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- PDB-7rxz: 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: 7rxz
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


positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane ...positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / protein insertion into mitochondrial outer membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / 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 / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / telomere maintenance via telomerase / protein unfolding / HSF1-dependent transactivation / response to unfolded protein / positive regulation of cell size / chaperone-mediated protein complex assembly / regulation of protein-containing complex assembly / HSF1 activation / Attenuation phase / RHOBTB2 GTPase cycle / positive regulation of defense response to virus by host / eNOS activation / positive regulation of lamellipodium assembly / axonal growth cone / DNA polymerase binding / activation of innate immune response / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Signaling by ERBB2 / response to salt stress / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of cardiac muscle contraction / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / protein tyrosine kinase binding / AURKA Activation by TPX2 / Constitutive Signaling by Overexpressed ERBB2 / lysosomal lumen / ESR-mediated signaling / VEGFR2 mediated vascular permeability / response to cocaine / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / neuron migration / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Downregulation of ERBB2 signaling / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Aggrephagy / Chaperone Mediated Autophagy / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / positive regulation of nitric oxide biosynthetic process / unfolded protein binding / melanosome
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
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: 3.152 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: J.Biomol.Struct.Dyn. / 年: 2022
タイトル: Structural basis of the key residue W320 responsible for Hsp90 conformational change.
著者: Peng, S. / 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12月28日Provider: repository / タイプ: Initial release
改定 1.12023年10月25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

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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
D: Heat shock protein HSP 90-alpha
E: Heat shock protein HSP 90-alpha
F: Heat shock protein HSP 90-alpha


分子量 (理論値)分子数
合計 (水以外)298,0736
ポリマ－298,0736
非ポリマー00
水00
1
A: Heat shock protein HSP 90-alpha
B: Heat shock protein HSP 90-alpha


分子量 (理論値)分子数
合計 (水以外)99,3582
ポリマ－99,3582
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-27 kcal/mol
Surface area40390 Å2
手法PISA
2
C: Heat shock protein HSP 90-alpha
D: Heat shock protein HSP 90-alpha


分子量 (理論値)分子数
合計 (水以外)99,3582
ポリマ－99,3582
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-29 kcal/mol
Surface area39620 Å2
手法PISA
3
E: Heat shock protein HSP 90-alpha
F: Heat shock protein HSP 90-alpha


分子量 (理論値)分子数
合計 (水以外)99,3582
ポリマ－99,3582
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-29 kcal/mol
Surface area40070 Å2
手法PISA
単位格子
Length a, b, c (Å)153.830, 87.987, 166.178
Angle α, β, γ (deg.)90.000, 114.360, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and ((resid 293 and (name O or name...
21(chain B and ((resid 293 and (name O or name...
31(chain C and ((resid 293 and (name O or name...
41(chain D and ((resid 293 and (name N or name...
51(chain E and ((resid 293 and (name O or name...
61(chain F and ((resid 293 and (name N or name...

NCSドメイン領域:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR

Dom-IDComponent-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR(chain A and ((resid 293 and (name O or name...AA2934
12ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
13ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
14ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
15ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
16ILEILE(chain A and ((resid 293 and (name O or name...AA293 - 6984 - 409
21THRTHR(chain B and ((resid 293 and (name O or name...BB2934
22ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
23ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
24ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
25ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
26ILEILE(chain B and ((resid 293 and (name O or name...BB293 - 6984 - 409
31THRTHR(chain C and ((resid 293 and (name O or name...CC2934
32ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
33ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
34ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
35ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
36ILEILE(chain C and ((resid 293 and (name O or name...CC293 - 6984 - 409
41THRTHR(chain D and ((resid 293 and (name N or name...DD2934
42ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
43ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
44ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
45ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
46ILEILE(chain D and ((resid 293 and (name N or name...DD293 - 6984 - 409
51THRTHR(chain E and ((resid 293 and (name O or name...EE2934
52ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
53ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
54ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
55ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
56ILEILE(chain E and ((resid 293 and (name O or name...EE293 - 6984 - 409
61THRTHR(chain F and ((resid 293 and (name N or name...FF2934
62ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
63ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
64ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
65ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 6984 - 409
66ILEILE(chain F and ((resid 293 and (name N or name...FF293 - 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: 6 / 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

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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: 3.7 Å3/Da / 溶媒含有率: 66.73 %
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 NaAc PH 6.0, 12 % PEG3350

