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- PDB-4tnw: C. elegans glutamate-gated chloride channel (GluCl) in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 4tnw
タイトルC. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and POPC in a lipid-modulated conformation
要素
  • (Mouse monoclonal Fab fragment, ...) x 2
  • Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
キーワードTRANSPORT PROTEIN/IMMUNE SYSTEM / membrane protein / ligand-gated ion channel / neurotransmitter receptor / Cys-loop receptor / TRANSPORT PROTEIN-IMMUNE SYSTEM complex
機能・相同性
機能・相同性情報


extracellularly glutamate-gated chloride channel activity / Neurotransmitter receptors and postsynaptic signal transmission / locomotion involved in locomotory behavior / glutamate binding / protein complex oligomerization / chloride transmembrane transport / transmembrane signaling receptor activity / postsynaptic membrane / identical protein binding / plasma membrane
類似検索 - 分子機能
Glutamate gated chloride channel, transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily ...Glutamate gated chloride channel, transmembrane domain / Neurotransmitter-gated ion-channel transmembrane domain / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-POV / Glutamate-gated chloride channel alpha
類似検索 - 構成要素
生物種Caenorhabditis elegans (センチュウ)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Althoff, T. / Hibbs, R.E. / Banerjee, S. / Gouaux, E.
資金援助 米国, ドイツ, 3件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM100400 米国
German Research Foundation (DFG)AL 1725-1/1 ドイツ
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS061404 米国
引用
ジャーナル: Nature / 年: 2014
タイトル: X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors.
著者: Althoff, T. / Hibbs, R.E. / Banerjee, S. / Gouaux, E.
#1: ジャーナル: Nature / 年: 2011
タイトル: Principles of activation and permeation in an anion-selective Cys-loop receptor.
著者: Hibbs, R.E. / Gouaux, E.
履歴
登録2014年6月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年8月13日Provider: repository / タイプ: Initial release
改定 1.12014年9月3日Group: Database references
改定 1.22017年9月27日Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
カテゴリ: citation / entity ...citation / entity / entity_src_gen / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
改定 1.32019年12月18日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42020年7月29日Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 1.52023年9月27日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.62024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: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
B: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
C: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
D: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
E: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
F: Mouse monoclonal Fab fragment, heavy chain
G: Mouse monoclonal Fab fragment, heavy chain
H: Mouse monoclonal Fab fragment, heavy chain
I: Mouse monoclonal Fab fragment, heavy chain
K: Mouse monoclonal Fab fragment, light chain
L: Mouse monoclonal Fab fragment, light chain
N: Mouse monoclonal Fab fragment, light chain
O: Mouse monoclonal Fab fragment, light chain
P: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
Q: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
R: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
S: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
T: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
U: Mouse monoclonal Fab fragment, heavy chain
V: Mouse monoclonal Fab fragment, heavy chain
W: Mouse monoclonal Fab fragment, heavy chain
X: Mouse monoclonal Fab fragment, heavy chain
Y: Mouse monoclonal Fab fragment, heavy chain
Z: Mouse monoclonal Fab fragment, light chain
f: Mouse monoclonal Fab fragment, light chain
g: Mouse monoclonal Fab fragment, light chain
h: Mouse monoclonal Fab fragment, light chain
i: Mouse monoclonal Fab fragment, light chain
J: Mouse monoclonal Fab fragment, heavy chain
M: Mouse monoclonal Fab fragment, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)881,90456
ポリマ－870,85530
非ポリマー11,04926
水00
1
A: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
B: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
C: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
D: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
E: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
F: Mouse monoclonal Fab fragment, heavy chain
G: Mouse monoclonal Fab fragment, heavy chain
H: Mouse monoclonal Fab fragment, heavy chain
I: Mouse monoclonal Fab fragment, heavy chain
K: Mouse monoclonal Fab fragment, light chain
L: Mouse monoclonal Fab fragment, light chain
N: Mouse monoclonal Fab fragment, light chain
O: Mouse monoclonal Fab fragment, light chain
J: Mouse monoclonal Fab fragment, heavy chain
M: Mouse monoclonal Fab fragment, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)440,22428
ポリマ－435,42815
非ポリマー4,79613
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
2
P: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
Q: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
R: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
S: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
T: Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
U: Mouse monoclonal Fab fragment, heavy chain
V: Mouse monoclonal Fab fragment, heavy chain
W: Mouse monoclonal Fab fragment, heavy chain
X: Mouse monoclonal Fab fragment, heavy chain
Y: Mouse monoclonal Fab fragment, heavy chain
Z: Mouse monoclonal Fab fragment, light chain
f: Mouse monoclonal Fab fragment, light chain
g: Mouse monoclonal Fab fragment, light chain
h: Mouse monoclonal Fab fragment, light chain
i: Mouse monoclonal Fab fragment, light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)441,68028
ポリマ－435,42815
非ポリマー6,25313
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)453.750, 192.870, 196.140
Angle α, β, γ (deg.)90.00, 92.27, 90.00
Int Tables number5
Space group name H-MC121
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain A and (resid 1:340 )
21chain B and (resid 1:340 )
31chain C and (resid 1:340 )
41chain D and (resid 1:340 )
51chain E and (resid 1:340 )
61chain P and (resid 1:340 )
71chain Q and (resid 1:340 )
81chain R and (resid 1:340 )
91chain S and (resid 1:340 )
101chain T and (resid 1:340 )
12chain F and (resid 1:120 )
22chain G and (resid 1:120 )
32chain H and (resid 1:120 )
42chain I and (resid 1:120 )
52chain J and (resid 1:120 )
62chain U and (resid 1:120 )
72chain V and (resid 1:120 )
82chain W and (resid 1:120 )
92chain X and (resid 1:120 )
102chain Y and (resid 1:120 )
13chain K and (resid 1:108 )
23chain L and (resid 1:108 )
33chain M and (resid 1:108 )
43chain N and (resid 1:108 )
53chain O and (resid 1:108 )
63chain Z and (resid 1:108 )
73chain f and (resid 1:108 )
83chain g and (resid 1:108 )
93chain h and (resid 1:108 )
103chain i and (resid 1:108 )

