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- PDB-7lv3: Crystal structure of human protein kinase G (PKG) R-C complex in ... -

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基本情報

登録情報
データベース: PDB / ID: 7lv3
タイトルCrystal structure of human protein kinase G (PKG) R-C complex in inhibited state
要素Isoform Beta of cGMP-dependent protein kinase 1
キーワードTRANSFERASE/INHIBITOR / Protein Kinase G / TRANSFERASE-INHIBITOR complex
機能・相同性
機能・相同性情報


negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle ...negative regulation of glutamate secretion / negative regulation of inositol phosphate biosynthetic process / cGMP-dependent protein kinase / cGMP-dependent protein kinase activity / cell growth involved in cardiac muscle cell development / regulation of testosterone biosynthetic process / collateral sprouting / negative regulation of platelet aggregation / positive regulation of circadian rhythm / relaxation of vascular associated smooth muscle / Rap1 signalling / regulation of GTPase activity / cGMP-mediated signaling / mitogen-activated protein kinase p38 binding / spermatid development / cGMP effects / negative regulation of vascular associated smooth muscle cell migration / negative regulation of vascular associated smooth muscle cell proliferation / dendrite development / cGMP binding / forebrain development / calcium channel regulator activity / cerebellum development / acrosomal vesicle / sarcolemma / neuron migration / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / Ca2+ pathway / protein kinase activity / protein phosphorylation / protein serine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
類似検索 - 分子機能
cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. ...cGMP-dependent protein kinase, N-terminal coiled-coil domain / Coiled-coil N-terminus of cGMP-dependent protein kinase / cGMP-dependent kinase / cGMP-dependent protein kinase, catalytic domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Extension to Ser/Thr-type protein kinases / Jelly Rolls / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / RmlC-like jelly roll fold / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Jelly Rolls / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / cGMP-dependent protein kinase 1
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.41 Å
データ登録者Sharma, R. / Lying, Q. / Casteel, D. / Kim, C.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090161 米国
引用ジャーナル: Elife / 年: 2022
タイトル: An auto-inhibited state of protein kinase G and implications for selective activation.
著者: Sharma, R. / Kim, J.J. / Qin, L. / Henning, P. / Akimoto, M. / VanSchouwen, B. / Kaur, G. / Sankaran, B. / MacKenzie, K.R. / Melacini, G. / Casteel, D.E. / Herberg, F.W. / Kim, C.W.
履歴
登録2021年2月23日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年8月24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11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
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: Isoform Beta of cGMP-dependent protein kinase 1
B: Isoform Beta of cGMP-dependent protein kinase 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)141,14111
ポリマ－139,7232
非ポリマー1,4189
水2,288127
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: mass spectrometry, Dimer
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-63 kcal/mol
Surface area52600 Å2
手法PISA
単位格子
Length a, b, c (Å)99.832, 112.824, 150.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID
11
21

