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- PDB-3nid: The Closed Headpiece of Integrin alphaIIB beta3 and its Complex w... -

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基本情報

登録情報
データベース: PDB / ID: 3nid
タイトルThe Closed Headpiece of Integrin alphaIIB beta3 and its Complex with an alpahIIB beta3 -Specific Antagonist That Does Not Induce Opening
要素
  • (Monoclonal antibody 10E5 ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3
キーワードCELL ADHESION/BLOOD CLOTTING / Integrin / headpiece / alphaIIB / beta3 / CELL ADHESION-BLOOD CLOTTING 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 / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization ...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 / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / alphav-beta3 integrin-PKCalpha complex / fibrinogen binding / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / glycinergic synapse / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / : / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / angiogenesis involved in wound healing / filopodium membrane / extracellular matrix binding / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / positive regulation of leukocyte migration / apoptotic cell clearance / wound healing, spreading of epidermal cells / integrin complex / heterotypic cell-cell adhesion / smooth muscle cell migration / Molecules associated with elastic fibres / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cell adhesion mediated by integrin / cellular response to insulin-like growth factor stimulus / Syndecan interactions / microvillus membrane / p130Cas linkage to MAPK signaling for integrins / positive regulation of smooth muscle cell migration / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / cell-substrate adhesion / positive regulation of osteoblast proliferation / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / fibronectin binding / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / ECM proteoglycans / Integrin cell surface interactions / positive regulation of bone resorption / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / coreceptor activity / cell adhesion molecule binding / cellular response to platelet-derived growth factor stimulus / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / Integrin signaling / embryo implantation / substrate adhesion-dependent cell spreading / protein kinase C binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / cell-matrix adhesion / Signal transduction by L1 / response to activity / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / positive regulation of smooth muscle cell proliferation / wound healing / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cell-cell adhesion / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / ruffle membrane / cellular response to mechanical stimulus / positive regulation of fibroblast proliferation / positive regulation of angiogenesis / Signaling by RAF1 mutants
類似検索 - 分子機能
ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / 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 beta tail domain ...ligand-binding face of the semaphorins, domain 2 / ntegrin, alpha v. Chain A, domain 3 / ligand-binding face of the semaphorins, domain 2 / Integrin alpha, N-terminal / 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 beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / Integrins beta chain EGF (I-EGF) domain profile. / Integrin alpha cytoplasmic region / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / 分子置換 / 解像度: 2.3 Å
データ登録者Zhu, J.H. / Zhu, J.Q. / Springer, T.A.
引用ジャーナル: Blood / 年: 2010
タイトル: Closed headpiece of integrin {alpha}IIb{beta}3 and its complex with an {alpha}IIb{beta}3-specific antagonist that does not induce opening.
著者: Zhu, J.H. / Zhu, J.Q. / Negri, A. / Provasi, D. / Filizola, M. / Coller, B.S. / Springer, T.A.
履歴
登録2010年6月15日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02010年12月22日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年9月6日Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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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 heavy chain
F: Monoclonal antibody 10E5 light chain
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)302,25547
ポリマ－297,1488
非ポリマー5,10839
水19,0781059
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,42425
ポリマ－148,5744
非ポリマー2,85021
水724
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 heavy chain
F: Monoclonal antibody 10E5 light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)150,83122
ポリマ－148,5744
非ポリマー2,25718
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)258.970, 144.490, 104.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11A
21C
12B
22D
13B
23D
14B
24D
15B
25D
16H
26E
17H
27E
18L
28F
19L
29F

NCSドメイン領域:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 454
2116C1 - 454
1126B1 - 57
2126D1 - 57
1146B109 - 352
2146D109 - 352
1156B433 - 466
2156D433 - 466
1166H1 - 119
2166E1 - 119
1176H120 - 221
2176E120 - 221
1186L1 - 108
2186F1 - 108
1196L109 - 214
2196F109 - 214

NCSアンサンブル:
ID
1
2
3
4
5
6
7
8
9

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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 / Platelet membrane glycoprotein IIb / GPalpha IIb / GPIIb / Integrin alpha-IIb heavy chain


