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- PDB-4z7o: Integrin alphaIIbbeta3 in complex with AGDV peptide -

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基本情報

登録情報
データベース: PDB / ID: 4z7o
タイトルIntegrin alphaIIbbeta3 in complex with AGDV peptide
要素
  • (Monoclonal antibody 10E5 Fab ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3
  • Tetrapeptide ALA-GLY-ASP-VAL
キーワードMembrane protein/Immune system / CELL ADHESION / PLATELET AGGREGATION / Membrane protein-Immune system complex
機能・相同性
機能・相同性情報


tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation ...tube development / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / negative regulation of lipid transport / vascular endothelial growth factor receptor 2 binding / glycinergic synapse / negative regulation of low-density lipoprotein receptor activity / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / apolipoprotein A-I-mediated signaling pathway / regulation of bone resorption / apoptotic cell clearance / positive regulation of cell adhesion mediated by integrin / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / cellular response to insulin-like growth factor stimulus / smooth muscle cell migration / microvillus membrane / negative chemotaxis / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / activation of protein kinase activity / cellular response to platelet-derived growth factor stimulus / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / GRB2:SOS provides linkage to MAPK signaling for Integrins / negative regulation of macrophage derived foam cell differentiation / platelet-derived growth factor receptor signaling pathway / negative regulation of lipid storage / fibronectin binding / ECM proteoglycans / positive regulation of T cell migration / positive regulation of bone resorption / Integrin cell surface interactions / coreceptor activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / positive regulation of endothelial cell migration / Integrin signaling / substrate adhesion-dependent cell spreading / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / Signaling by high-kinase activity BRAF mutants / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / ruffle membrane / VEGFA-VEGFR2 Pathway / cell-cell adhesion / cellular response to mechanical stimulus / positive regulation of angiogenesis / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / regulation of protein localization
類似検索 - 分子機能
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha cytoplasmic region / EGF-like domain, extracellular / EGF-like domain / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / 7 Propeller / Methylamine Dehydrogenase; Chain H / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
: / Integrin beta-3 / Integrin alpha-IIb
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 解像度: 2.85 Å
データ登録者Lin, F.Y. / Zhu, J. / Springer, T.A.
引用ジャーナル: J.Biol.Chem. / 年: 2016
タイトル: beta-Subunit Binding Is Sufficient for Ligands to Open the Integrin alpha IIb beta 3 Headpiece.
著者: Lin, F.Y. / Zhu, J. / Eng, E.T. / Hudson, N.E. / Springer, T.A.
履歴
登録2015年4月7日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年1月27日Provider: repository / タイプ: Initial release
改定 1.12016年3月9日Group: Database references
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation

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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: Integrin alpha-IIb
B: Integrin beta-3
C: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 Fab heavy chain
F: Monoclonal antibody 10E5 Fab light chain
H: Monoclonal antibody 10E5 Fab heavy chain
L: Monoclonal antibody 10E5 Fab light chain
G: Tetrapeptide ALA-GLY-ASP-VAL
I: Tetrapeptide ALA-GLY-ASP-VAL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)301,16934
ポリマ－297,24410
非ポリマー3,92524
水10,521584
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Monoclonal antibody 10E5 Fab heavy chain
L: Monoclonal antibody 10E5 Fab light chain
G: Tetrapeptide ALA-GLY-ASP-VAL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,69617
ポリマ－148,6225
非ポリマー2,07412
水905
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Integrin alpha-IIb
D: Integrin beta-3
E: Monoclonal antibody 10E5 Fab heavy chain
F: Monoclonal antibody 10E5 Fab light chain
I: Tetrapeptide ALA-GLY-ASP-VAL
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,47317
ポリマ－148,6225
非ポリマー1,85112
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)259.918, 144.524, 104.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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要素

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タンパク質 , 2種, 4分子 ACBD

#1: タンパク質 Integrin alpha-IIb / GPalpha IIb / GPIIb / Platelet membrane glycoprotein IIb


分子量: 49357.805 Da / 分子数: 2 / 断片: UNP residues 32-486 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGA2B, GP2B, ITGAB
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P08514
#2: タンパク質 Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


分子量: 51804.625 Da / 分子数: 2 / 断片: UNP residues 29-497 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGB3, GP3A
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P05106

