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- PDB-4nee: crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef -

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基本情報

登録情報
データベース: PDB / ID: 4nee
タイトルcrystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef
要素
  • AP-2 complex subunit alpha-2
  • AP-2 complex subunit sigma
  • Protein Nef
キーワードVIRAL PROTEIN/PROTEIN TRANSPORT / clathrin Adaptor AP-2 / HIV-1 Nef / CD4 downregulation / VIRAL PROTEIN-PROTEIN TRANSPORT complex
機能・相同性
機能・相同性情報


Nef mediated downregulation of CD28 cell surface expression / secretory vesicle / Late Phase of HIV Life Cycle / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / protein trimerization ...Nef mediated downregulation of CD28 cell surface expression / secretory vesicle / Late Phase of HIV Life Cycle / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / protein trimerization / negative regulation of glycoprotein biosynthetic process / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class I / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / symbiont-mediated suppression of host antigen processing and presentation of peptide antigen via MHC class II / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / membrane coat / symbiont-mediated suppression of host autophagy / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / symbiont-mediated suppression of host apoptosis / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / thioesterase binding / Nef Mediated CD4 Down-regulation / CD4 receptor binding / Nef and signal transduction / Neutrophil degranulation / Uncoating of the HIV Virion / Trafficking of GluR2-containing AMPA receptors / MHC class I protein binding / host cell Golgi membrane / synaptic vesicle endocytosis / Binding and entry of HIV virion / vesicle-mediated transport / viral life cycle / regulation of calcium-mediated signaling / phosphatidylinositol binding / protein serine/threonine kinase binding / Nef mediated downregulation of MHC class I complex cell surface expression / intracellular protein transport / Assembly Of The HIV Virion / Budding and maturation of HIV virion / SH3 domain binding / virion component / kinase binding / disordered domain specific binding / synaptic vesicle / ATPase binding / cytoplasmic vesicle / postsynapse / symbiont-mediated suppression of host innate immune response / signaling receptor binding / protein domain specific binding / intracellular membrane-bounded organelle / synapse / protein kinase binding / GTP binding / protein-containing complex binding / host cell plasma membrane / glutamatergic synapse / extracellular region / membrane / plasma membrane
類似検索 - 分子機能
Nef Regulatory Factor / Nef Regulatory Factor / Beta-Lactamase - #60 / 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 / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily ...Nef Regulatory Factor / Nef Regulatory Factor / Beta-Lactamase - #60 / 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 / HIV-1 Nef protein, anchor domain superfamily / HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / Adaptor protein complex, sigma subunit / : / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
Protein Nef / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit alpha / Protein Nef
類似検索 - 構成要素
生物種Rattus norvegicus (ドブネズミ)
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: 2.8841 Å
データ登録者Hurley, J.H. / Bonifacino, J.S. / Ren, X. / Park, S.Y.
引用ジャーナル: Elife / 年: 2014
タイトル: How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4.
著者: Ren, X. / Park, S.Y. / Bonifacino, J.S. / Hurley, J.H.
履歴
登録2013年10月29日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年1月29日Provider: repository / タイプ: Initial release
改定 1.12014年3月5日Group: Database references
改定 1.22023年9月20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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
D: AP-2 complex subunit sigma
L: AP-2 complex subunit sigma
F: AP-2 complex subunit sigma
I: AP-2 complex subunit sigma
G: AP-2 complex subunit alpha-2
B: AP-2 complex subunit alpha-2
J: AP-2 complex subunit alpha-2
A: AP-2 complex subunit alpha-2
E: Protein Nef
H: Protein Nef
K: Protein Nef
C: Protein Nef


分子量 (理論値)分子数
合計 (水以外)316,39612
ポリマ－316,39612
非ポリマー00
水00
1
D: AP-2 complex subunit sigma
B: AP-2 complex subunit alpha-2
C: Protein Nef