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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: 0.97922 Å
検出器タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2015年12月3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: 0.97922 Å / 相対比: 1
反射解像度: 3.15→50 Å / Num. obs: 70092 / % possible obs: 99.7 % / 冗長度: 3.3 % / Biso Wilson estimate: 76.89 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.086 / Rrim(I) all: 0.158 / Χ2: 1.625 / Net I/σ(I): 8.4 / Num. measured all: 231203
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
3.15-3.263.20.81169370.620.5310.9731.32499.7
3.26-3.393.20.62569740.7320.4090.751.42799.8
3.39-3.553.20.4269620.8560.2750.5041.66199.4
3.55-3.733.20.30569090.9110.1990.3661.74699.5
3.73-3.973.20.22570030.9470.1470.2691.85899.7
3.97-4.273.30.14969880.9730.0960.1771.74799.8
4.27-4.73.30.11470160.9820.0730.1361.72199.8
4.7-5.383.40.09970400.9850.0630.1171.679100
5.38-6.783.60.09670770.9860.0590.1131.456100
6.78-503.40.07371860.9850.0490.0881.64199.2

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解析

ソフトウェア
名称バージョン分類
PHENIX1.10.1_2155精密化
HKL-2000データスケーリング
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: 3.152→48.09 Å / SU ML: 0.45 / 交差検証法: THROUGHOUT / σ(F): 0 / 位相誤差: 27.45 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.248 1848 2.86 %
Rwork0.1911 62701 -
obs0.1927 64549 91.76 %
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: 195.87 Å2 / Biso mean: 88.8291 Å2 / Biso min: 40.24 Å2
精密化ステップサイクル: final / 解像度: 3.152→48.09 Å
タンパク質核酸リガンド溶媒全体
原子数19425 0 0 0 19425
残基数----2362
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01219744
X-RAY DIFFRACTIONf_angle_d1.40526515
X-RAY DIFFRACTIONf_chiral_restr0.0732946
X-RAY DIFFRACTIONf_plane_restr0.0083370
X-RAY DIFFRACTIONf_dihedral_angle_d13.11412291
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A8708X-RAY DIFFRACTION12.152TORSIONAL
12B8708X-RAY DIFFRACTION12.152TORSIONAL
13C8708X-RAY DIFFRACTION12.152TORSIONAL
14D8708X-RAY DIFFRACTION12.152TORSIONAL
15E8708X-RAY DIFFRACTION12.152TORSIONAL
16F8708X-RAY DIFFRACTION12.152TORSIONAL
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 (%)
3.152-3.2370.37361120.3259407578
3.237-3.33220.32491330.3043425482
3.3322-3.43970.4191410.2978431683
3.4397-3.56260.30731290.2617459088
3.5626-3.70520.3261380.256471790
3.7052-3.87380.31361450.2317474391
3.8738-4.07790.28161340.2103487993
4.0779-4.33320.24551470.1763505596
4.3332-4.66750.2281480.1579507497
4.6675-5.13680.18581510.1525514498
5.1368-5.87890.24541510.1688523799
5.8789-7.40250.24371630.1786525199
7.4025-48.090.17041560.1421536699
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)
16.4464-0.9146-0.30124.89571.99016.12680.13010.6938-0.0448-0.2553-0.10090.0136-0.4434-0.1868-0.15090.4783-0.07920.05840.5593-0.00010.466544.252423.1929139.4531
21.1579-1.35190.56184.91380.72470.81260.3167-0.30370.8407-0.3353-0.4074-0.85140.1989-0.54970.13980.71120.0885-0.00160.6572-0.04470.750532.515835.9968141.4844
34.95971.16733.41920.72960.28912.98050.1791-0.386-0.08270.6389-0.1818-0.20190.0865-0.23650.02040.7425-0.1147-0.02750.5474-0.02260.642462.938931.4761158.1157
43.9660.928-1.03992.5688-0.4273.80860.1308-0.44320.40640.4502-0.06640.34170.03170.0309-0.03950.69720.0086-0.16470.4519-0.07820.710785.595450.9232163.4777
54.527-0.79151.22032.984-0.22494.05480.0590.16260.12470.17680.0153-0.03870.2879-0.113-0.06350.61780.0427-0.04290.51870.11870.51963.57163.4968112.6753
63.2464-1.28892.42461.5716-1.37693.68230.04940.27310.1976-0.124-0.2524-0.2120.13450.17380.17830.5680.096-0.10660.60220.00560.712196.254347.457135.107