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERHISHISchain A and (resid 1:340 )AA1 - 3401 - 340
21SERSERHISHISchain B and (resid 1:340 )BB1 - 3401 - 340
31SERSERHISHISchain C and (resid 1:340 )CC1 - 3401 - 340
41SERSERHISHISchain D and (resid 1:340 )DD1 - 3401 - 340
51SERSERHISHISchain E and (resid 1:340 )EE1 - 3401 - 340
61SERSERHISHISchain P and (resid 1:340 )PN1 - 3401 - 340
71SERSERHISHISchain Q and (resid 1:340 )QO1 - 3401 - 340
81SERSERHISHISchain R and (resid 1:340 )RP1 - 3401 - 340
91SERSERHISHISchain S and (resid 1:340 )SQ1 - 3401 - 340
101SERSERHISHISchain T and (resid 1:340 )TR1 - 3401 - 340
12GLUGLUVALVALchain F and (resid 1:120 )FF1 - 1201 - 120
22GLUGLUVALVALchain G and (resid 1:120 )GG1 - 1201 - 120
32GLUGLUVALVALchain H and (resid 1:120 )HH1 - 1201 - 120
42GLUGLUVALVALchain I and (resid 1:120 )II1 - 1201 - 120
52GLUGLUVALVALchain J and (resid 1:120 )JCA1 - 1201 - 120
62GLUGLUVALVALchain U and (resid 1:120 )US1 - 1201 - 120
72GLUGLUVALVALchain V and (resid 1:120 )VT1 - 1201 - 120
82GLUGLUVALVALchain W and (resid 1:120 )WU1 - 1201 - 120
92GLUGLUVALVALchain X and (resid 1:120 )XV1 - 1201 - 120
102GLUGLUVALVALchain Y and (resid 1:120 )YW1 - 1201 - 120
13GLNGLNVALVALchain K and (resid 1:108 )KJ1 - 1081 - 108
23GLNGLNVALVALchain L and (resid 1:108 )LK1 - 1081 - 108
33GLNGLNVALVALchain M and (resid 1:108 )MDA1 - 1081 - 108
43GLNGLNVALVALchain N and (resid 1:108 )NL1 - 1081 - 108
53GLNGLNVALVALchain O and (resid 1:108 )OM1 - 1081 - 108
63GLNGLNVALVALchain Z and (resid 1:108 )ZX1 - 1081 - 108
73GLNGLNVALVALchain f and (resid 1:108 )fY1 - 1081 - 108
83GLNGLNVALVALchain g and (resid 1:108 )gZ1 - 1081 - 108
93GLNGLNVALVALchain h and (resid 1:108 )hAA1 - 1081 - 108
103GLNGLNVALVALchain i and (resid 1:108 )iBA1 - 1081 - 108