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タンパク質・ペプチド , 1種, 2分子 GI

#5: タンパク質・ペプチド Tetrapeptide ALA-GLY-ASP-VAL


分子量: 360.363 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)

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抗体 , 2種, 4分子 EHFL

#3: 抗体 Monoclonal antibody 10E5 Fab heavy chain


分子量: 23766.473 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
#4: 抗体 Monoclonal antibody 10E5 Fab light chain


分子量: 23332.686 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ)
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)

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糖 , 4種, 6分子

#6: 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
#7: 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: 2 / 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
#8: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 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
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#12: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / 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: 2 / 由来タイプ: 組換発現 / 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

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非ポリマー , 5種, 602分子

#9: 化合物 ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4
#10: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Ca
#11: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Mn
#13: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#14: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 584 / 由来タイプ: 天然 / 式: H2O

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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: 3.32 Å3/Da / 溶媒含有率: 62.91 %
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: 8.9
詳細: 11% PEG 8000, 0.2 M ammonium sulfate, 0.1 M Tris-HCl, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: 23-ID-B / 波長: 1 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2012年12月15日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 2.85→50 Å / Num. obs: 92354 / % possible obs: 99.6 % / 冗長度: 3.7 % / Net I/σ(I): 2.68

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2142: ???)精密化
XDSデータ削減
XDSデータスケーリング
PHASER位相決定
精密化解像度: 2.85→49.027 Å / SU ML: 0.51 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 31.56 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2566 1966 2.17 %
Rwork0.2232 --
obs0.2239 90699 97.8 %
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: 2.85→49.027 Å
タンパク質核酸リガンド溶媒全体
原子数20760 0 225 584 21569
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00621635
X-RAY DIFFRACTIONf_angle_d0.55529371
X-RAY DIFFRACTIONf_dihedral_angle_d8.66912890
X-RAY DIFFRACTIONf_chiral_restr0.0433278
X-RAY DIFFRACTIONf_plane_restr0.0033806
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8499-2.92120.41761120.39755041X-RAY DIFFRACTION78
2.9212-3.00020.41651350.38365876X-RAY DIFFRACTION92
3.0002-3.08840.4021400.38516388X-RAY DIFFRACTION99
3.0884-3.18810.39571410.34616395X-RAY DIFFRACTION100
3.1881-3.3020.33541420.31656415X-RAY DIFFRACTION100
3.302-3.43420.30351430.28296406X-RAY DIFFRACTION100
3.4342-3.59050.26491420.26356417X-RAY DIFFRACTION100
3.5905-3.77970.29381430.24746424X-RAY DIFFRACTION100
3.7797-4.01640.2421430.21766486X-RAY DIFFRACTION100
4.0164-4.32630.22541430.18826468X-RAY DIFFRACTION100
4.3263-4.76140.20361440.15976491X-RAY DIFFRACTION100