75.3058-0.3236-1.20965.01080.70343.5044-0.1948-0.0889-0.13940.34560.2262-0.11770.23530.501-0.01590.620.0336-0.01370.6067-0.00310.435934.242921.2762112.7267
83.78550.9591-2.47624.3668-2.8266.1368-0.02160.19780.40020.42070.0511-0.061-0.41710.3401-0.05810.80970.062-0.12320.5385-0.04930.577229.912533.1097108.0682
93.9816-1.5452-1.66521.2551.00792.7847-0.1490.2021-0.40290.1154-0.14960.57880.3689-0.26790.34170.66450.05560.15750.524-0.09080.87735.919729.7781124.6403
102.1021-1.6722-1.36571.390.79192.03810.1750.4817-0.2102-0.4521-0.34010.2223-0.3546-0.43710.2060.66510.13510.02190.7677-0.060.8714-6.713843.1084129.5983
111.9439-0.51081.22462.10930.17433.6686-0.2430.11620.09450.00150.07040.0093-0.03560.23680.15740.54190.07410.13930.5273-0.03820.6589-2.540449.5742144.0319
124.34240.3224-2.54885.1766-0.95544.8941-0.02230.73350.3928-0.00610.068-0.0412-0.18560.2517-0.08390.4705-0.0644-0.08580.61990.02670.4750.031869.5242139.2372
133.094-2.9106-1.82422.93611.79991.07670.02490.4068-0.31520.11610.04480.21220.69320.00320.22240.8528-0.0916-0.10840.6186-0.02170.642555.210354.8857141.5426
144.31042.1352-2.59930.5679-0.92021.40120.2906-0.47110.11840.6672-0.22740.1147-0.38480.0866-0.05110.7954-0.10480.13090.54630.04210.656530.809758.8676158.3263
153.2018-0.18450.59213.0334-0.0082.95060.174-0.1609-0.22170.5133-0.03940.010.02680.0333-0.13460.5534-0.01090.17560.58360.09830.70447.4739.5681164.1466
162.03740.6340.77962.15070.74836.0355-0.2518-0.2713-0.1164-0.1406-0.0050.01810.20440.17830.34630.48430.1113-0.03830.56760.10250.598864.826726.9569117.4465
171.84170.5927-0.033.9334-3.18696.7398-0.03270.4394-0.1515-0.82-0.2064-0.39260.4320.46970.21320.76480.11840.04380.580.03030.54867.520332.675185.8353
184.5562-1.0284-0.63973.4887-0.92913.8243-0.0854-0.09050.2627-0.04610.0371-0.1386-0.19480.12170.00340.91130.0019-0.09290.6380.04930.494557.40550.246668.2828
192.92751.4019-0.09563.6479-0.59316.5657-0.1947-0.55510.12410.0047-0.20310.32560.07750.05430.37560.34120.09530.01650.6073-0.08720.612229.000663.0865118.0242
201.2918-0.7016-0.99331.47111.94774.8202-0.0480.2274-0.0282-0.383-0.25190.40980.0235-0.45740.37120.8146-0.0462-0.13530.5357-0.02170.591529.549248.378277.2295
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 385 )A293 - 385
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 407 )A386 - 407
3X-RAY DIFFRACTION3chain 'A' and (resid 408 through 543 )A408 - 543
4X-RAY DIFFRACTION4chain 'A' and (resid 544 through 698 )A544 - 698
5X-RAY DIFFRACTION5chain 'B' and (resid 293 through 451 )B293 - 451
6X-RAY DIFFRACTION6chain 'B' and (resid 452 through 698 )B452 - 698
7X-RAY DIFFRACTION7chain 'C' and (resid 293 through 371 )C293 - 371
8X-RAY DIFFRACTION8chain 'C' and (resid 372 through 429 )C372 - 429
9X-RAY DIFFRACTION9chain 'C' and (resid 430 through 513 )C430 - 513
10X-RAY DIFFRACTION10chain 'C' and (resid 514 through 582 )C514 - 582
11X-RAY DIFFRACTION11chain 'C' and (resid 583 through 698 )C583 - 698
12X-RAY DIFFRACTION12chain 'D' and (resid 293 through 371 )D293 - 371
13X-RAY DIFFRACTION13chain 'D' and (resid 372 through 407 )D372 - 407
14X-RAY DIFFRACTION14chain 'D' and (resid 408 through 543 )D408 - 543
15X-RAY DIFFRACTION15chain 'D' and (resid 544 through 698 )D544 - 698
16X-RAY DIFFRACTION16chain 'E' and (resid 293 through 429 )E293 - 429
17X-RAY DIFFRACTION17chain 'E' and (resid 430 through 555 )E430 - 555
18X-RAY DIFFRACTION18chain 'E' and (resid 556 through 698 )E556 - 698
19X-RAY DIFFRACTION19chain 'F' and (resid 293 through 427 )F293 - 427
20X-RAY DIFFRACTION20chain 'F' and (resid 428 through 698 )F428 - 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