分子量 (理論値)分子数
合計 (水以外)79,0993
ポリマ－79,0993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-21 kcal/mol
Surface area29580 Å2
手法PISA
2
L: AP-2 complex subunit sigma
J: AP-2 complex subunit alpha-2
K: Protein Nef


分子量 (理論値)分子数
合計 (水以外)79,0993
ポリマ－79,0993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-22 kcal/mol
Surface area29890 Å2
手法PISA
3
F: AP-2 complex subunit sigma
A: AP-2 complex subunit alpha-2
E: Protein Nef


分子量 (理論値)分子数
合計 (水以外)79,0993
ポリマ－79,0993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-22 kcal/mol
Surface area29270 Å2
手法PISA
4
I: AP-2 complex subunit sigma
G: AP-2 complex subunit alpha-2
H: Protein Nef


分子量 (理論値)分子数
合計 (水以外)79,0993
ポリマ－79,0993
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-22 kcal/mol
Surface area29640 Å2
手法PISA
単位格子
Length a, b, c (Å)109.558, 168.034, 200.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

#1: タンパク質
AP-2 complex subunit sigma / Adapter-related protein complex 2 subunit sigma / Adaptor protein complex AP-2 subunit sigma / ...Adapter-related protein complex 2 subunit sigma / Adaptor protein complex AP-2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


分子量: 17038.688 Da / 分子数: 4 / 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: Ap2s1, Ap17, Claps2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P62744
#2: タンパク質
AP-2 complex subunit alpha-2 / Adaptor-related protein complex 2 / alpha 2 subunit


分子量: 44389.285 Da / 分子数: 4 / Fragment: Residues 1-396 / 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: Ap17, Ap2a2, Ap2s1, Claps2 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q66HM2, UniProt: P18484*PLUS
#3: タンパク質
Protein Nef


分子量: 17670.990 Da / 分子数: 4 / Fragment: HIV-1 Nef, residues 54-203 / 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: P04601*PLUS
配列の詳細THE N-TERMINAL SEQUENCE OF THE PROTEIN is GAMGSACAWLEAQE. DUE TO THE PRESENCE OF A FLEXIBLE LOOP ...THE N-TERMINAL SEQUENCE OF THE PROTEIN is GAMGSACAWLEAQE. DUE TO THE PRESENCE OF A FLEXIBLE LOOP THE REGISTRATION OF THE MODEL SEQUENCE IS UNKNOWN.

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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: 2.91 Å3/Da / 溶媒含有率: 57.76 %
結晶化温度: 288 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 9.5
詳細: 70mM CHES pH 9.5, 140mM NaCl, 7% PEG8000, 21% glycerol, 0.2mM inositol hexakisphosphate (IP6), VAPOR DIFFUSION, SITTING DROP, temperature 288K

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データ収集

回折平均測定温度: 200 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年7月10日
放射モノクロメーター: Si (111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.884→50 Å / Num. all: 83709 / Num. obs: 80188 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / 冗長度: 5.2 % / Rmerge(I) obs: 0.184
反射 シェル解像度: 2.884→3 Å / % possible all: 80.2

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解析

ソフトウェア
名称バージョン分類
HKL-2000データ収集
PHASER位相決定
PHENIX(phenix.refine: 1.8.3_1479)精密化
HKL-2000データ削減
HKL-2000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: PDB ENTRY 3REA