NCSアンサンブル:
ID
1
2
3

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要素

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タンパク質 , 1種, 10分子 ABCDEPQRST

#1: タンパク質
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha / Protein GLC-1


分子量: 39636.629 Da / 分子数: 10 / 断片: UNP RESIDUES 62-363,UNP RESIDUES 422-455 / 由来タイプ: 組換発現
由来: (組換発現) Caenorhabditis elegans (センチュウ)
遺伝子: glc-1, CELE_F11A5.10, F11A5.10 / プラスミド: pFastBac1 / 細胞株 (発現宿主): Sf9 / 器官 (発現宿主): ovary
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
組織 (発現宿主): ovary / 参照: UniProt: G5EBR3

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抗体 , 2種, 20分子 FGHIUVWXYJKLNOZfghiM

#2: 抗体
Mouse monoclonal Fab fragment, heavy chain


分子量: 24297.170 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: Hybridoma
#3: 抗体
Mouse monoclonal Fab fragment, light chain


分子量: 23151.738 Da / 分子数: 10 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 細胞株: Hybridoma

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糖 , 2種, 16分子

#4: 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: 9 / 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
#8: 糖
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE / ドデシルβ-D-マルトシド


タイプ: D-saccharide / 分子量: 510.615 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C24H46O11 / コメント: 可溶化剤*YM

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非ポリマー , 3種, 10分子

#5: 化合物
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


分子量: 760.076 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C42H82NO8P / コメント: リン脂質*YM
#6: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Cl
#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3

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詳細

Has protein modificationY
配列の詳細UNP G5EBR3 RESIDUES 364-421 ARE REPLACED WITH RESIDUES AGT

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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: 4.92 Å3/Da / 溶媒含有率: 75.02 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5
詳細: 35-36% pentaerythritol propoxylate (5/4 PO/OH), 50 mM sodium citrate pH 5.5, 100 mM potassium chloride, Crystals were obtained after incubation of protein with lipid and detergent for 4 weeks at 4 degC

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9793 Å
検出器タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2011年11月10日
詳細: Mirrors: bent cylinders, stripes of Pt, Rh and clear
放射モノクロメーター: Cryo-cooled double Si(111) crystal monochromator
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: 0.9793 Å / 相対比: 1
反射解像度: 3.2→58.7 Å / Num. obs: 256166 / % possible obs: 92.2 % / 冗長度: 1.92 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 7.26
反射 シェル解像度: 3.2→3.24 Å / 冗長度: 1.6 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.43 / % possible all: 83.5

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.8.4_1496)精密化
ADSCデータ収集
HKL-2000データ削減
HKL-2000データスケーリング
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
直接法位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 3RHW

