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- PDB-7ry1: human Hsp90_MC domain structure -

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基本情報

登録情報
データベース: PDB / ID: 7ry1
タイトルhuman Hsp90_MC domain structure
要素Heat shock protein HSP 90-alpha
キーワードCHAPERONE / Hsp90 / hexamer
機能・相同性
機能・相同性情報


sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / TPR domain binding / PIWI-interacting RNA (piRNA) biogenesis / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / regulation of postsynaptic membrane neurotransmitter receptor levels / regulation of protein-containing complex assembly / HSF1 activation / telomere maintenance via telomerase / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / cardiac muscle cell apoptotic process / positive regulation of telomere maintenance via telomerase / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy / disordered domain specific binding / MHC class II protein complex binding / The role of GTSE1 in G2/M progression after G2 checkpoint
類似検索 - 分子機能
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold
類似検索 - ドメイン・相同性
Chem-MDC / Heat shock protein HSP 90-alpha
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: 3.523 Å
データ登録者Peng, S. / Deng, J. / Matts, R.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)1R15CA219907-01 米国
引用ジャーナル: Acta Crystallogr D Struct Biol / 年: 2022
タイトル: Crystal structure of the middle and C-terminal domains of Hsp90 alpha labeled with a coumarin derivative reveals a potential allosteric binding site as a drug target.
著者: Peng, S. / Woodruff, J. / Pathak, P.K. / Matts, R.L. / Deng, J.
履歴
登録2021年8月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年5月11日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
改定 1.22024年12月25日Group: Advisory / Derived calculations / Structure summary
カテゴリ: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
C: Heat shock protein HSP 90-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,1876
ポリマ－149,0363
非ポリマー1,1503
水00
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,1244
ポリマ－99,3582
非ポリマー7672
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-26 kcal/mol
Surface area42350 Å2
手法PISA
2
C: Heat shock protein HSP 90-alpha
ヘテロ分子

C: Heat shock protein HSP 90-alpha
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)100,1244
ポリマ－99,3582
非ポリマー7672
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5440 Å2
ΔGint-29 kcal/mol
Surface area43280 Å2
手法PISA
単位格子
Length a, b, c (Å)159.850, 311.964, 88.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resseq 293 or resseq 295:296 or (resid...
21(chain B and (resseq 293 or resseq 295:296 or (resid...
31(chain C and (resseq 293 or resseq 295:296 or (resid...

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
11THRTHRTHRTHR(chain A and (resseq 293 or resseq 295:296 or (resid...AA2934
12PROPROILEILE(chain A and (resseq 293 or resseq 295:296 or (resid...AA295 - 2966 - 7
13TRPTRPTRPTRP(chain A and (resseq 293 or resseq 295:296 or (resid...AA2978
14THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
15THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
16THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
17THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
18THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
19THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
110THRTHRASPASP(chain A and (resseq 293 or resseq 295:296 or (resid...AA293 - 6994 - 410
21THRTHRTHRTHR(chain B and (resseq 293 or resseq 295:296 or (resid...BB2934
22PROPROILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB295 - 2966 - 7
23TRPTRPTRPTRP(chain B and (resseq 293 or resseq 295:296 or (resid...BB2978
24THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
25THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
26THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
27THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
28THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
29THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
210THRTHRILEILE(chain B and (resseq 293 or resseq 295:296 or (resid...BB293 - 6984 - 409
31THRTHRTHRTHR(chain C and (resseq 293 or resseq 295:296 or (resid...CC2934
32PROPROILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC295 - 2966 - 7
33TRPTRPTRPTRP(chain C and (resseq 293 or resseq 295:296 or (resid...CC2978
34THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
35THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
36THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
37THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
38THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
39THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409
310THRTHRILEILE(chain C and (resseq 293 or resseq 295:296 or (resid...CC293 - 6984 - 409

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要素

#1: タンパク質 Heat shock protein HSP 90-alpha / Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS- ...Heat shock 86 kDa / HSP 86 / HSP86 / Lipopolysaccharide-associated protein 2 / LAP-2 / LPS-associated protein 2 / Renal carcinoma antigen NY-REN-38