3rea


解像度: 2.8841→48.88 Å / SU ML: 0.4 / σ(F): 1.42 / 位相誤差: 25.12 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2668 4014 5.01 %Random
Rwork0.2194 ---
obs0.2218 80121 95.53 %-
all-80188 --
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
精密化ステップサイクル: LAST / 解像度: 2.8841→48.88 Å
タンパク質核酸リガンド溶媒全体
原子数21530 0 0 0 21530
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01521985
X-RAY DIFFRACTIONf_angle_d1.15929768
X-RAY DIFFRACTIONf_dihedral_angle_d14.2868144
X-RAY DIFFRACTIONf_chiral_restr0.0693364
X-RAY DIFFRACTIONf_plane_restr0.0073802
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8841-2.9180.3936810.3521442X-RAY DIFFRACTION54
2.918-2.95360.40291220.33822394X-RAY DIFFRACTION87
2.9536-2.9910.35831260.32572466X-RAY DIFFRACTION91
2.991-3.03030.34841470.31152542X-RAY DIFFRACTION94
3.0303-3.07180.35451370.30452525X-RAY DIFFRACTION93
3.0718-3.11570.33151300.29432565X-RAY DIFFRACTION94
3.1157-3.16220.34251350.28472551X-RAY DIFFRACTION95
3.1622-3.21160.31851380.28762624X-RAY DIFFRACTION96
3.2116-3.26420.31481570.27172584X-RAY DIFFRACTION96
3.2642-3.32050.32231230.27482648X-RAY DIFFRACTION97
3.3205-3.38090.3351370.25822625X-RAY DIFFRACTION97
3.3809-3.44590.29821530.25112637X-RAY DIFFRACTION96
3.4459-3.51620.28541450.24722608X-RAY DIFFRACTION96
3.5162-3.59260.29661350.23562673X-RAY DIFFRACTION98
3.5926-3.67620.32691400.24472650X-RAY DIFFRACTION97
3.6762-3.76810.32031350.21912670X-RAY DIFFRACTION98
3.7681-3.86990.2411400.21422675X-RAY DIFFRACTION98
3.8699-3.98370.27571550.22812664X-RAY DIFFRACTION98
3.9837-4.11230.24951410.19342720X-RAY DIFFRACTION99
4.1123-4.25920.20021290.17332745X-RAY DIFFRACTION100
4.2592-4.42960.23631460.17292745X-RAY DIFFRACTION100
4.4296-4.6310.19871420.16942719X-RAY DIFFRACTION100
4.631-4.8750.2121350.16842771X-RAY DIFFRACTION100
4.875-5.18010.24331610.18252735X-RAY DIFFRACTION100
5.1801-5.57950.2391200.22805X-RAY DIFFRACTION100
5.5795-6.14010.27971580.20272767X-RAY DIFFRACTION100
6.1401-7.02630.22971360.19872799X-RAY DIFFRACTION100
7.0263-8.84380.18421460.16782838X-RAY DIFFRACTION100
8.8438-48.88680.19051640.1592920X-RAY DIFFRACTION99
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)
12.01130.2262-0.84594.09341.53562.31990.0685-0.19070.22210.1415-0.3711.18830.3379-0.45850.2970.24530.024-0.01110.3791-0.0270.41552.8538-14.9206-18.4448
21.9964-2.4738-2.61020.9624-1.01768.0786-0.1777-1.32411.50191.83481.1513-0.6965-1.1194-0.3726-0.61870.81370.24330.17820.40760.06740.733813.9726-23.0327-5.2696
34.8973-1.74332.3694.62232.15687.4576-0.2885-0.7787-1.08560.4366-0.65850.7011.3823-0.564-0.66420.218-0.0266-0.09850.58230.16670.12489.4755-23.341-14.7626
41.8046-1.3131-0.1862.6689-0.04752.48130.0250.18750.2847-0.1267-0.1145-0.1341-0.14710.1140.15670.15290.029-0.04840.3227-0.00310.248417.5041-11.4096-25.8369
53.6740.8324-0.41442.8106-0.26130.14050.4187-1.16610.31811.3653-0.43240.32120.2909-0.3591-0.11740.5645-0.11730.08630.5327-0.05550.328636.60178.17529.2029
