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- PDB-4tnv: 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: 4tnv
タイトルC. elegans glutamate-gated chloride channel (GluCl) in complex with Fab in a non-conducting 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / 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
CITRATE ANION / 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: 3.6 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_assembly / pdbx_struct_assembly_gen / 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_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _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10月16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
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
I: 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)878,62354
ポリマ－870,85530
非ポリマー7,76724
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
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
I: 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)439,27626
ポリマ－435,42815
非ポリマー3,84811
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)439,34728
ポリマ－435,42815
非ポリマー3,91913
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)455.810, 195.680, 196.180
Angle α, β, γ (deg.)90.00, 93.15, 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 (resseq 1:300 )
21chain B and (resseq 1:300 )
31chain C and (resseq 1:300 )
41chain D and (resseq 1:300 )
51chain E and (resseq 1:300 )
61chain P and (resseq 1:300 )
71chain Q and (resseq 1:300 )
81chain R and (resseq 1:300 )
91chain S and (resseq 1:300 )
101chain T and (resseq 1:300 )
12chain A and (resseq 314:340 )
22chain B and (resseq 314:340 )
32chain C and (resseq 314:340 )
42chain D and (resseq 314:340 )
52chain E and (resseq 314:340 )
62chain P and (resseq 314:340 )
72chain Q and (resseq 314:340 )
82chain R and (resseq 314:340 )
92chain S and (resseq 314:340 )
102chain T and (resseq 314:340 )
13chain F and (resseq 1:120 )
23chain G and (resseq 1:120 )
33chain H and (resseq 1:120 )
43chain I and (resseq 1:120 )
53chain J and (resseq 1:120 )
63chain U and (resseq 1:120 )
73chain V and (resseq 1:120 )
83chain W and (resseq 1:120 )
93chain X and (resseq 1:120 )
103chain Y and (resseq 1:120 )
14chain K and (resseq 1:108 )
24chain L and (resseq 1:108 )
34chain M and (resseq 1:108 )
44chain N and (resseq 1:108 )
54chain O and (resseq 1:108 )
64chain Z and (resseq 1:108 )
74chain f and (resseq 1:108 )
84chain g and (resseq 1:108 )