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
11LYSLYSPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA75 - 836 - 14
12ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA9021
13PROPROSERSER(chain 'A' and (resid 75 through 84 or resid 90...AA97 - 10228 - 33
14SERSERLEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA105 - 10836 - 39
15GLUGLULEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA111 - 12242 - 53
16SERSERPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA125 - 13656 - 67
17TYRTYRTYRTYR(chain 'A' and (resid 75 through 84 or resid 90...AA13970
18SERSERILEILE(chain 'A' and (resid 75 through 84 or resid 90...AA143 - 14574 - 76
19GLYGLYMETMET(chain 'A' and (resid 75 through 84 or resid 90...AA149 - 15880 - 89
110GLYGLYLYSLYS(chain 'A' and (resid 75 through 84 or resid 90...AA161 - 16292 - 93
111VALVALVALVAL(chain 'A' and (resid 75 through 84 or resid 90...AA16596
112GLYGLYGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA169100
113CYSCYSPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA173 - 177104 - 108
114VALVALTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA180 - 195111 - 126
115LEULEUARGARG(chain 'A' and (resid 75 through 84 or resid 90...AA204 - 209135 - 140
116CYSCYSMETMET(chain 'A' and (resid 75 through 84 or resid 90...AA211 - 216142 - 147
117THRTHRPHEPHE(chain 'A' and (resid 75 through 84 or resid 90...AA219 - 230150 - 161
118SERSERPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA233 - 241164 - 172
119ILEILEVALVAL(chain 'A' and (resid 75 through 84 or resid 90...AA244 - 251175 - 182
120GLUGLUGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA254 - 267185 - 198
121GLYGLYSERSER(chain 'A' and (resid 75 through 84 or resid 90...AA270 - 288201 - 219
122ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA292223
123PHEPHELEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA295 - 299226 - 230
124GLYGLYPHEPHE(chain 'A' and (resid 75 through 84 or resid 90...AA302 - 336233 - 267
125GLUGLULYSLYS(chain 'A' and (resid 75 through 84 or resid 90...AA355 - 357286 - 288
126TYRTYRGLUGLU(chain 'A' and (resid 75 through 84 or resid 90...AA360 - 361291 - 292
127ALAALALEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA364 - 370295 - 301
128SERSERGLYGLY(chain 'A' and (resid 75 through 84 or resid 90...AA373 - 384304 - 315
129GLYGLYLEULEU(chain 'A' and (resid 75 through 84 or resid 90...AA387 - 407318 - 338
130ARGARGARGARG(chain 'A' and (resid 75 through 84 or resid 90...AA410341
131ILEILEHISHIS(chain 'A' and (resid 75 through 84 or resid 90...AA412 - 420343 - 351
132SERSERTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA423 - 442354 - 373
133ASPASPASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA445376
134TYRTYRTHRTHR(chain 'A' and (resid 75 through 84 or resid 90...AA448 - 530379 - 461
135TPOTPOPROPRO(chain 'A' and (resid 75 through 84 or resid 90...AA532 - 578463 - 509
136THRTHRASNASN(chain 'A' and (resid 75 through 84 or resid 90...AA581 - 613512 - 544
137GLUGLUASPASP(chain 'A' and (resid 75 through 84 or resid 90...AA616 - 685547 - 616
138ANPANPANPANP(chain 'A' and (resid 75 through 84 or resid 90...AE803
21LYSLYSPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB75 - 836 - 14
22ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB9021
23PROPROSERSER(chain 'B' and (resid 75 through 91 or resid 97...BB97 - 10228 - 33
24SERSERLEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB105 - 10836 - 39
25GLUGLULEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB111 - 12242 - 53
26SERSERPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB125 - 13656 - 67
27TYRTYRTYRTYR(chain 'B' and (resid 75 through 91 or resid 97...BB13970
28SERSERILEILE(chain 'B' and (resid 75 through 91 or resid 97...BB143 - 14574 - 76
29GLYGLYMETMET(chain 'B' and (resid 75 through 91 or resid 97...BB149 - 15880 - 89
210GLYGLYLYSLYS(chain 'B' and (resid 75 through 91 or resid 97...BB161 - 16292 - 93
211VALVALVALVAL(chain 'B' and (resid 75 through 91 or resid 97...BB16596
212GLYGLYGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB169100
213CYSCYSPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB173 - 177104 - 108
214VALVALTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB180 - 195111 - 126
215LEULEUARGARG(chain 'B' and (resid 75 through 91 or resid 97...BB204 - 209135 - 140
216CYSCYSMETMET(chain 'B' and (resid 75 through 91 or resid 97...BB211 - 216142 - 147
217THRTHRPHEPHE(chain 'B' and (resid 75 through 91 or resid 97...BB219 - 230150 - 161
218SERSERPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB233 - 241164 - 172
219ILEILEVALVAL(chain 'B' and (resid 75 through 91 or resid 97...BB244 - 251175 - 182
220GLUGLUGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB254 - 267185 - 198
221GLYGLYSERSER(chain 'B' and (resid 75 through 91 or resid 97...BB270 - 288201 - 219
222ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB292223
223PHEPHELEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB295 - 299226 - 230
224GLYGLYPHEPHE(chain 'B' and (resid 75 through 91 or resid 97...BB302 - 336233 - 267
225ALAALAALAALA(chain 'B' and (resid 75 through 91 or resid 97...BB356 - 358287 - 289
226TYRTYRGLUGLU(chain 'B' and (resid 75 through 91 or resid 97...BB360 - 361291 - 292
227ALAALALEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB364 - 370295 - 301
228SERSERGLYGLY(chain 'B' and (resid 75 through 91 or resid 97...BB373 - 384304 - 315
229GLYGLYLEULEU(chain 'B' and (resid 75 through 91 or resid 97...BB387 - 407318 - 338
230ARGARGARGARG(chain 'B' and (resid 75 through 91 or resid 97...BB410341
231ILEILEHISHIS(chain 'B' and (resid 75 through 91 or resid 97...BB412 - 420343 - 351
232SERSERTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB423 - 442354 - 373
233ASPASPASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB445376
234TYRTYRTHRTHR(chain 'B' and (resid 75 through 91 or resid 97...BB448 - 530379 - 461
235TPOTPOPROPRO(chain 'B' and (resid 75 through 91 or resid 97...BB532 - 578463 - 509
236THRTHRASNASN(chain 'B' and (resid 75 through 91 or resid 97...BB581 - 613512 - 544
237GLUGLUASPASP(chain 'B' and (resid 75 through 91 or resid 97...BB616 - 685547 - 616
238ANPANPANPANP(chain 'B' and (resid 75 through 91 or resid 97...BI803