62.91180.5568-2.39555.6771-3.82794.01190.5658-0.5297-1.0112-0.6082-0.59111.37531.559-2.0137-0.18090.7804-0.1535-0.25840.88730.04110.833224.350115.68416.6826
74.2708-2.6949-0.1222.03960.18012.4696-0.1243-1.14060.11070.65890.43560.4865-0.068-0.7791-0.19410.4127-0.00580.1450.6648-0.0480.821730.929220.967528.4661
82.226-1.21710.90614.8925-0.441.81120.1620.16240.1578-0.0369-0.140.12270.18990.0452-0.08520.1724-0.0226-0.00180.3243-0.02280.240243.375510.23217.4226
97.7162-4.50242.4689.0867-2.00346.3696-0.0885-0.15690.1867-0.35830.0008-0.90440.47240.75160.03370.26730.09410.03440.49640.00290.302358.87826.099112.3657
101.86511.0930.7115.3391-1.55121.4461-0.26340.3301-0.26810.19860.2115-1.71890.09210.33050.10320.36080.07160.12850.44950.06940.662173.9617-55.9119-33.2853
112.1432-2.86891.47463.838-1.87671.601-0.2311-0.4631-0.0908-0.1558-0.5289-0.28410.30360.29040.41270.38770.75730.29480.58370.28211.221564.7916-55.3883-16.65
121.77970.6143-2.68291.0906-1.79315.50970.2954-0.66420.32080.0576-0.4732-0.2408-0.38360.76660.10880.49020.0530.03070.45370.09730.414667.9196-50.4866-25.0372
132.68480.1289-0.6981.11190.6712.584-0.23870.0464-0.034-0.24350.0332-0.37620.1862-0.22720.08450.42260.00510.11920.25350.0940.392360.0372-55.9392-37.176
144.7586-2.9711-4.82144.42594.05715.3325-0.54430.8693-0.3451-0.3418-0.1633-0.57820.8953-0.6710.70650.5299-0.08110.11510.40780.02070.49951.4018-57.3767-50.1832
153.1719-0.0861-0.35126.37780.77422.14730.10940.72750.2599-0.9861-0.0657-0.0678-0.26010.460.09710.2832-0.0078-0.01880.3830.02780.2257-11.706115.672-1.0945
163.3961-2.47991.60328.7821-2.79433.58380.21490.27320.4177-1.4007-0.0614-0.28890.33060.7418-0.2820.33160.01890.07550.434-0.01990.2571-3.337315.9621-3.7251
173.07522.7535-1.73415.27891.11795.3434-0.11680.9550.4926-0.5414-0.0523-1.38061.15631.1574-0.39950.41940.09490.07940.6634-0.05390.4274-0.189420.52969.389
181.79090.25540.19781.98851.28042.3761-0.02780.00880.0619-0.07590.0732-0.04130.0801-0.0598-0.08910.1545-0.00290.00720.2380.04220.2178-16.557713.12168.4241
191.9143-1.22032.2841.2478-0.14297.13510.2237-0.2185-0.31560.0098-0.36730.73861.4301-0.58830.14690.1819-0.14510.02490.35130.01440.3248-32.94738.05359.2779
203.0281-2.1256-0.27233.89550.66351.67420.13870.4878-0.0828-0.3911-0.23750.22820.0543-0.14940.08790.26960.0037-0.04970.35250.01190.2589-26.03985.971-11.8048
211.49860.47390.34841.1325-0.02523.74510.0360.18630.359-0.0682-0.07770.187-0.3217-0.40680.10670.22920.06560.00860.3598-0.02760.4512-31.271431.20272.0219
224.162-0.54680.87882.36510.34042.14740.0432-0.3830.48320.38940.01010.0255-0.1417-0.0586-0.09410.2785-0.07440.03290.2991-0.06760.3228-16.630132.18422.9657
232.88740.99980.08435.76260.78354.1985-0.01160.04070.5495-0.0673-0.0966-0.0937-0.22110.28740.06440.2975-0.1076-0.05380.4684-0.10740.74635.734934.715921.3868