94chain h and (resseq 1:108 )
104chain i and (resseq 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
11SERSERILEILEchain A and (resseq 1:300 )AA1 - 3001 - 300
21SERSERILEILEchain B and (resseq 1:300 )BB1 - 3001 - 300
31SERSERILEILEchain C and (resseq 1:300 )CC1 - 3001 - 300
41SERSERILEILEchain D and (resseq 1:300 )DD1 - 3001 - 300
51SERSERILEILEchain E and (resseq 1:300 )EE1 - 3001 - 300
61SERSERILEILEchain P and (resseq 1:300 )PM1 - 3001 - 300
71SERSERILEILEchain Q and (resseq 1:300 )QN1 - 3001 - 300
81SERSERILEILEchain R and (resseq 1:300 )RO1 - 3001 - 300
91SERSERILEILEchain S and (resseq 1:300 )SP1 - 3001 - 300
101SERSERILEILEchain T and (resseq 1:300 )TQ1 - 3001 - 300
12ARGARGHISHISchain A and (resseq 314:340 )AA314 - 340314 - 340
22ARGARGHISHISchain B and (resseq 314:340 )BB314 - 340314 - 340
32ARGARGHISHISchain C and (resseq 314:340 )CC314 - 340314 - 340
42ARGARGHISHISchain D and (resseq 314:340 )DD314 - 340314 - 340
52ARGARGHISHISchain E and (resseq 314:340 )EE314 - 340314 - 340
62ARGARGHISHISchain P and (resseq 314:340 )PM314 - 340314 - 340
72ARGARGHISHISchain Q and (resseq 314:340 )QN314 - 340314 - 340
82ARGARGHISHISchain R and (resseq 314:340 )RO314 - 340314 - 340
92ARGARGHISHISchain S and (resseq 314:340 )SP314 - 340314 - 340
102ARGARGHISHISchain T and (resseq 314:340 )TQ314 - 340314 - 340
13GLUGLUVALVALchain F and (resseq 1:120 )FF1 - 1201 - 120
23GLUGLUVALVALchain G and (resseq 1:120 )GG1 - 1201 - 120
33GLUGLUVALVALchain H and (resseq 1:120 )HH1 - 1201 - 120
43GLUGLUVALVALchain I and (resseq 1:120 )ICA1 - 1201 - 120
53GLUGLUVALVALchain J and (resseq 1:120 )JBA1 - 1201 - 120
63GLUGLUVALVALchain U and (resseq 1:120 )UR1 - 1201 - 120
73GLUGLUVALVALchain V and (resseq 1:120 )VS1 - 1201 - 120
83GLUGLUVALVALchain W and (resseq 1:120 )WT1 - 1201 - 120
93GLUGLUVALVALchain X and (resseq 1:120 )XU1 - 1201 - 120
103GLUGLUVALVALchain Y and (resseq 1:120 )YV1 - 1201 - 120
14GLNGLNVALVALchain K and (resseq 1:108 )KI1 - 1081 - 108
24GLNGLNVALVALchain L and (resseq 1:108 )LJ1 - 1081 - 108
34GLNGLNVALVALchain M and (resseq 1:108 )MDA1 - 1081 - 108
44GLNGLNVALVALchain N and (resseq 1:108 )NK1 - 1081 - 108
54GLNGLNVALVALchain O and (resseq 1:108 )OL1 - 1081 - 108
64GLNGLNVALVALchain Z and (resseq 1:108 )ZW1 - 1081 - 108
74GLNGLNVALVALchain f and (resseq 1:108 )fX1 - 1081 - 108
84GLNGLNVALVALchain g and (resseq 1:108 )gY1 - 1081 - 108
94GLNGLNVALVALchain h and (resseq 1:108 )hZ1 - 1081 - 108
104GLNGLNVALVALchain i and (resseq 1:108 )iAA1 - 1081 - 108