NCS oper: (Code: givenMatrix: (-0.999862992821, -0.00464271658216, -0.015888384753), (-0.00431572040351, -0.853544078958, 0.521002763748), (-0.0159803049007, 0.520999952456, 0.853407100625) ...NCS oper: (Code: given
Matrix: (-0.999862992821, -0.00464271658216, -0.015888384753), (-0.00431572040351, -0.853544078958, 0.521002763748), (-0.0159803049007, 0.520999952456, 0.853407100625)
ベクター: -36.4786579281, 52.573469838, -14.7335605279)

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要素

#1: タンパク質 Isoform Beta of cGMP-dependent protein kinase 1 / cGK 1 / cGK1 / cGMP-dependent protein kinase I / cGKI


分子量: 69861.539 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PRKG1, PRKG1B, PRKGR1A, PRKGR1B / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q13976, cGMP-dependent protein kinase
#2: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Mn
#3: 化合物 ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP


分子量: 506.196 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C10H17N6O12P3 / タイプ: SUBJECT OF INVESTIGATION
コメント: AMP-PNP, エネルギー貯蔵分子類似体*YM
#4: 化合物 ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C2H6O2
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 127 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationY

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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: 3.05 Å3/Da / 溶媒含有率: 59.61 %
結晶化温度: 293 K / 手法: 蒸気拡散法 / pH: 8.5
詳細: 120 mM ethylene glycol, 100 mM Bicine (pH 8.5), 20 % w/v PEG 8,000

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データ収集

回折平均測定温度: 77 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALS / ビームライン: 8.2.1 / 波長: 0.987 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2018年8月25日
放射モノクロメーター: M / 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: 0.987 Å / 相対比: 1
反射解像度: 2.41→49.11 Å / Num. obs: 66393 / % possible obs: 99.95 % / 冗長度: 13.4 % / Biso Wilson estimate: 69.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1027 / Net I/σ(I): 20.93
反射 シェル解像度: 2.41→2.496 Å / Rmerge(I) obs: 0.1 / Num. unique obs: 6568 / CC1/2: 0.2999

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17.1_3660精密化
MOSFLMデータ削減
Aimless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: 2QCS, 4Z07

