[日本語] English
万見
- PDB-8jbk: Crystal structure of Na+,K+-ATPase in the E1.3Na+ state -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 8jbk
タイトルCrystal structure of Na+,K+-ATPase in the E1.3Na+ state
要素
  • (Sodium/potassium-transporting ATPase subunit ...) x 2
  • FXYD domain-containing ion transport regulator
キーワードMEMBRANE PROTEIN / ion pump / P-type ATPase
機能・相同性
機能・相同性情報


Basigin interactions / Ion homeostasis / P-type potassium transmembrane transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex ...Basigin interactions / Ion homeostasis / P-type potassium transmembrane transporter activity / positive regulation of sodium ion export across plasma membrane / positive regulation of potassium ion import across plasma membrane / regulation of monoatomic ion transport / Ion transport by P-type ATPases / transporter activator activity / P-type sodium:potassium-exchanging transporter activity / sodium:potassium-exchanging ATPase complex / membrane repolarization / establishment or maintenance of transmembrane electrochemical gradient / sodium ion export across plasma membrane / positive regulation of potassium ion transmembrane transport / regulation of calcium ion transmembrane transport / intracellular sodium ion homeostasis / ion channel regulator activity / intracellular potassium ion homeostasis / regulation of cardiac muscle contraction by calcium ion signaling / relaxation of cardiac muscle / positive regulation of sodium ion transmembrane transport / sodium ion transport / organelle membrane / potassium ion import across plasma membrane / ATPase activator activity / sperm flagellum / intercalated disc / lateral plasma membrane / ATP metabolic process / cardiac muscle contraction / T-tubule / proton transmembrane transport / protein localization to plasma membrane / sarcolemma / transmembrane transport / intracellular calcium ion homeostasis / melanosome / ATPase binding / regulation of gene expression / protein-macromolecule adaptor activity / basolateral plasma membrane / cell adhesion / protein stabilization / apical plasma membrane / axon / innate immune response / protein kinase binding / ATP hydrolysis activity / ATP binding / metal ion binding
類似検索 - 分子機能
: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / : / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. ...: / Ion-transport regulator, FXYD motif / : / ATP1G1/PLM/MAT8 family / FXYD family signature. / Sodium/potassium-transporting ATPase subunit beta / Sodium/potassium-transporting ATPase subunit beta superfamily / : / Sodium / potassium ATPase beta chain / Sodium and potassium ATPases beta subunits signature 1. / Sodium and potassium ATPases beta subunits signature 2. / P-type ATPase subfamily IIC, subunit alpha / Cation-transporting P-type ATPase, C-terminal / Cation transporting ATPase, C-terminus / Cation transporter/ATPase, N-terminus / Cation-transporting P-type ATPase, N-terminal / Cation transporter/ATPase, N-terminus / Cation transport ATPase (P-type) / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / HAD superfamily / HAD-like superfamily
類似検索 - ドメイン・相同性
CHOLESTEROL / : / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium/potassium-transporting ATPase subunit alpha / Sodium/potassium-transporting ATPase subunit beta-1 / FXYD domain-containing ion transport regulator
類似検索 - 構成要素
生物種Sus scrofa (ブタ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Kanai, R. / Vilsen, B. / Cornelius, F. / Toyoshima, C.
資金援助 日本, 2件
組織認可番号国
Japan Society for the Promotion of Science (JSPS)JP19H00975 日本
Japan Society for the Promotion of Science (JSPS)JP21K06109 日本
引用ジャーナル: FEBS Lett / 年: 2023
タイトル: Crystal structures of Na ,K -ATPase reveal the mechanism that converts the K -bound form to Na -bound form and opens and closes the cytoplasmic gate.
著者: Ryuta Kanai / Bente Vilsen / Flemming Cornelius / Chikashi Toyoshima /
要旨: Na ,K -ATPase (NKA) plays a pivotal role in establishing electrochemical gradients for Na and K across the cell membrane by alternating between the E1 (showing high affinity for Na and low affinity ...Na ,K -ATPase (NKA) plays a pivotal role in establishing electrochemical gradients for Na and K across the cell membrane by alternating between the E1 (showing high affinity for Na and low affinity for K ) and E2 (low affinity to Na and high affinity to K ) forms. Presented here are two crystal structures of NKA in E1·Mg and E1·3Na states at 2.9 and 2.8 Å resolution, respectively. These two E1 structures fill a gap in our description of the NKA reaction cycle based on the atomic structures. We describe how NKA converts the K -bound E2·2K form to an E1 (E1·Mg ) form, which allows high-affinity Na binding, eventually closing the cytoplasmic gate (in E1 ~ P·ADP·3Na ) after binding three Na , while keeping the extracellular ion pathway sealed. We now understand previously unknown functional roles for several parts of NKA and that NKA uses even the lipid bilayer for gating the ion pathway.
履歴
登録2023年5月9日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年8月9日Provider: repository / タイプ: Initial release
改定 1.12023年8月16日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
改定 1.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
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