243.3814-1.33360.54052.82651.26923.33540.19150.00310.1587-0.3397-0.15430.4188-0.6035-0.4851-0.04380.36570.0827-0.02880.33280.08580.36310.70076.9769-28.5023
250.8897-1.3610.25524.0158-1.09761.63210.14470.3512-0.1851-0.5236-0.16180.07790.28790.0762-0.00070.32010.0192-0.01510.3893-0.0860.228516.2357-24.7416-36.8434
262.62760.566-0.27651.9953-0.76634.5763-0.0397-0.0554-0.26140.2330.08570.07320.1541-0.0446-0.05450.32270.0541-0.01780.31450.05530.416518.7069-41.7417-10.095
273.53321.406-1.03463.73730.20844.30880.129-0.4103-0.60740.3412-0.1615-0.19950.8093-0.18360.10750.51750.0324-0.03240.45950.0170.331150.0767-11.635830.1254
281.448-0.92691.19014.1872-1.10851.8195-0.0448-0.20010.2170.4744-0.0562-0.1872-0.17870.28530.12950.1757-0.07760.02340.4780.00720.320559.76518.589128.9862
292.9454-1.28050.74847.57492.48986.71440.16070.02550.459-0.270.3595-0.399-0.08480.2469-0.34860.24250.02520.04870.3936-0.03110.344149.876429.715213.1959
300.9785-1.5909-0.17482.96590.32662.57230.09690.35340.1788-0.2117-0.1636-0.0231-0.3317-0.04110.02780.2456-0.031-0.01380.36370.05570.469937.059635.145811.9146
315.3481.9256-1.11352.8266-0.86554.34530.14580.5886-0.1651-0.1172-0.0417-0.2072-0.1944-0.65420.01190.36640.0714-0.02480.42640.02890.519920.843335.597218.4158
321.0307-0.2883-0.47121.67910.3662.0888-0.01520.17290.0636-0.3399-0.0663-0.2571-0.03720.16550.06110.32150.01270.11850.40230.12550.412761.8047-45.8587-41.986
336.9375-1.95861.48113.6188-0.5575.39170.2361-0.47320.2272-0.2204-0.31790.07460.7199-0.0474-0.0460.4612-0.07450.06150.4527-0.03130.399962.9266-37.4446-7.37
340.2202-0.3440.28640.6752-0.47670.5140.41070.1439-0.3452-0.5247-0.18150.36410.0772-0.7647-0.37960.71410.0553-0.26320.47320.04080.438728.7665-64.1921-19.1533
352.3532-2.1627-2.39328.17493.5264.4346-0.3191-0.1628-0.5225-0.2226-0.00260.82930.50250.67460.23070.40820.0421-0.04230.55060.18730.348731.4759-71.6615-10.5461
364.666-0.85731.3570.61540.75852.42150.2742-0.1088-0.1948-0.0813-0.39720.29060.3783-0.1298-0.03990.4636-0.0193-0.00320.224-0.01910.627938.3815-65.2959-20.1886
376.1630.51022.22673.34850.27173.87770.1303-0.52040.89280.4289-0.51980.2187-1.1644-0.15370.33380.5210.05610.12710.23080.12750.315539.7465-60.9677-9.2746
380.43161.5626-0.00266.0923-1.7726.5712-0.2029-0.3241-0.37910.0158-0.3069-1.51080.9421.04420.55950.32690.06620.01580.44410.14990.469155.6938-70.4949-14.6333
390.53670.15930.5031.46042.33894.6495-0.1334-0.1563-0.25-0.25980.53450.1755-0.08270.77510.10180.39970.0130.12220.33120.09250.532455.8715-65.2027-24.4207
403.48792.3313-1.14161.5496-0.74710.9133-0.0933-0.2484-0.24250.1851-0.0324-0.6210.27510.46360.19960.42260.0570.04310.28160.00190.455245.5349-68.645-8.2613
415.99411.6752-1.33033.23042.46573.59810.7034-0.97030.73680.4586-0.2785-0.1197-0.76310.14410.06120.6824-0.12310.0610.7233-0.10070.302141.8498-57.41821.3847
424.507-1.1915-1.48222.0561-0.85881.8348-0.1196-0.916-0.25471.09660.35030.48230.230.3282-0.02280.7974-0.02750.00780.38960.0130.444-8.7146-3.42939.6719