分子量: 49678.781 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HSP90AA1, HSP90A, HSPC1, HSPCA / 発現宿主: Escherichia coli (大腸菌)
参照: UniProt: P07900, non-chaperonin molecular chaperone ATPase
#2: 化合物 ChemComp-MDC / N-[2-(1-MALEIMIDYL)ETHYL]-7-DIETHYLAMINOCOUMARIN-3-CARBOXAMIDE


分子量: 383.398 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C20H21N3O5 / タイプ: SUBJECT OF INVESTIGATION
研究の焦点であるリガンドがあるかY
Has protein modificationN

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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: 3.69 Å3/Da / 溶媒含有率: 66.64 %
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 Succinic acid PH 6.5, 12% PEG3350, 20mM CaCl2

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 19-ID / 波長: 0.97951 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2019年12月4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: 0.97951 Å / 相対比: 1
反射解像度: 3.5→50 Å / Num. obs: 27438 / % possible obs: 99.9 % / 冗長度: 6.4 % / Biso Wilson estimate: 127.52 Å2 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.063 / Rrim(I) all: 0.161 / Χ2: 0.688 / Net I/σ(I): 3.9 / Num. measured all: 176259
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.5-3.636.41.36627080.5360.5811.4870.466100
3.63-3.776.30.84426860.7090.3620.920.484100
3.77-3.946.10.64527160.8120.2830.7060.511100
3.94-4.156.30.44527090.9220.1920.4850.55799.9
4.15-4.416.70.29127220.9550.1210.3160.647100
4.41-4.756.60.22427210.9780.0930.2430.695100
4.75-5.236.30.18127260.9830.0780.1980.77499.9
5.23-5.986.80.17727590.9870.0730.1920.716100
5.98-7.536.60.11627890.9940.0480.1250.757100
7.53-506.10.05529020.9980.0230.061.24699.8

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解析

ソフトウェア
名称バージョン分類
HKL-2000データスケーリング
PHENIX1.10.1_2155精密化
PDB_EXTRACT3.27データ抽出
HKL-3000データ削減
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3Q6M