3rhw


解像度: 3.2→58.7 Å / SU ML: 0.49 / 交差検証法: FREE R-VALUE / σ(F): 1.23 / 位相誤差: 27.36 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2506 21267 5 %Random
Rwork0.2269 ---
obs0.2281 425172 77.58 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 3.2→58.7 Å
タンパク質核酸リガンド溶媒全体
原子数60274 0 544 0 60818
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00362464
X-RAY DIFFRACTIONf_angle_d0.73985197
X-RAY DIFFRACTIONf_dihedral_angle_d10.50722087
X-RAY DIFFRACTIONf_chiral_restr0.039864
X-RAY DIFFRACTIONf_plane_restr0.00310588
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A16369X-RAY DIFFRACTION8.489TORSIONAL
12B16369X-RAY DIFFRACTION8.489TORSIONAL
13C16369X-RAY DIFFRACTION8.489TORSIONAL
14D16369X-RAY DIFFRACTION8.489TORSIONAL
15E16369X-RAY DIFFRACTION8.489TORSIONAL
16P16369X-RAY DIFFRACTION8.489TORSIONAL
17Q16369X-RAY DIFFRACTION8.489TORSIONAL
18R16369X-RAY DIFFRACTION8.489TORSIONAL
19S16369X-RAY DIFFRACTION8.489TORSIONAL
110T16369X-RAY DIFFRACTION8.489TORSIONAL
21F5682X-RAY DIFFRACTION8.489TORSIONAL
22G5682X-RAY DIFFRACTION8.489TORSIONAL
23H5682X-RAY DIFFRACTION8.489TORSIONAL
24I5682X-RAY DIFFRACTION8.489TORSIONAL
25J5682X-RAY DIFFRACTION8.489TORSIONAL
26U5682X-RAY DIFFRACTION8.489TORSIONAL
27V5682X-RAY DIFFRACTION8.489TORSIONAL
28W5682X-RAY DIFFRACTION8.489TORSIONAL
29X5682X-RAY DIFFRACTION8.489TORSIONAL
210Y5682X-RAY DIFFRACTION8.489TORSIONAL
31K4826X-RAY DIFFRACTION8.489TORSIONAL
32L4826X-RAY DIFFRACTION8.489TORSIONAL
33M4826X-RAY DIFFRACTION8.489TORSIONAL
34N4826X-RAY DIFFRACTION8.489TORSIONAL
35O4826X-RAY DIFFRACTION8.489TORSIONAL
36Z4826X-RAY DIFFRACTION8.489TORSIONAL
37f4826X-RAY DIFFRACTION8.489TORSIONAL
38g4826X-RAY DIFFRACTION8.489TORSIONAL
39h4826X-RAY DIFFRACTION8.489TORSIONAL
310i4826X-RAY DIFFRACTION8.489TORSIONAL
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.39715510.384510316X-RAY DIFFRACTION60
3.2364-3.27440.38865550.374810575X-RAY DIFFRACTION61
3.2744-3.31440.38585700.364610696X-RAY DIFFRACTION62
3.3144-3.35630.35785840.355811026X-RAY DIFFRACTION64
3.3563-3.40050.38015930.360311177X-RAY DIFFRACTION64
3.4005-3.44710.36745970.35611338X-RAY DIFFRACTION65
3.4471-3.49630.37146010.349511729X-RAY DIFFRACTION68
3.4963-3.54850.33756300.338211998X-RAY DIFFRACTION69
3.5485-3.60390.3376580.31812517X-RAY DIFFRACTION72
3.6039-3.6630.34346900.313112644X-RAY DIFFRACTION73
3.663-3.72610.33486790.317712845X-RAY DIFFRACTION74
3.7261-3.79390.31577000.305813212X-RAY DIFFRACTION76
3.7939-3.86680.3066860.279913352X-RAY DIFFRACTION77
3.8668-3.94580.28747180.269513573X-RAY DIFFRACTION79
3.9458-4.03150.26277260.262313967X-RAY DIFFRACTION80
4.0315-4.12530.26697520.235514214X-RAY DIFFRACTION82
4.1253-4.22840.24287590.21914386X-RAY DIFFRACTION83
4.2284-4.34270.2557650.222114547X-RAY DIFFRACTION84
4.3427-4.47050.22867850.202214775X-RAY DIFFRACTION85
4.4705-4.61470.21497720.194514748X-RAY DIFFRACTION85
4.6147-4.77960.19697860.18514959X-RAY DIFFRACTION86
4.7796-4.97080.21287780.175415039X-RAY DIFFRACTION87
4.9708-5.19690.19757940.167115050X-RAY DIFFRACTION87
5.1969-5.47080.20417950.174415083X-RAY DIFFRACTION87
5.4708-5.81320.21938030.193815001X-RAY DIFFRACTION87
5.8132-6.26160.21467900.208115017X-RAY DIFFRACTION87
6.2616-6.89090.26017790.215715051X-RAY DIFFRACTION87
6.8909-7.88590.24157940.200515014X-RAY DIFFRACTION87
7.8859-9.92770.18327940.16515092X-RAY DIFFRACTION87