432.73833.0942-0.07324.1656-1.17145.52850.2748-0.40870.20921.97850.2433-0.1749-0.6013-0.9052-0.42730.75910.0373-0.15090.3322-0.00250.5871-6.79244.483137.6457
441.5647-0.85681.74671.9876-1.32484.780.0791-0.04060.15080.40120.1331-0.3593-0.17990.6697-0.16720.3707-0.08-0.13610.4380.01430.4830.94094.207927.3346
455.9229-3.38190.10818.1959-2.95727.3944-0.0082-0.4006-0.5324-0.86190.99461.21090.7954-0.9073-0.86380.4163-0.0311-0.15960.5810.15370.770438.36094.4357-11.5074
468.8553-2.02930.29315.92531.30381.3791-0.33390.63250.047-1.04460.57371.25990.0892-0.4971-0.75760.6701-0.0627-0.02230.70010.23640.571237.99717.673-20.7243
475.4255-1.00021.60144.4917-0.56757.50640.77741.2886-0.4639-1.0860.0408-0.25730.7010.3108-0.70420.5280.0065-0.16020.3576-0.0970.587226.61888.5995-15.1902
484.9435-0.75241.49031.96680.03527.76480.08380.62680.7825-0.4255-0.153-0.3184-0.34740.52220.09580.3443-0.0177-0.00690.31210.05370.536229.745716.2533-10.3441
493.2386-1.10331.82511.79650.05864.3469-0.87290.1937-0.5569-0.2726-0.0191-0.14770.2597-0.18230.38730.08630.0851-0.06540.4243-0.1460.353720.42719.3926-2.6351
502.1023.45510.44526.8395-1.42044.10880.2276-0.5952-0.94380.3038-0.4325-0.23491.2955-1.39550.43660.5867-0.25090.05850.57680.03940.370922.50790.70359.3062
511.74690.15011.78480.2884-0.34644.7757-0.3808-0.3220.4551-0.07760.1789-0.1713-0.4511-0.60220.23110.3703-0.0079-0.0960.3286-0.06590.51623.621812.7819-1.6871
520.0621-0.15880.17040.6672-0.60530.57460.37430.02640.3047-0.3817-0.4686-0.4032-0.29220.3795-0.08790.63730.23190.01710.4092-0.0540.82849.7479-13.4106-7.624
530.4638-0.27440.06333.8364-2.90442.30660.03610.20830.3858-0.3416-0.5075-0.69190.16240.40910.07090.37010.0745-0.11910.4777-0.13730.383548.4574-11.82974.169
545.43380.4538-0.18710.487-0.15692.5180.0940.1838-0.49090.1713-0.2353-0.5847-0.05760.33590.10750.52090.0201-0.07990.3096-0.06440.34141.1532-14.6799-5.92
554.9197-1.38131.5841.3613-0.64253.56860.1393-1.09660.05270.11240.1668-0.0567-0.02170.0017-0.26310.3505-0.0577-0.10890.292-0.00130.250830.1946-15.94833.8884
562.0477-0.06541.0993.56790.37890.44420.2268-0.42140.0272-0.2630.04330.63930.2632-0.4328-0.20860.4341-0.02410.03480.40590.01730.316424.5517-11.5674-5.2585
577.4492-2.7217-1.05488.49311.73295.418-0.7166-0.9182-0.80561.32550.69390.6311.0593-0.823-0.18090.87770.0121-0.09560.4610.08560.396839.4114-25.433210.1677
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 41 )
2X-RAY DIFFRACTION2chain 'D' and (resid 42 through 48 )
3X-RAY DIFFRACTION3chain 'D' and (resid 49 through 62 )
4X-RAY DIFFRACTION4chain 'D' and (resid 63 through 142 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 41 )
6X-RAY DIFFRACTION6chain 'L' and (resid 42 through 48 )
7X-RAY DIFFRACTION7chain 'L' and (resid 49 through 55 )
8X-RAY DIFFRACTION8chain 'L' and (resid 56 through 127 )
9X-RAY DIFFRACTION9chain 'L' and (resid 128 through 142 )
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 41 )