3q6m


解像度: 3.523→47.421 Å / SU ML: 0.52 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 28.79 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.272 1995 7.28 %
Rwork0.2164 25399 -
obs0.2204 27394 98.7 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 319.62 Å2 / Biso mean: 141.4972 Å2 / Biso min: 72.89 Å2
精密化ステップサイクル: final / 解像度: 3.523→47.421 Å
タンパク質核酸リガンド溶媒全体
原子数9949 0 84 0 10033
Biso mean--180.8 --
残基数----1207
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00410205
X-RAY DIFFRACTIONf_angle_d0.80613701
X-RAY DIFFRACTIONf_chiral_restr0.0471504
X-RAY DIFFRACTIONf_plane_restr0.0041743
X-RAY DIFFRACTIONf_dihedral_angle_d14.8996323
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5296X-RAY DIFFRACTION8.528TORSIONAL
12B5296X-RAY DIFFRACTION8.528TORSIONAL
13C5296X-RAY DIFFRACTION8.528TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.523-3.61080.38911180.3429149884
3.6108-3.70840.34111430.32621819100
3.7084-3.81740.33861440.30981829100
3.8174-3.94060.33221400.30291784100
3.9406-4.08140.32841420.29561816100
4.0814-4.24470.32931420.26141812100
4.2447-4.43770.29251450.24211828100
4.4377-4.67150.25231440.23511835100
4.6715-4.96390.28681420.22511815100
4.9639-5.34670.25791450.20321826100
5.3467-5.88380.25951460.21851861100
5.8838-6.73320.29031460.21851857100
6.7332-8.47520.26081470.18991861100
8.4752-47.420.21211510.142195899
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)
18.24581.44432.90412.4932-1.97439.3351-0.17321.55980.3043-3.2550.0777-0.55160.157-0.5309-0.0051.56740.1301-0.04281.39090.20071.12-11.4122-39.2473-7.6209
28.57382.31292.02352.44553.73839.7126-0.57340.5710.3546-2.14970.4276-0.5722-0.6730.27420.28241.0334-0.05460.14581.10140.13451.0015-16.6525-37.7801-0.537
39.24252.7445-1.98654.60513.8759.43210.5341-1.8296-0.39152.1534-0.79740.18551.95431.16170.26841.67830.1032-0.12581.11910.0421.2189-11.8231-43.441710.5408
46.17774.2925-1.87048.8379-0.33747.59780.7244-0.98041.18160.9001-0.48390.31730.10380.3436-0.1991.2537-0.0213-0.14831.0595-0.12350.9407-18.0828-33.685410.1674
59.39742.7957-2.7075.9321-0.58126.2202-0.22860.56090.0296-0.26420.08840.6558-0.2104-1.53510.18091.11720.0567-0.07741.4284-0.00181.0704-42.2292-51.63077.8703
62.4317-0.7195-2.05246.6608-0.44613.0531-0.0379-1.26880.57720.14640.66641.2331-0.8737-1.5379-0.47621.43390.39010.10322.07720.24921.3088-48.6351-49.209917.2611
76.55121.70775.98466.9501-0.18885.9011-1.5487-3.74771.1165-1.53980.23692.41430.308-0.31531.29321.49530.16450.71233.54210.74522.212-66.3199-62.335528.6932
88.4913.2317-0.18975.8115-4.07862.9536-0.351-1.3552-0.2905-0.61520.4654-0.53560.4285-1.0438-0.07951.2823-0.00660.11081.76820.36131.5282-47.8834-62.11326.3735
90.2219-1.170.90276.1623-2.47749.0856-0.4576-0.571-0.30980.51911.1933-0.2432-0.0665-1.3414-0.95331.5689-0.21340.03552.20910.25691.4388-53.4395-68.980629.486
104.4302-1.40541.13482.2934-1.03247.80991.00010.0467-0.33220.36380.36840.53491.5541-0.8609-1.31221.4086-0.2943-0.10611.68810.43451.813-50.9043-79.845728.0664
117.535.08450.49535.16090.27453.25410.124-1.53370.23571.486-0.3571-0.7420.19310.20160.22551.31420.0624-0.1591.09480.05391.05663.9861-66.799148.5569
124.19510.8976-2.64439.4813.58858.50320.1740.89180.2609-1.3578-0.2618-0.0385-1.6243-0.65080.07721.40950.08540.01620.89840.06711.21912.0828-62.952435.5788
135.6002-0.61623.71128.85381.19765.4095-0.36810.5286-0.306-0.30810.5801-0.9717-0.24870.1891-0.08881.0108-0.00630.03221-0.01310.85575.6948-72.83634.3449
148.07543.14762.66489.31720.78135.80680.3088-0.5091-0.99730.68120.20750.43611.4113-1.3436-0.4561.2921-0.2830.04791.18370.24461.1675-21.2165-85.52337.318
156.0433-0.52483.32333.98640.19024.53070.23370.778-1.592-1.27580.19620.52692.3882-0.5235-0.32972.1863-0.58290.00681.5395-0.12481.6008-31.7964-95.637421.7012
