.230838338254.651849151371.708976882564.7510922514-0.599978651019-0.1355285889290.287653074998-0.3923589368170.3952127569390.346607901789-0.1037576730080.007050306116840.2326839228140.5419414403790.07269370930040.1016158156090.639425639806-0.07824947874330.5052308474315.2705374358-13.2134043755-0.302475357449
135.679834542295.429900282090.07109256544219.086522403425.738547487888.55533358898-0.5405297226960.255442717380.606636836844-1.738675961251.070335152541.05237201185-0.676540621309-0.471958228481-0.2617554664490.8678791383890.168345972445-0.1039368871191.636384359610.2811593001281.081129243334.49734038436-10.2807865846-15.1898724635
141.067648292910.484215082910.04672501941217.19391919986-7.609100436655.90486532355-0.160871472099-0.02927867153080.5002390860380.870578113090.5043453724950.745928974529-0.137963596219-1.19081540714-0.2904962481771.719293705340.1796541925980.2200981345951.52238965123-0.4281881756011.0909521566310.302962214716.7968586954-9.90011559888
153.512931993040.5335856292490.01773581336442.21882365727-1.29752355861-0.0925676491338-0.1943566300370.1809050834750.4506815749730.9162950864870.1462263328220.2153504180620.0187512824898-0.348327584832-0.0262576071013.10838936027-0.3061644240750.5930155580461.48041644067-0.3763051659871.1783134025441.276821227642.1670388323-17.5354192091
162.638471246570.565034414718-0.324084956644.05227432063-0.2152136405973.852393381260.90671178493-0.8344426582180.4276240057731.92395214426-0.740968159645-0.283684786548-0.4778822720750.680698985469-0.2344146993731.78148954574-0.4679172759180.05114972413780.727441460501-0.1082736504080.68982425376974.463946885820.2367720198-28.9328961427
174.29896784796-0.945672742582-3.95161341991.063160206670.9681401090924.546588801480.949175033464-0.06904136723730.6558741490031.03990847008-0.3749973216350.299238727849-1.82618538813-0.351643162964-0.6610723332652.96030492296-0.1450518190720.8124540502270.952358213715-0.115035331731.368246109357.950524597430.8886669234-32.0126476512
184.54548777899-0.4388620469563.221089212822.006521546571.990373870279.54129855013.02025658021.35954067763-0.607419352296-1.91789660401-2.526268472870.3302911310510.8699547736041.36732534068-0.003990439488452.791207821620.9526320795711.390036517811.613792525210.2247427434731.7904181277533.448190844520.5403908503-9.01992618237
197.150741732541.675917269827.819599730126.330451808641.049929010858.816260019160.603424310306-2.770241951081.243772320551.90142666766-0.572191743416-0.648910181357-1.18148679928-2.22507339845-0.07280185905431.69759070236-0.2147071897030.3794727806691.39294675347-0.1952880585191.1867249330534.362763816813.1734423362-1.93390166812
205.794309929496.555245953342.632542849647.641114372974.372540451249.371774576070.998149568859-0.638302231989-1.51438674656-2.68573887142-0.612289491298-0.2104271777861.63465914922-0.6111036919830.1129489980051.96162675288-0.05237602731340.1324730892141.17467781352-0.5927158887492.209220135734.781050573313.2836546604-13.2425790849
211.209683283121.00996994969-0.126224532770.938442752809-0.0975609064340.00192148015193-0.07237917616370.0503972011576-1.082825105190.387016280181.16120037093-0.916404168235-0.5227341701121.32417951859-0.9587556702332.82493005376-0.1346672564890.4325480727061.4176900346-0.5288331663691.5232216397446.24593600417.5179771761-12.6525904741
226.0735803871-2.604604094118.003058382783.66222404386-2.664032924811.97696470144-1.336558027290.0696316889141-1.95383121522-0.457188851036-1.04868163426-0.80822810794-0.388068248751-2.592049458221.929660574062.144754397180.403573929020.8631141881671.31339059387-0.0766390509951.6950554379441.809118691121.8952045887-7.83189405955