NCSアンサンブル:
ID
1
2
3
4

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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 FGHUVWXYJIKLNOZfghiM

#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, 20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: 10 / 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
#5: 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: 10 / 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 , 2種, 4分子

#6: 化合物 ChemComp-FLC / CITRATE ANION / シトラ-ト


分子量: 189.100 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C6H5O7
#7: 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

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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: 5.02 Å3/Da / 溶媒含有率: 75.48 %
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

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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18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: 3.6→58.44 Å / Num. obs: 175651 / % possible obs: 88.4 % / 冗長度: 1.85 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 5.82
反射 シェル解像度: 3.6→3.64 Å / 冗長度: 1.54 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 1.37 / % possible all: 78.9

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)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
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: 3.6→58.438 Å / SU ML: 0.75 / 交差検証法: FREE R-VALUE / σ(F): 1.39 / 位相誤差: 33.11 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2829 8778 5 %random
Rwork0.2611 ---
obs0.2622 175580 88.34 %-
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: 3.6→58.438 Å
タンパク質核酸リガンド溶媒全体
原子数60008 0 400 0 60408
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00462049
X-RAY DIFFRACTIONf_angle_d0.78384673
X-RAY DIFFRACTIONf_dihedral_angle_d11.15521778
X-RAY DIFFRACTIONf_chiral_restr0.0319851
X-RAY DIFFRACTIONf_plane_restr0.00510524
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDタイプRms dev position (Å)
11A2360X-RAY DIFFRACTIONPOSITIONAL0.013
12B2360X-RAY DIFFRACTIONPOSITIONAL0.013
13C2360X-RAY DIFFRACTIONPOSITIONAL0.012
14D2360X-RAY DIFFRACTIONPOSITIONAL0.012
15E2360X-RAY DIFFRACTIONPOSITIONAL0.012
16P2360X-RAY DIFFRACTIONPOSITIONAL0.014
17Q2360X-RAY DIFFRACTIONPOSITIONAL0.013
18R2360X-RAY DIFFRACTIONPOSITIONAL0.013
19S2360X-RAY DIFFRACTIONPOSITIONAL0.017
110T2360X-RAY DIFFRACTIONPOSITIONAL0.013
21A237X-RAY DIFFRACTIONPOSITIONAL0.011
22B237X-RAY DIFFRACTIONPOSITIONAL0.011
23C237X-RAY DIFFRACTIONPOSITIONAL0.01
24D237X-RAY DIFFRACTIONPOSITIONAL0.01
25E237X-RAY DIFFRACTIONPOSITIONAL0.012
26P237X-RAY DIFFRACTIONPOSITIONAL0.013
27Q237X-RAY DIFFRACTIONPOSITIONAL0.013
28R237X-RAY DIFFRACTIONPOSITIONAL0.013
29S237X-RAY DIFFRACTIONPOSITIONAL0.014
210T237X-RAY DIFFRACTIONPOSITIONAL0.012
31F949X-RAY DIFFRACTIONPOSITIONAL0.104
32G949X-RAY DIFFRACTIONPOSITIONAL0.104
33H949X-RAY DIFFRACTIONPOSITIONAL0.148
34I949X-RAY DIFFRACTIONPOSITIONAL0.104
35J949X-RAY DIFFRACTIONPOSITIONAL0.237
36U949X-RAY DIFFRACTIONPOSITIONAL0.104
37V949X-RAY DIFFRACTIONPOSITIONAL0.104
38W949X-RAY DIFFRACTIONPOSITIONAL0.104
39X949X-RAY DIFFRACTIONPOSITIONAL0.104
310Y949X-RAY DIFFRACTIONPOSITIONAL0.012
41K804X-RAY DIFFRACTIONPOSITIONAL0.439
42L804X-RAY DIFFRACTIONPOSITIONAL0.439
43M804X-RAY DIFFRACTIONPOSITIONAL0.165
44N804X-RAY DIFFRACTIONPOSITIONAL0.192