163.468-3.37251.32223.7205-2.17516.5053-0.08550.90570.8317-0.9097-0.4939-1.69760.06570.24640.58921.5667-0.3398-0.21781.77920.34041.9524-27.898-80.434619.2727
176.3831-4.83441.04325.70933.18697.7856-0.24810.0463-0.5981-1.1031-0.5219-1.19190.9129-1.38330.9881.5171-0.3852-0.33421.7173-0.07121.3122-33.5798-82.410817.1537
186.2041-6.56620.83817.14650.22845.10820.19460.9604-0.7411-0.72330.0630.96450.6467-0.7906-0.17231.5018-0.7659-0.20792.14980.19511.5464-50.3907-85.744815.9042
198.9833-0.9231.80216.1737-1.26753.991-0.1657-1.3802-0.74031.3389-0.018-0.09590.2207-0.4890.41481.44210.15690.15291.18350.00631.1103-15.1872-44.157649.1903
208.088-2.28164.66539.09162.18438.4915-0.09521.2938-0.9566-1.03290.4111-0.46330.22351.00250.0441.2410.05630.10791.1243-0.1321.2004-14.1867-45.016833.67
219.49122.85690.43853.4608-0.02983.1149-0.56680.47580.0912-0.0996-0.06191.96670.1603-0.3120.60211.4358-0.0227-0.11920.9350.02981.0224-24.9274-38.786937.8057
224.77250.10020.958510.0721-3.72553.8757-0.3574-0.23730.34130.32720.03340.1251-0.5473-0.19640.37631.140.124-0.15970.9112-0.1711.0599-18.9096-13.623136.9987
232.973-0.4636-1.71146.8311-1.31552.08340.2370.61971.2617-0.0210.07791.5732-0.9783-0.8906-0.08361.64190.3087-0.59971.5508-0.13152.0272-26.32143.720923.4961
246.8750.4441-0.73468.7199-0.6265.0416-0.30890.60310.3736-0.9663-0.47061.1132-0.5238-0.91370.51451.50670.0562-0.11841.05550.13531.5705-17.04890.897118.4434
254.52742.8375-1.01453.83622.45025.8061-0.8130.4383-0.6157-0.3185-0.11290.36960.27130.67731.20871.9551-0.1053-0.11461.21690.07381.4211-10.0349-8.762117.3676
266.95613.0648-3.25352.34150.26066.91430.63450.49671.5869-0.3222-0.0738-0.1513-1.2781-0.1727-0.48312.37720.0879-0.38961.05640.00652.0749-4.980411.819415.9325
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 317 )A293 - 317
2X-RAY DIFFRACTION2chain 'A' and (resid 318 through 343 )A318 - 343
3X-RAY DIFFRACTION3chain 'A' and (resid 344 through 377 )A344 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 429 )A378 - 429
5X-RAY DIFFRACTION5chain 'A' and (resid 430 through 523 )A430 - 523
6X-RAY DIFFRACTION6chain 'A' and (resid 524 through 556 )A524 - 556
7X-RAY DIFFRACTION7chain 'A' and (resid 557 through 578 )A557 - 578
8X-RAY DIFFRACTION8chain 'A' and (resid 579 through 617 )A579 - 617
9X-RAY DIFFRACTION9chain 'A' and (resid 618 through 656 )A618 - 656
10X-RAY DIFFRACTION10chain 'A' and (resid 657 through 699 )A657 - 699
11X-RAY DIFFRACTION11chain 'B' and (resid 293 through 343 )B293 - 343
12X-RAY DIFFRACTION12chain 'B' and (resid 344 through 377 )B344 - 377
13X-RAY DIFFRACTION13chain 'B' and (resid 378 through 429 )B378 - 429
14X-RAY DIFFRACTION14chain 'B' and (resid 430 through 523 )B430 - 523
15X-RAY DIFFRACTION15chain 'B' and (resid 524 through 596 )B524 - 596
16X-RAY DIFFRACTION16chain 'B' and (resid 597 through 618 )B597 - 618
17X-RAY DIFFRACTION17chain 'B' and (resid 619 through 640 )B619 - 640
18X-RAY DIFFRACTION18chain 'B' and (resid 641 through 698 )B641 - 698
19X-RAY DIFFRACTION19chain 'C' and (resid 293 through 343 )C293 - 343
20X-RAY DIFFRACTION20chain 'C' and (resid 344 through 402 )C344 - 402
21X-RAY DIFFRACTION21chain 'C' and (resid 403 through 429 )C403 - 429
22X-RAY DIFFRACTION22chain 'C' and (resid 430 through 532 )C430 - 532
23X-RAY DIFFRACTION23chain 'C' and (resid 533 through 578 )C533 - 578
24X-RAY DIFFRACTION24chain 'C' and (resid 579 through 607 )C579 - 607
25X-RAY DIFFRACTION25chain 'C' and (resid 608 through 640 )C608 - 640
26X-RAY DIFFRACTION26chain 'C' and (resid 641 through 698 )C641 - 698

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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