11X-RAY DIFFRACTION11chain 'F' and (resid 42 through 48 )
12X-RAY DIFFRACTION12chain 'F' and (resid 49 through 62 )
13X-RAY DIFFRACTION13chain 'F' and (resid 63 through 127 )
14X-RAY DIFFRACTION14chain 'F' and (resid 128 through 142 )
15X-RAY DIFFRACTION15chain 'I' and (resid 1 through 24 )
16X-RAY DIFFRACTION16chain 'I' and (resid 25 through 41 )
17X-RAY DIFFRACTION17chain 'I' and (resid 42 through 54 )
18X-RAY DIFFRACTION18chain 'I' and (resid 55 through 127 )
19X-RAY DIFFRACTION19chain 'I' and (resid 128 through 142 )
20X-RAY DIFFRACTION20chain 'G' and (resid 9 through 140 )
21X-RAY DIFFRACTION21chain 'G' and (resid 141 through 219 )
22X-RAY DIFFRACTION22chain 'G' and (resid 220 through 358 )
23X-RAY DIFFRACTION23chain 'G' and (resid 359 through 396 )
24X-RAY DIFFRACTION24chain 'B' and (resid 9 through 87 )
25X-RAY DIFFRACTION25chain 'B' and (resid 88 through 320 )
26X-RAY DIFFRACTION26chain 'B' and (resid 321 through 396 )
27X-RAY DIFFRACTION27chain 'J' and (resid 9 through 87 )
28X-RAY DIFFRACTION28chain 'J' and (resid 88 through 238 )
29X-RAY DIFFRACTION29chain 'J' and (resid 239 through 273 )
30X-RAY DIFFRACTION30chain 'J' and (resid 274 through 358 )
31X-RAY DIFFRACTION31chain 'J' and (resid 359 through 396 )
32X-RAY DIFFRACTION32chain 'A' and (resid 9 through 358 )
33X-RAY DIFFRACTION33chain 'A' and (resid 359 through 396 )
34X-RAY DIFFRACTION34chain 'E' and (resid 55 through 80 )
35X-RAY DIFFRACTION35chain 'E' and (resid 81 through 94 )
36X-RAY DIFFRACTION36chain 'E' and (resid 95 through 118 )
37X-RAY DIFFRACTION37chain 'E' and (resid 119 through 142 )
38X-RAY DIFFRACTION38chain 'E' and (resid 143 through 157 )
39X-RAY DIFFRACTION39chain 'E' and (resid 158 through 177 )
40X-RAY DIFFRACTION40chain 'E' and (resid 178 through 191 )
41X-RAY DIFFRACTION41chain 'E' and (resid 192 through 203 )
42X-RAY DIFFRACTION42chain 'H' and (resid 56 through 103 )
43X-RAY DIFFRACTION43chain 'H' and (resid 104 through 142 )
44X-RAY DIFFRACTION44chain 'H' and (resid 143 through 203 )
45X-RAY DIFFRACTION45chain 'K' and (resid 55 through 64 )
46X-RAY DIFFRACTION46chain 'K' and (resid 65 through 80 )
47X-RAY DIFFRACTION47chain 'K' and (resid 81 through 103 )
48X-RAY DIFFRACTION48chain 'K' and (resid 104 through 142 )
49X-RAY DIFFRACTION49chain 'K' and (resid 143 through 149 )
50X-RAY DIFFRACTION50chain 'K' and (resid 150 through 156 )
51X-RAY DIFFRACTION51chain 'K' and (resid 157 through 203 )
52X-RAY DIFFRACTION52chain 'C' and (resid 55 through 80 )
53X-RAY DIFFRACTION53chain 'C' and (resid 81 through 93 )
54X-RAY DIFFRACTION54chain 'C' and (resid 94 through 128 )
55X-RAY DIFFRACTION55chain 'C' and (resid 129 through 156 )
56X-RAY DIFFRACTION56chain 'C' and (resid 157 through 185 )
57X-RAY DIFFRACTION57chain 'C' and (resid 186 through 203 )

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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