4.7614-5.44960.17181440.16476520X-RAY DIFFRACTION100
5.4496-6.86290.23741470.20366609X-RAY DIFFRACTION100
6.8629-49.03420.25591470.19816797X-RAY DIFFRACTION99
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)
15.5099-1.639-1.78272.77710.13894.2189-0.12930.28270.0689-0.20570.16720.08010.2199-0.3505-0.00690.74870.00410.02390.63930.02690.698148.937488.325938.7782
26.0962-2.7237-3.25028.57925.85524.67210.62590.51070.3045-1.2553-0.70010.4464-1.0149-0.9709-0.15440.92210.0924-0.02790.77290.13090.801540.594295.427339.0308
32.92540.0961-0.11771.39980.15131.78960.1103-0.23510.06850.399-0.13760.32260.1147-0.3360.0320.8036-0.03030.15660.6059-0.01370.768442.375994.895262.802
43.82661.6135-0.64226.34651.38255.95080.2673-0.3186-0.09350.5557-0.1386-0.39670.33270.374-0.1450.70650.09470.04680.47860.09080.594166.63985.595860.182
52.49940.7077-0.1491.86810.3152.9307-0.0577-0.072-0.37140.24010.0225-0.14190.32070.10450.01290.78410.0880.08020.49710.0370.713162.720182.896245.5798
67.0125-1.77462.25035.8088-4.69774.81552.23082.81640.8473-2.8226-3.4051-2.01381.51170.67770.72561.07130.17560.26450.7435-0.00870.879760.000872.887233.0186
77.6895-4.6013-4.33514.89452.98692.6585-0.3507-0.00020.16550.51180.7219-1.20120.65631.7644-0.25791.2170.3751-0.01512.7088-0.16411.7895122.950689.061935.4175
83.0609-2.8515-2.64136.62526.66269.32710.0375-0.4321.0053-0.36450.9239-1.1067-0.63131.4343-1.19021.0969-0.2084-0.03181.6858-0.00051.5354103.7106113.241252.256
92.39820.99760.11173.72140.52932.0840.0963-0.30270.31030.2071-0.0031-0.1197-0.42050.1188-0.08980.85610.02310.08350.5194-0.00570.763568.0224117.824763.3943
107.6062-6.0968-6.78337.61256.10276.004-1.012-0.5583-0.1010.91360.74810.23611.34881.46760.33091.0390.1759-01.28160.10861.373797.5314103.883760.4624
114.980.3584-2.35253.84953.79579.1694-0.12390.06390.12960.03840.0432-0.0930.64090.88910.10070.9720.0542-0.04491.4270.11071.3886100.7373104.268348.2019
123.79082.087-1.62093.9741-2.56433.714-0.1019-0.6206-0.3227-1.1906-0.3009-0.93370.75541.12360.23781.39070.41650.16732.7706-0.03611.4919116.224188.526719.0174
135.72841.2466-2.72285.5966-1.84615.3527-0.0601-0.10160.11920.06060.1309-0.31890.32191.0625-0.06280.81610.08960.04861.0539-0.0160.752688.17294.5747131.7442
143.5310.4623-0.36731.3653-0.37582.7015-0.22240.8693-0.1291-0.4085-0.0899-0.30420.37390.57330.32921.05170.15320.25691.44010.01550.892592.380290.0347107.4822
156.019-2.0431-1.14663.66350.56815.6139-0.16721.0556-0.8752-0.5648-0.06950.05251.4168-0.37340.26981.4368-0.08310.27871.0162-0.23180.962571.749475.7193115.2614
164.084-0.77740.19422.74340.12754.174-0.2215-0.0547-0.8734-0.27620.2176-0.19021.08590.0730.02931.1630.01940.21810.8954-0.11570.932773.104576.2788126.1772
175.2899-0.0616-0.17984.3433-0.81354.6012-0.51790.2448-0.486-0.00910.10890.01780.8727-0.05590.39490.91460.04280.08630.94930.00290.727675.83284.7284132.4602
184.4223-3.20881.62138.5688-4.08446.0212-0.0072-0.3155-0.32440.8051-0.2198-0.33760.38260.34810.23420.81550.02630.15120.9804-0.05410.766882.2285.5692136.8298
197.68911.2031-5.57717.1701-1.57994.1725-0.84760.7972-0.7882-0.28380.28011.24782.0941-1.70770.87491.6892-0.64870.34552.0513-0.12451.717315.931569.3059141.4911
204.08341.253-2.66711.226-1.20563.6447-0.15081.49280.4696-0.24690.3920.4210.3171-1.4256-0.28341.216-0.2532-0.09031.89190.150.973844.593698.3222105.2271