238.40645177788-2.43456157897-0.6291141015162.15145737815-0.1763987990040.0956596118841-0.157252054275-0.434404158773-0.3012851774520.3823871794261.26895454736-0.480040842906-3.1597173050.569838482748-1.00878822282.3591881073-0.1547704511590.3882157390090.926789787504-0.3154649996630.97492875372638.610547177122.5326423696-9.86783280532
245.36688790822-2.574901346192.572060045426.8830641163-5.584017115654.601635696960.63217858494-3.0749130811-0.720888886817-1.570603797911.37957700831-0.827290299423-1.828312377280.0286400655763-1.082821815452.78521621114-0.004002830023990.8657239620840.968891357849-0.4567845352091.1030120499733.988852279425.26062863481.8180006403
251.51539878022.581149414740.4045689107966.684031881030.9146383237570.110307320477-0.350676281768-0.307939990454-0.269716464757-1.450346570590.1199529427761.78302817174-0.372938631078-0.6848511094830.4141138338193.662791376970.8366908804480.7489561778091.48473821393-0.07078760438721.8512911191724.741419584627.5028505641-5.85015106684
261.998340521247.507726390047.052538089254.64646884424.47227385516.6544125414-0.9791568964364.01536251605-2.89832278027-0.7513863784860.1603439115450.0923218446775-0.6634196667870.5185713331270.8016327696791.020432451220.352428991867-0.1492485316291.72684722907-0.6241462017741.717315705430.0443316528099-22.182847505-11.1027422557
271.99214724569-2.516245634119.870451744560.113079565853-0.5397010563532.1077689786-0.9843672590682.03887820822-0.0476450184931-1.253322733841.98087662992-1.432106848290.09194541471491.54540229713-0.8709520917990.8545626539050.600653781465-1.795898994272.73678264388-2.240597140462.83278266811.63566539187-29.4065786668-12.8253805113
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 358 )
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 619 )
3X-RAY DIFFRACTION3chain 'S' and (resid 1 through 24 )
4X-RAY DIFFRACTION4chain 'S' and (resid 25 through 48 )
5X-RAY DIFFRACTION5chain 'S' and (resid 49 through 54 )
6X-RAY DIFFRACTION6chain 'S' and (resid 55 through 71 )
7X-RAY DIFFRACTION7chain 'S' and (resid 72 through 76 )
8X-RAY DIFFRACTION8chain 'S' and (resid 77 through 117 )
9X-RAY DIFFRACTION9chain 'S' and (resid 118 through 142 )
10X-RAY DIFFRACTION10chain 'N' and (resid 34 through 52 )
11X-RAY DIFFRACTION11chain 'N' and (resid 53 through 103 )
12X-RAY DIFFRACTION12chain 'N' and (resid 104 through 191 )
13X-RAY DIFFRACTION13chain 'N' and (resid 192 through 203 )
14X-RAY DIFFRACTION14chain 'B' and (resid 13 through 134 )
15X-RAY DIFFRACTION15chain 'B' and (resid 135 through 349 )
16X-RAY DIFFRACTION16chain 'B' and (resid 350 through 532 )
17X-RAY DIFFRACTION17chain 'B' and (resid 533 through 582 )
18X-RAY DIFFRACTION18chain 'M' and (resid 1 through 8 )
19X-RAY DIFFRACTION19chain 'M' and (resid 9 through 19 )
20X-RAY DIFFRACTION20chain 'M' and (resid 20 through 35 )
21X-RAY DIFFRACTION21chain 'M' and (resid 36 through 52 )
22X-RAY DIFFRACTION22chain 'M' and (resid 53 through 60 )
23X-RAY DIFFRACTION23chain 'M' and (resid 61 through 74 )
24X-RAY DIFFRACTION24chain 'M' and (resid 75 through 105 )
25X-RAY DIFFRACTION25chain 'M' and (resid 106 through 124 )
26X-RAY DIFFRACTION26chain 'D' and (resid 406 through 411 )
27X-RAY DIFFRACTION27chain 'D' and (resid 412 through 419 )

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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://pdbjlvh1.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