-
集合体

登録構造単位
A: Sodium/potassium-transporting ATPase subunit alpha
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
C: Sodium/potassium-transporting ATPase subunit alpha
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)330,24545
ポリマ－310,3436
非ポリマー19,90339
水57632
1
A: Sodium/potassium-transporting ATPase subunit alpha
B: Sodium/potassium-transporting ATPase subunit beta-1
G: FXYD domain-containing ion transport regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)166,34223
ポリマ－155,1713
非ポリマー11,17120
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area17140 Å2
ΔGint-92 kcal/mol
Surface area62680 Å2
手法PISA
2
C: Sodium/potassium-transporting ATPase subunit alpha
D: Sodium/potassium-transporting ATPase subunit beta-1
E: FXYD domain-containing ion transport regulator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)163,90322
ポリマ－155,1713
非ポリマー8,73219
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area13660 Å2
ΔGint-106 kcal/mol
Surface area61320 Å2
手法PISA
単位格子
Length a, b, c (Å)193.740, 74.490, 162.560
Angle α, β, γ (deg.)90.000, 115.720, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
要素

-
Sodium/potassium-transporting ATPase subunit ... , 2種, 4分子 ACBD

#1: タンパク質 Sodium/potassium-transporting ATPase subunit alpha


分子量: 112872.766 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: D2WKD6
#2: タンパク質 Sodium/potassium-transporting ATPase subunit beta-1 / Sodium/potassium-dependent ATPase subunit beta-1


分子量: 35204.402 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: P05027

-
タンパク質 , 1種, 2分子 GE

#3: タンパク質 FXYD domain-containing ion transport regulator / Na+/K+ ATPase gamma subunit transcript variant a


分子量: 7094.115 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Sus scrofa (ブタ) / 参照: UniProt: Q58K79

-
糖 , 5種, 5分子

#4: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 910.823 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 424.401 Da / 分子数: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#12: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#13: 糖 ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE / デシルβ-マルトシド


タイプ: D-saccharide / 分子量: 482.562 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C22H42O11 / コメント: 可溶化剤*YM

-
非ポリマー , 6種, 66分子

#7: 化合物 ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mn
#8: 化合物
ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Na / タイプ: SUBJECT OF INVESTIGATION
#9: 化合物
ChemComp-CLR / CHOLESTEROL / コレステロ-ル


分子量: 386.654 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C27H46O
#10: 化合物 ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


分子量: 790.145 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C44H88NO8P / コメント: リン脂質*YM
#11: 化合物
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE / DOPC


分子量: 787.121 Da / 分子数: 15 / 由来タイプ: 合成 / 式: C44H85NO8P / コメント: DOPC, リン脂質*YM
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 32 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかY
Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.41 Å3/Da / 溶媒含有率: 63.88 %
結晶化温度: 283 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.2
詳細: 285 mM NaCl, 25 mM MgCl2, 15.4% (w/v) PEG2000MME, 7% (w/v) glycerol, 5 mM GSH, 0.1 mM DTT and 1 mg/ml butylhydroxytoluen, 100 mM MES

-
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: SPring-8 / ビームライン: BL41XU / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年7月3日
放射モノクロメーター: Si double crystal / 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: 2.8→30 Å / Num. obs: 67058 / % possible obs: 64.8 % / 冗長度: 3.5 % / Biso Wilson estimate: 68.82 Å2 / CC1/2: 0.922 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.04
反射 シェル解像度: 2.8→2.89 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 472 / CC1/2: 0.775 / % possible all: 5.1