213.85590.25640.22492.1408-0.54164.4439-0.23091.16650.4322-0.47160.27170.0860.0166-0.7994-0.02691.0083-0.1091-0.00261.59990.17550.791660.7631100.5633101.5377
224.57220.4082-1.11892.8166-0.18426.0355-0.50441.1612-0.4202-0.0557-0.12240.1521.1218-0.78310.54551.3582-0.42310.04351.84-0.08321.063733.417484.3047118.6267
239.71492.81523.91349.72924.00142.8445-0.73030.0159-0.27010.5765-0.53360.13152.2165-2.15471.21481.6548-0.24870.29521.65620.01591.406720.428479.1396157.2602
246.26750.76160.33224.8204-4.79634.94440.66140.4854-4.23191.38941.40780.81772.6138-2.5311-1.68091.3396-0.4590.06671.6910.57422.87129.640872.5271159.1869
254.2672-2.20362.23815.97260.10461.4749-0.13260.8066-1.2157-0.9698-0.68840.33811.48091.52880.82621.61520.23190.45941.87810.05571.6952120.801682.638483.8939
262.0852-0.2404-0.90496.84121.76020.791-0.0862.77210.4585-2.6441-0.27540.5720.9742-0.28650.43092.59750.05040.0742.8629-0.19861.1813116.116884.895578.501
275.4748-2.298-0.75072.2412.24873.2350.5970.43960.7234-1.0441-0.5681-0.07510.80280.01370.04751.36730.05420.37382.2690.30361.258112.659893.014987.9964
284.8859-0.5473-1.92713.71440.53484.7928-0.1051.28430.0074-0.7048-0.2955-0.28241.0760.10710.18191.39330.16010.4352.31210.13121.2743115.9689.721485.7789
292.3974-1.6836-1.966.5645-0.08522.4874-0.37440.74380.1209-0.8466-0.0381-1.86070.69610.4370.45841.95730.46690.36343.04580.21872.0499150.015582.579279.9806
302.3255-0.49882.17623.09531.28343.31411.58282.30770.30820.1912-0.6442-0.14470.83391.3631-1.00751.97811.06410.27783.56320.11262.0222151.108281.278979.653
317.2861-1.50672.55814.9357-1.65445.9850.1850.61041.46540.1934-0.8065-1.1908-0.59621.1430.49041.3162-0.06540.29941.92730.23751.907126.9072107.25296.1477
327.2952-3.4141-0.11282.4198-1.18366.38060.04870.05582.56650.6852-0.0908-1.09770.47750.7869-0.01740.92360.0056-0.09162.10820.13012.0024133.7464102.6526106.7312
335.4945-2.62810.96843.2705-0.03132.2996-0.2402-0.25120.84940.14130.0056-0.84830.26880.86290.27311.1689-0.01780.24752.22580.12381.3891122.792198.6756102.4199
344.67060.8629-4.30350.2208-0.85774.0403-0.670.6040.6243-0.3938-1.0144-0.39790.53442.44561.3281.24060.33120.34533.83430.2472.1269150.735597.259894.9214
353.16040.0993-0.03054.4030.90134.04540.23370.90920.2267-0.9757-0.2152-0.44-0.39212.2039-0.13252.08690.31910.56723.16990.4212.0937152.416997.738778.7008
361.42041.1836-0.79881.47470.41444.01180.06821.20880.101-0.87770.379-0.9929-0.2820.6132-0.39481.65350.06170.64913.73610.4512.4767156.460998.503180.1195
378.8291-3.8024-5.96312.50323.23768.9208-0.4446-0.9331-0.18331.28950.3664-0.0541.34350.4170.35461.4628-0.04950.20391.54090.01941.170119.368889.910285.8022
384.02812.97522.19574.4218-0.30243.8761-0.0723-0.77240.73940.28540.15270.4312-0.24490.0535-0.13080.95690.03810.1751.197-0.15411.095918.0113101.729980.0463
399.2424-0.19-3.87542.2074-0.64454.54580.0592-0.97050.17430.94960.09250.4381-0.1128-0.3056-0.14771.0660.03080.26471.2588-0.03641.005117.361896.062683.3068
408.55871.64772.93764.09772.84955.2709-0.0462-1.1426-1.77290.74740.07210.68130.8805-0.0098-0.00261.32070.04780.22941.51130.57682.2243-17.41283.897594.1014
419.37097.55643.96046.47412.02034.8653-0.2169-0.1389-2.84080.12830.3952-0.6430.7110.6057-0.27621.00310.2450.30241.63520.22612.5531-8.68882.706689.8095
425.28752.08892.04180.96681.7956.65020.295-0.2148-2.41120.2924-0.07140.00211.4916-0.3743-0.23821.4433-0.0060.1881.49920.6252.9166-16.037877.631593.5091