2qcs

4z07


解像度: 2.41→47.38 Å / SU ML: 0.3817 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.9407
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2383 1809 2.73 %
Rwork0.1997 64563 -
obs0.2008 66372 99.97 %
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 mean: 87.98 Å2
精密化ステップサイクル: LAST / 解像度: 2.41→47.38 Å
タンパク質核酸リガンド溶媒全体
原子数9227 0 78 127 9432
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00549506
X-RAY DIFFRACTIONf_angle_d0.877912912
X-RAY DIFFRACTIONf_chiral_restr0.05171443
X-RAY DIFFRACTIONf_plane_restr0.00491656
X-RAY DIFFRACTIONf_dihedral_angle_d8.70691295
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.480.40531370.3484917X-RAY DIFFRACTION99.82
2.48-2.550.33771370.33034897X-RAY DIFFRACTION99.94
2.55-2.630.36191380.30244924X-RAY DIFFRACTION99.98
2.63-2.720.33691370.2944863X-RAY DIFFRACTION100
2.72-2.830.33141380.27374947X-RAY DIFFRACTION100
2.83-2.960.31771380.26714926X-RAY DIFFRACTION100
2.96-3.120.31061390.25534930X-RAY DIFFRACTION100
3.12-3.310.2961370.24074927X-RAY DIFFRACTION99.98
3.31-3.570.27131400.22424978X-RAY DIFFRACTION100
3.57-3.930.24531390.19234962X-RAY DIFFRACTION100
3.93-4.50.18961400.1575007X-RAY DIFFRACTION100
4.5-5.660.19791420.1675045X-RAY DIFFRACTION100
5.66-47.380.19711470.17045240X-RAY DIFFRACTION99.87
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)
12.437054990650.0862546900470.4070126084844.16901593306-0.1670678551573.377770684310.01575704059780.4723173277830.0218786400229-0.8026808450960.0882094210204-0.508551812391-0.2615121294130.122114675327-0.0963163115310.719950868053-0.02422293608990.1864915944910.647643009642-0.1741070425270.6021695921625.8184968150658.7074719336-35.8696648907
20.2589424687590.882259108680.1034384370666.71374062183-0.04116504886680.749696222227-0.244445749505-0.0977776850526-0.287705833824-0.2201620702090.223495995366-0.758102426990.148848022309-0.120428523774-0.008554936107430.6901823265580.1288206776760.001198630521920.618171798334-0.06179069247860.84627748419721.152471793231.3510039576-16.7060919247
33.063352827320.114723630383-0.4074669738362.243725371310.248470421322.66102253615-0.03986010890670.1140962071140.443845715007-0.127354531306-0.0744192575274-0.1793714563920.08147139964350.3297581737390.1084054876580.4368917020120.0003986805212840.04609588736760.420122001340.07974221842420.501318597689-17.529078711-5.91116346687-3.61518246737
44.777071470371.498295811630.4088530621957.6941484141-0.403976543951.48153427755-0.08102345851360.3540910432080.0755724406676-0.5170235482070.276335758430.661758019749-0.068868336935-0.389674426303-0.178066687670.457007156779-0.0209510414870.0318517164080.6217667309320.03883696820440.374715892216-41.7628771921-25.788095881-13.1437367414
50.675357398736-0.646314539577-0.1620922889843.59227948539-0.1143438237060.5558519064210.0508208432270.1603215701450.344674504102-0.3211259197820.07388597096650.237546176781-0.188007474225-0.342384457631-0.1209275973320.8397014147090.078499258654-0.137261421820.8407066787890.1552300614590.718174258797-52.60639738719.21459879246-14.5287462087
64.96239710636-0.532561958239-0.7517021819362.39451355476-0.01401067290691.836319664540.002391570869670.230151532675-0.463840912893-0.368405296983-0.1427984344240.4225928246940.175314602167-0.3799122562110.103870625790.565643079842-0.0610318749793-0.02799680510290.54409821627-0.1680441333920.477165165665-18.611825731656.0945355528-20.2973566855
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 73 through 257 )
2X-RAY DIFFRACTION2chain 'A' and (resid 258 through 369 )
3X-RAY DIFFRACTION3chain 'A' and (resid 370 through 686 )
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 201 )
5X-RAY DIFFRACTION5chain 'B' and (resid 202 through 369 )
6X-RAY DIFFRACTION6chain 'B' and (resid 370 through 686 )

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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

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