45O804X-RAY DIFFRACTIONPOSITIONAL0.236
46Z804X-RAY DIFFRACTIONPOSITIONAL0.235
47f804X-RAY DIFFRACTIONPOSITIONAL0.167
48g804X-RAY DIFFRACTIONPOSITIONAL0.237
49h804X-RAY DIFFRACTIONPOSITIONAL0.169
410i804X-RAY DIFFRACTIONPOSITIONAL0.242
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.64090.40092590.40874929X-RAY DIFFRACTION78
3.6409-3.68370.41412620.41184960X-RAY DIFFRACTION79
3.6837-3.72860.40452610.40014976X-RAY DIFFRACTION80
3.7286-3.77580.41682690.39635100X-RAY DIFFRACTION81
3.7758-3.82550.39342660.39035048X-RAY DIFFRACTION81
3.8255-3.87790.39162670.38515088X-RAY DIFFRACTION81
3.8779-3.93330.40852710.38375152X-RAY DIFFRACTION83
3.9333-3.9920.39292760.37385234X-RAY DIFFRACTION83
3.992-4.05430.37192810.36585336X-RAY DIFFRACTION85
4.0543-4.12080.33462840.33565403X-RAY DIFFRACTION86
4.1208-4.19180.32372930.32445561X-RAY DIFFRACTION88
4.1918-4.2680.33372940.32255594X-RAY DIFFRACTION89
4.268-4.35010.34852940.31565588X-RAY DIFFRACTION89
4.3501-4.43890.31352980.29425652X-RAY DIFFRACTION90
4.4389-4.53540.26143020.28375739X-RAY DIFFRACTION92
4.5354-4.64080.293010.2675719X-RAY DIFFRACTION91
4.6408-4.75680.2553050.25665806X-RAY DIFFRACTION92
4.7568-4.88540.2633070.24595818X-RAY DIFFRACTION92
4.8854-5.02910.25343060.23675821X-RAY DIFFRACTION93
5.0291-5.19130.25513080.23815861X-RAY DIFFRACTION93
5.1913-5.37670.26733090.24915861X-RAY DIFFRACTION93
5.3767-5.59180.27493100.24695889X-RAY DIFFRACTION93
5.5918-5.84610.26663070.24295834X-RAY DIFFRACTION93
5.8461-6.1540.26463090.25175865X-RAY DIFFRACTION93
6.154-6.53910.27593070.24135840X-RAY DIFFRACTION92
6.5391-7.04320.25863090.24465867X-RAY DIFFRACTION93
7.0432-7.75050.27413110.21635913X-RAY DIFFRACTION93
7.7505-8.86870.22613090.1915872X-RAY DIFFRACTION93
8.8687-11.16090.1693100.15335881X-RAY DIFFRACTION93
11.1609-58.44590.2852930.24025595X-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)
12.02920.62891.48862.37541.07983.3227-0.05-0.36270.15150.2841-0.269-0.1372-0.5361-0.00680.33120.681-0.03980.01370.78360.23721.0702-65.3085-31.505614.0097
22.8517-0.61020.25521.2782-0.90762.9897-0.2130.06510.28550.1705-0.3051-0.3294-0.12720.81430.5020.74910.0116-0.00310.80780.17250.9016-84.9197-31.283830.5929
32.1264-0.33641.24731.93110.19753.6920.26860.08080.0030.4527-0.0358-0.42330.08770.6616-0.1421.075-0.15450.07330.8788-0.10670.7483-91.0812-6.911534.773
41.4322-0.12720.91921.3495-0.45423.83750.3881-0.2658-0.5430.4305-0.1677-0.16180.28950.0051-0.1871.0895-0.3723-0.10620.9086-0.1391.1894-75.30537.915721.1687
51.84740.2550.211.54060.33592.869-0.1482-0.67140.07780.1014-0.1775-0.048-0.1380.0150.38730.6999-0.1582-0.07660.95980.06531.1881-59.3285-7.53978.4657
61.7572-0.009-0.27540.97830.92312.07320.5116-0.8362-0.27220.5848-0.5190.22120.0692-0.06990.03761.3871-0.29610.08511.52120.0921.1955-133.7583-40.144947.0154
70.8673-0.52340.03221.31070.35831.09860.4299-0.13290.9192-0.69070.1064-0.683-1.0574-0.2918-0.23642.0441-0.02850.45041.10230.07521.3555-124.105433.979435.6571
81.43830.3740.51194.0077-0.58051.71820.5173-0.0587-0.2026-0.1512-0.26820.66940.334-0.2812-0.22510.70220.018-0.00930.84470.11281.1299-80.5595-80.57121.8069
92.53740.1265-1.30141.9437-1.23242.23580.3241-0.0880.26060.3689-0.6213-0.6414-0.55620.43430.32591.2191-0.1809-0.13090.99560.0111.331-61.987842.4088-15.7129