435.29962.84950.68566.83360.61061.0255-0.07020.80011.24140.0106-0.19551.98920.0104-0.76440.15390.91340.0640.17191.63-0.25621.67312.082100.203963.2242
445.49830.5199-0.68453.90540.18563.5344-0.08590.4685-0.6128-0.0873-0.1130.75990.2321-0.90720.25660.8388-0.0750.09271.2758-0.17471.148912.000994.076963.2313
456.60962.451.33175.23621.38293.6421-0.06150.1952-0.27860.1393-0.25041.15210.3-1.18860.35670.832-0.02410.16171.4781-0.14211.34976.015595.187166.5149
464.4889-0.11691.05031.75971.78894.8353-0.3971-0.087-1.5310.26980.05490.41030.61230.19350.44820.9687-0.00540.23591.50370.13762.0041-20.145689.281883.8499
476.6583-1.7693-0.15481.66060.7834.4468-0.1295-1.1536-1.7664-0.36650.46820.1912-0.4910.5233-0.20150.8631-0.09760.18881.37490.38081.7642-17.771394.450784.3208
484.82160.9378-0.58083.16052.18356.0317-0.008-0.4472-0.94290.5693-0.35130.84830.1995-1.59760.4071.00850.09650.33811.69550.18621.8995-29.076295.280588.9322
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:44)
2X-RAY DIFFRACTION2(chain A and resid 45:73)
3X-RAY DIFFRACTION3(chain A and resid 74:274)
4X-RAY DIFFRACTION4(chain A and resid 275:334)
5X-RAY DIFFRACTION5(chain A and resid 335:448)
6X-RAY DIFFRACTION6(chain A and resid 449:454)
7X-RAY DIFFRACTION7(chain B and resid 3:62)
8X-RAY DIFFRACTION8(chain B and resid 63:108)
9X-RAY DIFFRACTION9(chain B and resid 109:349)
10X-RAY DIFFRACTION10(chain B and resid 350:390)
11X-RAY DIFFRACTION11(chain B and resid 391:432)
12X-RAY DIFFRACTION12(chain B and resid 433:466)
13X-RAY DIFFRACTION13(chain C and resid 1:68)
14X-RAY DIFFRACTION14(chain C and resid 69:274)
15X-RAY DIFFRACTION15(chain C and resid 275:334)
16X-RAY DIFFRACTION16(chain C and resid 335:399)
17X-RAY DIFFRACTION17(chain C and resid 400:428)
18X-RAY DIFFRACTION18(chain C and resid 429:453)
19X-RAY DIFFRACTION19(chain D and resid 3:50)
20X-RAY DIFFRACTION20(chain D and resid 51:176)
21X-RAY DIFFRACTION21(chain D and resid 177:353)
22X-RAY DIFFRACTION22(chain D and resid 354:440)
23X-RAY DIFFRACTION23(chain D and resid 441:465)
24X-RAY DIFFRACTION24(chain D and resid 466:471)
25X-RAY DIFFRACTION25(chain E and resid 1:15)
26X-RAY DIFFRACTION26(chain E and resid 16:22)
27X-RAY DIFFRACTION27(chain E and resid 23:64)
28X-RAY DIFFRACTION28(chain E and resid 65:119)
29X-RAY DIFFRACTION29(chain E and resid 120:170)
30X-RAY DIFFRACTION30(chain E and resid 171:219)
31X-RAY DIFFRACTION31(chain F and resid 1:11)
32X-RAY DIFFRACTION32(chain F and resid 12:24)
33X-RAY DIFFRACTION33(chain F and resid 25:102)
34X-RAY DIFFRACTION34(chain F and resid 103:118)
35X-RAY DIFFRACTION35(chain F and resid 119:164)
36X-RAY DIFFRACTION36(chain F and resid 165:214)
37X-RAY DIFFRACTION37(chain H and resid 1:31)
38X-RAY DIFFRACTION38(chain H and resid 32:64)
39X-RAY DIFFRACTION39(chain H and resid 65:120)
40X-RAY DIFFRACTION40(chain H and resid 121:151)
41X-RAY DIFFRACTION41(chain H and resid 152:179)
42X-RAY DIFFRACTION42(chain H and resid 180:219)
43X-RAY DIFFRACTION43(chain L and resid 1:27)
44X-RAY DIFFRACTION44(chain L and resid 28:71)
45X-RAY DIFFRACTION45(chain L and resid 72:106)
46X-RAY DIFFRACTION46(chain L and resid 107:145)
47X-RAY DIFFRACTION47(chain L and resid 146:182)
48X-RAY DIFFRACTION48(chain L and resid 183:214)

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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://pdbjlvh1.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