-
解析

ソフトウェア
名称バージョン分類
BSSデータ収集
HKL-2000データ削減
STARANISOデータスケーリング
PHASER位相決定
PHENIX1.19.2_4158精密化
精密化構造決定の手法: 分子置換
開始モデル: 3WGU

3wgu


解像度: 2.8→15 Å / SU ML: 0.377 / 交差検証法: FREE R-VALUE / σ(F): 1.37 / 位相誤差: 32.0193
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2704 3326 5.01 %
Rwork0.2285 63093 -
obs0.2306 66419 64.6 %
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: 83.89 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→15 Å
タンパク質核酸リガンド溶媒全体
原子数20772 0 878 32 21682
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00422079
X-RAY DIFFRACTIONf_angle_d0.748229932
X-RAY DIFFRACTIONf_chiral_restr0.3683426
X-RAY DIFFRACTIONf_plane_restr0.00573758
X-RAY DIFFRACTIONf_dihedral_angle_d18.61578481
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.2988110.3846179X-RAY DIFFRACTION4.47
2.84-2.880.3666110.3758229X-RAY DIFFRACTION5.77
2.88-2.930.2414120.3614263X-RAY DIFFRACTION6.55
2.93-2.980.4769210.3095397X-RAY DIFFRACTION9.74
2.98-3.030.3214250.3489489X-RAY DIFFRACTION12.34
3.03-3.080.3315410.33759X-RAY DIFFRACTION18.73
3.08-3.140.3696500.3313940X-RAY DIFFRACTION23.27
3.14-3.20.3484760.31351396X-RAY DIFFRACTION34.67
3.2-3.270.3263960.33221862X-RAY DIFFRACTION46.11
3.27-3.350.31621180.31512224X-RAY DIFFRACTION55.13
3.35-3.430.34721370.30722688X-RAY DIFFRACTION66.11
3.43-3.520.34531630.30443095X-RAY DIFFRACTION76.19
3.52-3.620.30431930.28583548X-RAY DIFFRACTION88.11
3.62-3.740.30932080.27694017X-RAY DIFFRACTION97.91
3.74-3.870.3362120.26214060X-RAY DIFFRACTION99.98
3.87-4.020.27262130.25134020X-RAY DIFFRACTION100
4.02-4.20.26962160.23044094X-RAY DIFFRACTION100
4.2-4.420.27082150.20784086X-RAY DIFFRACTION100
4.42-4.690.23572170.19194087X-RAY DIFFRACTION100
4.69-5.040.25662120.19424067X-RAY DIFFRACTION100
5.04-5.520.28572200.21394094X-RAY DIFFRACTION100
5.52-6.270.27142170.23464149X-RAY DIFFRACTION100
6.27-7.710.25762170.21464127X-RAY DIFFRACTION100
7.71-150.19312250.16054223X-RAY DIFFRACTION99.82
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)
10.2190773927410.09821226835050.06425712555270.062028098475-0.08937967056390.213508356597-0.1031294859580.198458865591-0.03259513485190.01664115935820.06427778184090.1398140692650.0677160962765-0.207650211174-0.002162422194090.405718537137-0.02738766347670.01259486205770.179995840303-0.0007733094716330.406569008569-13.309-21.444110.441
20.7592565081160.043398690728-0.1046097793490.1360485859530.06124345139120.9137747703960.0442408980761-0.251959112581-0.1655502565010.1935545153830.0168319037376-0.110409074659-0.1482567018890.04316957422170.1020662624650.005337388081670.107083108144-0.1104964765610.05060064630210.1355304612190.2891329967654.173.55127.755
3-0.02062468641370.09326254109160.05575183096420.4987966368550.3146535708710.290618546273-0.0581063810450.0750920837776-0.0530514100282-0.08426505871690.09786124150220.0279526275082-0.424072138773-0.00918651703378-75.24557468610.146041043855-0.005895915119050.008625026849220.216896141208-0.01639890914190.140272282952-5.5236.72576.929
40.00184631750241-0.000122073910539-0.00100460752605-0.0001915883235948.45126012154E-60.000443571832131-0.02374367468730.01141641722670.00050515423003-0.0267717658363-0.05155753089770.01618104146860.02101596906730.00985150633499-0.8759615630761.34742301120.1781059966880.06013262127651.43426296635-0.1283705844561.39990266761-25.53427.65492.248
50.000798485690570.00510798778434-0.001589243170480.0290433765286-0.01007639221460.00367534684331-0.2448523734530.06815543635250.06279296502050.00512048587819-0.0196996877855-0.014462877469-0.0574332388163-0.04164809682050.5837424618321.119138120130.0536188654548-0.1134889680850.4020896742780.01511259013640.437005352876-8.53625.06971.564