9.9277-58.70.24087830.21714964X-RAY DIFFRACTION86
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)
11.29670.22051.31721.16620.53143.6366-0.133-0.15190.09250.1112-0.1371-0.1949-0.0890.3530.27030.57010.04240.00510.59140.09580.8052-64.3966-28.611914.3656
22.51160.2961.17481.21420.22782.01640.0758-0.305-0.22050.3777-0.0862-0.18060.04860.2625-0.0160.60890.0001-0.00070.61270.14410.6006-83.6926-28.856530.9184
33.69880.10921.79921.17850.08732.52460.2155-0.4664-0.01390.3388-0.1722-0.15720.07170.2055-0.07110.6822-0.06950.0870.64690.01420.5193-90.1195-4.801435.7933
42.4751-0.64272.00031.0123-0.66913.33350.0844-0.3820.13330.2946-0.0417-0.1811-0.03110.0725-0.04960.6646-0.12060.01860.6203-0.08860.7086-74.744310.269422.3798
51.6066-0.09221.46181.0952-0.35694.0817-0.0867-0.19850.13180.1433-0.1669-0.3281-0.14230.30840.24550.5284-0.0126-0.02180.46670.03650.7652-58.7761-4.46159.206
64.18761.4326-0.76781.0564-0.17291.45230.1846-0.9677-0.34680.4454-0.36680.18440.2654-0.050.18210.8255-0.16170.13010.78340.05760.786-133.1656-37.274347.5429
73.2481-1.9689-0.78822.49371.40352.58650.2288-0.23810.9935-0.02060.0676-0.0624-1.6496-0.4189-0.25921.75560.13910.35660.79770.02751.0962-121.705337.511936.092
81.6716-0.23220.53247.37750.52051.55070.2678-0.1473-0.38670.3081-0.06960.63440.5056-0.2347-0.1880.6628-0.0782-0.02190.66290.110.6266-80.6438-77.71772.9924
91.35121.0266-0.6523.7295-2.17672.52680.1489-0.07310.35660.2455-0.3564-0.4802-0.47670.33440.20670.7505-0.06550.07750.6975-0.02850.992-61.271344.3813-15.8701
102.2405-0.33-1.04221.59061.37653.53430.0459-0.05420.1863-0.3586-0.35230.5717-1.3853-0.83260.34271.15410.24730.05560.7759-0.05840.8388-134.765726.188639.3992
111.6285-0.37090.09564.77310.50832.84770.39280.2668-0.2847-0.7041-0.1020.16920.4868-0.0575-0.28980.70430.0809-0.07060.5540.0390.5839-72.5075-75.6646-12.3042
123.99272.1405-1.04371.2073-0.38370.5616-0.0558-0.6225-1.0550.375-0.2098-0.41460.3629-0.0410.23811.0073-0.06760.11160.74970.19381.0971-132.4167-52.497239.0958
131.59560.505-0.57263.9895-2.12481.62930.2125-0.02210.51210.6543-0.0041-0.3138-0.59870.0828-0.19950.8325-0.06590.16650.618-0.17440.9024-75.795853.4378-11.9882
142.46090.26762.18261.10550.45164.3274-0.01640.0460.0543-0.03720.02190.09310.0852-0.09410.00710.4714-0.00960.06940.68010.01290.4907-48.563999.655568.398
151.8811-0.00951.67391.0967-0.04653.5217-0.1155-0.02280.0554-0.1256-0.00370.1973-0.0634-0.23870.14560.4857-0.06220.02520.66960.01390.5395-51.448474.539270.5323
162.5789-0.18981.84521.3913-0.23112.5713-0.1733-0.060.0229-0.19370.07440.07040.149-0.26360.09060.5663-0.080.05540.5369-0.00520.4947-33.655663.38156.188
172.4356-0.37471.9320.736-0.32512.18050.2034-0.036-0.0898-0.1441-0.0983-0.03520.29440.0637-0.14370.65340.00760.04570.6849-0.03240.5701-19.938781.709545.0684
182.78970.19562.38871.13260.14832.88360.00170.01010.1136-0.0305-0.0721-0.0371-0.0148-0.02610.03220.4763-0.00580.05750.6164-0.01870.4892-28.9723104.155652.7473
191.1550.1490.283.7321-1.36592.42510.0508-0.1587-0.4785-0.18790.21340.52760.9911-0.651-0.19771.1184-0.2823-0.0360.93560.18810.8229-50.678527.461494.0602
202.1417-3.0474-1.55474.26362.14861.40830.02130.1908-0.121-0.3320.0422-0.47990.20160.314-0.07160.84510.09770.20470.8843-0.17971.108910.15935.531345.725