102.6887-1.1448-1.18961.33611.65882.2144-0.2053-0.181-0.2059-0.3188-0.15570.3973-0.6752-0.34850.01481.58980.08370.20291.0245-0.02521.0994-136.651622.691739.2391
110.1687-0.5502-0.10594.55190.12371.72350.31980.2074-0.2795-1.06810.090.33910.37680.0487-0.36840.95210.2227-0.1650.85850.14151.0681-71.8626-78.7659-13.3333
121.08551.196-0.29681.30550.18541.16290.0724-0.5141-0.70430.6397-0.4634-0.16390.4044-0.02760.2091.4923-0.08690.07741.12630.21111.5258-133.0558-55.488639.0465
130.9352-0.2427-0.51822.3499-1.04210.65380.1980.10210.37540.51570.0083-0.5178-0.6798-0.0632-0.0661.0822-0.225-0.06940.9564-0.1751.082-76.569851.4825-11.8144
140.6663-0.32670.38721.67790.53583.71260.0175-0.0622-0.01360.18720.05930.0267-0.04330.2721-0.1270.68260.12160.07981.00650.00460.7246-50.431996.970468.6049
152.4470.02831.29171.5326-0.37473.0888-0.1251-0.47730.07660.02990.1110.1899-0.08010.02650.01060.6236-0.01140.05930.90030.05690.8582-52.309971.519469.9861
162.8953-0.56522.16142.0908-1.11542.9039-0.169-0.0498-0.18760.20210.1025-0.1004-0.17730.0050.02130.6915-0.01840.05890.7801-0.11680.7907-33.971861.365855.3967
173.3750.17251.8260.83670.32172.01180.147-0.7318-0.05050.0144-0.0131-0.06880.1755-0.2785-0.15280.6946-0.04830.05190.902-0.070.5625-20.734680.67444.7273
181.94480.62011.18071.69530.3223.29650.1235-0.38350.05430.1923-0.161-0.1678-0.30710.17270.02020.81780.0388-0.05530.6503-0.04380.5855-30.7931102.514252.9955
190.1798-0.35430.09541.45930.43090.10820.2471-0.3466-0.471-0.29220.05410.50110.7216-0.4258-0.08291.7534-0.18730.04261.69680.55022.027-51.490124.787493.7902
20-0.2021-0.2424-0.3750.02530.45650.75030.12260.4705-0.0232-0.2221-0.256-0.68560.29190.14620.00261.19170.2010.43611.3227-0.3432.02249.402833.359745.7227
211.1270.2619-0.9529-0.05520.11131.2289-0.05390.1075-0.1242-0.1031-0.0684-0.14820.3015-0.38220.22481.44950.09530.42411.29790.05010.9753-76.807296.3512114.2558
221.64891.4518-0.84540.4807-1.15620.8473-0.16750.13960.4680.11640.10650.134-0.04610.01120.05980.9108-0.18390.20331.1179-0.14521.486621.7218109.573234.8215
231.4282-0.98370.25750.4689-0.139-0.52490.14580.61561.37830.25220.15210.1051-1.19550.49590.38952.94580.182-1.78311.5574-0.55491.3422-29.7809148.858677.1682
24-0.0443-1.1334-0.13291.83290.5902-0.084-0.81940.4306-0.73930.28550.2670.57910.48690.38590.28061.29920.11020.31561.1794-0.29521.92563.697521.728857.4945
250.7177-0.0626-0.4724-0.04380.74021.1630.24960.02750.13020.0038-0.1404-0.0234-0.1193-0.16760.02231.46270.18060.30251.04340.13121.0003-70.9491112.5646116.6065
261.8696-0.6419-0.00320.6224-0.1871-0.1379-0.09140.76692.92230.1990.7093-0.6065-1.8311-0.51320.43844.28-0.722-2.40671.22110.29330.8171-13.4332151.020771.2643
270.0253-0.0981-0.30050.25570.28480.40570.1599-0.4175-0.44310.34690.14260.61080.6491-0.6163-0.07581.7093-0.25810.15262.01180.58131.8132-59.769832.529107.1531
281.92851.3305-0.7653-0.0296-0.77960.7199-0.32270.1674-0.421-0.2124-0.0178-0.13070.2773-0.15120.28211.0741-0.2630.39560.9576-0.24671.301630.682494.587934.4758
291.55970.78390.10141.9101-1.24590.7985-0.5140.4708-0.9135-1.14950.2385-0.4210.54280.66650.27721.4417-0.01760.45671.10380.03051.5644-37.347-28.8881-34.1811
301.9223-0.0761-0.5141.0745-1.36021.8517-0.20160.8375-0.3216-1.02150.0446-0.4087-0.0470.51380.31021.6254-0.25350.27791.2309-0.01661.4636-38.4619-13.013-41.535
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

-
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