60.0912177492032-0.08159290094860.0150227725720.0739465139489-0.01495186447740.001297940700820.09946938523950.0685018590837-0.0263660691429-0.245350982496-0.1189751981650.277027265477-0.29420617569-0.08823261049430.00104818122060.774210619821-0.0572264848506-0.1239550631470.7801349255070.006819042241820.421259013683-20.5653.55738.96
70.003436239991780.001851457933280.001793198538810.00179149572431-0.0002484936712840.001691121920080.0576123599785-0.01696314792150.0166771862177-0.0434168408297-0.006129136162870.047171752955-0.0463979053529-0.0034709568644-13.09477736921.072847645380.138745560776-0.4106135759341.06358802058-0.006882312891710.836700805867-29.2159.59831.778
80.000941587176615-0.00300906769910.002598443843970.00397495073393-0.003689651356380.00341127066031-0.0516068649888-0.006238610200430.0814684832530.012261225214-0.00539502614049-0.004610055989-0.07004217774790.004645213244190.2401386399971.52426232445-0.1803362354190.01229123340781.0766133670.1733124297080.827026809719-13.70715.9220.253
90.0155949521114-0.0132193794209-0.02161964132950.01038434193540.01981599130280.02684432303680.08809365839820.003756197748190.139884499792-0.142754529636-0.0510037608775-0.0056492608743-0.187472203378-0.0361974847302-0.2171792034571.42558666479-0.235408497452-0.1758664931061.18040254223-0.0115715346020.576033734275-14.53712.10624.307
100.01663680633860.01631670182720.00124251118660.0163714243806-0.004013062732310.0268715355063-0.004519348865450.0477841082146-0.069292515856-0.04488355656390.09038220420110.10529471249-0.02060110417640.00228891992806-73.96863694580.951782325906-0.0738018633698-0.2347059106960.78256088431-0.05456280267120.536132001739-17.7950.53529.037
11-0.0003800659759810.0001956799073815.17157496336E-50.0008039737156130.0008363745309610.0005044566912770.0579484932976-0.0596750171072-0.1095122082160.01252966245090.0278254036959-0.02601755509350.01864397428580.04675249041943.08815058643E-61.11320687982-0.156370903430.02729899862381.25109142938-0.1111826502591.03458464232-8.139-11.23120.919
120.01370671644150.0104651778159-0.01889900608750.01358405951680.007468640010560.04585150436540.08803394072260.0992356755095-0.0218359832566-0.083571717388-0.05502571813220.0946660726393-0.0873879013347-0.045979632476-0.2226732771181.10799988863-0.0922500470775-0.1554675514520.8795665795560.06505275149720.672407072106-17.877-3.46526.772
130.00488378918111-0.00512931799172-0.004735786053490.005791941296950.002226335340510.03032864414090.1634141593230.0360541666345-0.0681752787928-0.0455008726016-0.001426311830450.162480094076-0.171109380058-0.177936648724-5.185091165081.13186124249-0.0669675430939-0.1797722150470.7993147231610.02400891746970.530100366924-24.8310.56527.488
140.00303867708526-0.00158895730405-0.007142828002120.0104693370187-0.007447188858950.0401283053984-6.69196932667E-50.0508089949633-0.04204167132-0.02130164815090.0628263200563-0.08645298683010.0179647779295-0.2437957963655.60372290246E-70.803036542952-0.111820697612-0.1855355472080.837257719295-0.03685964055720.531791319722-21.04-8.73735.94
150.000475438835434-0.000340989236479-0.00141145299680.001408884505570.0002675386958320.002662797053530.0256243238655-0.02262525036080.002342094372610.005842481861670.0347425894843-0.0093164673231-0.01098998292060.00933810591249-50.09481746540.976112829013-0.03528344692530.04516351639460.848999455546-0.06380767543520.6759194300772.922-1.85742.018