214.29-1.5842-3.97320.60351.62424.4838-0.29410.2325-0.41590.3161-0.1230.23930.3619-0.6080.42320.7784-0.03230.17870.8565-0.02550.6399-74.7198.5733114.3954
225.82582.7774-3.57421.3508-1.91062.76570.01690.36810.3561-0.05530.1685-0.0249-0.2479-0.1111-0.15260.6269-0.0860.18860.6393-0.02980.819222.5642110.710534.7104
231.38710.29980.30996.02690.51671.1273-0.4333-0.03940.75160.3178-0.0040.243-0.67370.04590.39751.1080.0625-0.39740.851-0.1080.9303-28.9342150.431677.6373
242.1411-2.1334-1.00583.0120.44090.7241-0.56550.0088-0.68010.2960.3040.35370.50770.25910.24710.88770.09160.14680.8144-0.13671.0984.735123.993358.0178
252.431-0.7094-2.54740.65541.34483.3860.4005-0.15620.2947-0.0244-0.07310.0442-0.5155-0.0018-0.28410.8571-0.02270.19020.83480.04270.7592-68.2823114.5443117.2431
261.31840.39960.32733.94670.71680.4805-0.4093-0.08460.51590.05150.156-0.6135-0.5736-0.25390.23271.2190.0235-0.38330.98240.03680.9901-12.3973152.510871.9797
270.2829-0.36380.27113.0839-1.90622.22380.1157-0.2991-0.44530.50510.11840.7080.3303-0.5187-0.25861.0999-0.14960.09221.240.28081.0691-58.14835.4368107.8596
284.69211.984-2.10830.9117-1.11781.4347-0.14690.1618-0.53-0.1859-0.0158-0.35310.0440.00950.14260.673-0.05480.17980.6244-0.09170.929631.626795.686635.0015
292.45090.31420.03932.15760.03132.3836-0.30.6852-0.8387-1.11580.1493-0.97850.61650.9810.15861.35330.17470.53161.0213-0.03261.3653-37.8883-26.9847-33.9331
302.91390.7424-0.58553.023-0.7292.4102-0.03160.9591-0.3978-1.21050.0856-0.6793-0.14580.3372-0.08731.1838-0.05910.26480.8970.01440.9307-38.898-11.1662-41.5215
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 340 )
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 340 )
3X-RAY DIFFRACTION3chain 'C' and (resid 1 through 340 )
4X-RAY DIFFRACTION4chain 'D' and (resid 1 through 340 )
5X-RAY DIFFRACTION5chain 'E' and (resid 1 through 340 )
6X-RAY DIFFRACTION6chain 'F' and (resid 1 through 221 )
7X-RAY DIFFRACTION7chain 'G' and (resid 1 through 221 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 221 )
9X-RAY DIFFRACTION9chain 'I' and (resid 1 through 221 )
10X-RAY DIFFRACTION10chain 'K' and (resid 1 through 210 )
11X-RAY DIFFRACTION11chain 'L' and (resid 1 through 210 )
12X-RAY DIFFRACTION12chain 'N' and (resid 1 through 210 )
13X-RAY DIFFRACTION13chain 'O' and (resid 1 through 210 )
14X-RAY DIFFRACTION14chain 'P' and (resid 1 through 340 )
15X-RAY DIFFRACTION15chain 'Q' and (resid 1 through 340 )
16X-RAY DIFFRACTION16chain 'R' and (resid 1 through 340 )
17X-RAY DIFFRACTION17chain 'S' and (resid 1 through 340 )
18X-RAY DIFFRACTION18chain 'T' and (resid 1 through 340 )
19X-RAY DIFFRACTION19chain 'U' and (resid 1 through 221 )
20X-RAY DIFFRACTION20chain 'V' and (resid 1 through 221 )
21X-RAY DIFFRACTION21chain 'W' and (resid 1 through 221 )
22X-RAY DIFFRACTION22chain 'X' and (resid 1 through 221 )
23X-RAY DIFFRACTION23chain 'Y' and (resid 1 through 221 )
24X-RAY DIFFRACTION24chain 'Z' and (resid 1 through 210 )
25X-RAY DIFFRACTION25chain 'f' and (resid 1 through 210 )
26X-RAY DIFFRACTION26chain 'g' and (resid 1 through 210 )
27X-RAY DIFFRACTION27chain 'h' and (resid 1 through 210 )
28X-RAY DIFFRACTION28chain 'i' and (resid 1 through 210 )
29X-RAY DIFFRACTION29chain 'J' and (resid 1 through 221 )
30X-RAY DIFFRACTION30chain 'M' and (resid 1 through 210 )

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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