160.00505759454990.001081039759130.004172795271460.0066041553932-0.002482186556510.00359676135007-0.0695304474617-0.006657984140010.01049260309-0.1211984357960.0576008772603-0.06202000413610.0576220238167-0.0231308799469-0.2436454600890.2847171841440.01783629840250.009114188374660.473644500646-0.03541086170090.283123362556.839-8.21465.489
170.001035828027540.00115862413592-0.001154689062760.00133185427215-0.001416295457030.00115164137625-0.00354718847922-0.02713377825240.0011377682710.00581423721724-0.000951519400931-0.00242071660.001999504276140.00661567160243-70.43009192990.615771014834-0.0725738350767-0.03510210062880.7066104721070.07179309830480.67491001643913.854-10.09386.367
180.36342540895-0.01121911824220.01727561390080.08263557057560.185793820490.382285054442-0.124772840011-0.241381247834-0.0488013566834-0.08073374079720.0620676749146-0.0716109602730.1169619312120.443347130651-0.0001195214380460.4735860355540.09427198878520.1085166306490.314167154558-0.05269148951720.37873587617944.704-15.30230.644
190.6566382724370.0940604464764-0.0909878672733-0.137430425274-0.0456986962540.7606848163190.0545232184014-0.05099710895660.0703286302017-0.379635719749-0.01587828634630.199433873829-6.68616092375E-7-0.038931129294-0.006423431510.471892006916-0.00364012640758-0.001722689317050.0198358661962-0.05395988434180.2880164057229.2019.10112.999
200.572168550932-0.4577857774930.04720594419631.783234966260.4816599384720.1857027471570.23489156607-0.1923467982150.0636288836695-0.3686346338150.0231097142353-0.00975985137363-0.2678841316130.3967610349360.415384114092-0.16525142211-0.1863265053730.2274759075230.609639778327-0.2100758718830.27162117915131.39813.63668.722
210.00182210543624-9.0654925539E-5-0.00110051937663-0.000284776620331-7.60575134768E-50.000638542096275-0.0007069764856430.0383744558449-0.004088928540.0369387276063-0.00175973575176-0.003680760987-0.004367664401710.0223673780074-18.03760864131.27052438149-0.1943031456720.1572604671081.447856735160.07587727414781.1488610727650.41836.56851.166
220.603527527970.127199613854-0.09219862741730.4148164329830.2732201214910.233832795802-0.164771120838-0.236955439972-0.031954348309-0.180485177999-0.0438266021885-0.0457563250984-0.1625066768230.207989879237-0.1920625752240.443994145537-0.3117348026160.1247176620080.713465609384-0.2427481423470.47902548387330.82922.07682.098
230.00206741377424-0.0006011001980110.002161832561470.003854595418380.008831534014130.01481026574290.1104004784660.006240461149310.05899459253390.0703200300022-0.0264611463436-0.0886520132587-0.01058915471730.05741967953278.112046401490.729185584712-0.245241558567-0.1753439032271.76614476155-0.2359137052150.90538615535454.80313.119109.588
240.00155644565271-0.000166270493650.002042540239250.001373975170170.00159238540770.00795604323876-0.001718853831780.01215797012760.0278641382982-0.04849582351950.04658954229810.0726387590999-0.080635110605-0.0645547890963-1.49965940391.04145329899-0.2060812470760.1660281426311.44153903927-0.3953174454230.82026032710731.17520.922120.123
250.02307725243780.00434060140923-0.02791702450980.00178719340749-0.005094903446440.03375817890850.0908544973972-0.0934487749550.1798515874340.08418629715370.05016877606090.106954348418-0.0973260146080.04433079174360.0002554060982960.451563362013-0.0593640017522-0.03056500819041.43162700779-0.2100508668830.70794872573833.13217.32116.054
260.00219391754121-0.002106635999710.006474371548260.00527840046151-0.01315443243830.0250065593434-0.025216817967-0.07820954707090.04790393556310.08384319938710.0533515810264-0.1107280906850.09480860236040.1159314225660.005676383827780.432437441133-0.0647569986935-0.109195009951.34949238906-0.1892283324190.521328424638.7176.612111.619
270.000588523152071-0.002428107380240.0005615518204730.00302374065956-0.000352623040831-0.0002101152196130.0216699069546-0.00954209801376-0.124809284876-0.00129413716789-0.00451080199658-0.04936351360.05923407728080.0105006342111-2.2975827692E-61.37380444407-0.01618862311870.05514842270661.530809183690.05758108076861.1495721903530.411-6.892118.466
280.0765302929889-0.0008966556031940.01945064990250.04446508412140.001106445908580.02654668041060.310542578005-0.400546812046-0.008233709466830.121699316601-0.222861060807-0.004703844801750.1823778765130.3632154183080.001769676304870.519955405243-0.0255781096583-0.08459826323781.52472414916-0.1198451310760.55418400610742.3832.235110.912
290.00233182477749-0.0003495762265530.000403859149687-0.000104575049514-0.0001563608297722.85204446794E-50.0383867962627-0.01805411024930.02142886132890.0204241003190.0544751447552-0.009366394589360.01411495033650.000405415416138-67.64122013950.3827888385030.01604435542090.1183041489110.843759831607-0.1748502563850.56143074850820.9321.50296.476
300.015261922706-0.009585307254450.05220577414610.0943729258299-0.0700292146050.188440896210.01559076772570.0215670545421-0.159201838357-0.06290922427960.07558716257810.1341845912540.063835266997-0.03590024832130.007460985527240.114329715141-0.04986839872780.006177412759060.41836780628-0.1689700579330.46142138430619.942-4.8770.173
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 22:275 )A22 - 275
2X-RAY DIFFRACTION2( CHAIN A AND RESID 276:720 )A276 - 720
3X-RAY DIFFRACTION3( CHAIN A AND RESID 721:1016 )A721 - 1016
4X-RAY DIFFRACTION4( CHAIN B AND RESID 13:28 )B13 - 28
5X-RAY DIFFRACTION5( CHAIN B AND RESID 29:58 )B29 - 58
6X-RAY DIFFRACTION6( CHAIN B AND RESID 59:98 )B59 - 98
7X-RAY DIFFRACTION7( CHAIN B AND RESID 99:112 )B99 - 112
8X-RAY DIFFRACTION8( CHAIN B AND RESID 113:132 )B113 - 132
9X-RAY DIFFRACTION9( CHAIN B AND RESID 133:168 )B133 - 168
10X-RAY DIFFRACTION10( CHAIN B AND RESID 169:192 )B169 - 192
11X-RAY DIFFRACTION11( CHAIN B AND RESID 193:207 )B193 - 207
12X-RAY DIFFRACTION12( CHAIN B AND RESID 208:250 )B208 - 250
13X-RAY DIFFRACTION13( CHAIN B AND RESID 251:270 )B251 - 270
14X-RAY DIFFRACTION14( CHAIN B AND RESID 271:303 )B271 - 303
15X-RAY DIFFRACTION15( CHAIN G AND RESID 16:22 )G16 - 22
16X-RAY DIFFRACTION16( CHAIN G AND RESID 23:45 )G23 - 45
17X-RAY DIFFRACTION17( CHAIN G AND RESID 46:51 )G46 - 51
18X-RAY DIFFRACTION18( CHAIN C AND RESID 22:275 )C22 - 275
19X-RAY DIFFRACTION19( CHAIN C AND RESID 276:772 )C276 - 772
20X-RAY DIFFRACTION20( CHAIN C AND RESID 773:1016 )C773 - 1016
21X-RAY DIFFRACTION21( CHAIN D AND RESID 13:28 )D13 - 28
22X-RAY DIFFRACTION22( CHAIN D AND RESID 29:83 )D29 - 83
23X-RAY DIFFRACTION23( CHAIN D AND RESID 84:112 )D84 - 112
24X-RAY DIFFRACTION24( CHAIN D AND RESID 113:132 )D113 - 132
25X-RAY DIFFRACTION25( CHAIN D AND RESID 133:168 )D133 - 168
26X-RAY DIFFRACTION26( CHAIN D AND RESID 169:192 )D169 - 192
27X-RAY DIFFRACTION27( CHAIN D AND RESID 193:207 )D193 - 207
28X-RAY DIFFRACTION28( CHAIN D AND RESID 208:303 )D208 - 303
29X-RAY DIFFRACTION29( CHAIN E AND RESID 16:22 )E16 - 22
30X-RAY DIFFRACTION30( CHAIN E AND RESID 23:48 )E23 - 48

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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