分子量: 49515.965 Da / 分子数: 2 / 断片: Integrin alpha-IIb, residues 32-488 / 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 / プラスミド: pCDNA 3.1, pEF1 / Cell (発現宿主): CHO / 細胞株 (発現宿主): Lec 3.2.8.1
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 / CD61


分子量: 51958.789 Da / 分子数: 2 / 断片: Integrin beta-3, residues 27-497 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGB3, GP3A / プラスミド: pCDNA 3.1, pEF1 / Cell (発現宿主): CHO / 細胞株 (発現宿主): Lec 3.2.8.1
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P05106

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抗体 , 2種, 4分子 EHFL

#3: 抗体 Monoclonal antibody 10E5 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) / 株: BALB/C / 細胞株: 10E5 HYBRIDOMA
#4: 抗体 Monoclonal antibody 10E5 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) / 株: BALB/C / 細胞株: 10E5 HYBRIDOMA

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糖 , 4種, 6分子

#5: 多糖 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/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: 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
#7: 多糖 alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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: 586.542 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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}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: 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, 1092分子

#8: 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: 12 / 由来タイプ: 合成 / 式: Ca
#9: 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: 9 / 由来タイプ: 合成 / 式: C3H8O3
#10: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 10 / 由来タイプ: 合成 / 式: SO4
#11: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#13: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1059 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.28 Å3/Da / 溶媒含有率: 62.5 %
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-D / 波長: 1.00695 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2008年12月9日
放射モノクロメーター: Double 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: 1.00695 Å / 相対比: 1
反射解像度: 2.3→50 Å / Num. all: 173699 / Num. obs: 169848 / % possible obs: 97.7 % / 冗長度: 5.6 % / Rmerge(I) obs: 0.01 / Rsym value: 0.01 / Net I/σ(I): 11.7
反射 シェル解像度: 2.3→2.36 Å / 冗長度: 4.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.839 / % possible all: 96.9

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解析

ソフトウェア
名称バージョン分類
Blu-Iceデータ収集
PHASER位相決定
REFMAC5.5.0102精密化
XDSデータ削減
XDSデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 2VDR

2vdr


解像度: 2.3→48.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.963 / SU ML: 0.123 / 交差検証法: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.179 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.21474 1029 0.6 %RANDOM
Rwork0.17929 ---
obs0.1795 168819 100 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: MASK
原子変位パラメータBiso mean: 51.822 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.05 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→48.21 Å
タンパク質核酸リガンド溶媒全体
原子数20715 0 302 1059 22076
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02221579
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214427
X-RAY DIFFRACTIONr_angle_refined_deg1.0681.97129409
X-RAY DIFFRACTIONr_angle_other_deg0.783.00435078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71352712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89724.355930
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.463153360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.19115112
X-RAY DIFFRACTIONr_chiral_restr0.0670.23263
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124094
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024269
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.845513454
X-RAY DIFFRACTIONr_mcbond_other0.39155484
X-RAY DIFFRACTIONr_mcangle_it3.3271021723
X-RAY DIFFRACTIONr_scbond_it6.419208125
X-RAY DIFFRACTIONr_scangle_it8.437207676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-ID数タイプRms dev position (Å)Weight position
1A5857LOOSE POSITIONAL0.310
1A5857LOOSE THERMAL3.1520
2B719LOOSE POSITIONAL0.5110
2B719LOOSE THERMAL2.8220
3B1651LOOSE POSITIONAL0.4410
3B1651LOOSE THERMAL2.7420
4B3151LOOSE POSITIONAL0.2610
4B3151LOOSE THERMAL2.7520
5B418LOOSE POSITIONAL0.5510
5B418LOOSE THERMAL2.9620
6H1555LOOSE POSITIONAL0.2710
6H1555LOOSE THERMAL2.0520
7H1166LOOSE POSITIONAL0.4310
7H1166LOOSE THERMAL2.1120
8L1358LOOSE POSITIONAL0.2210
8L1358LOOSE THERMAL2.1820
9L1388LOOSE POSITIONAL0.6110
9L1388LOOSE THERMAL3.8520
LS精密化 シェル解像度: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.253 87 -
Rwork0.243 12241 -
obs--100 %
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)
13.1594-1.2771-1.17322.82551.02272.37990.02980.22770.0685-0.2728-0.09250.3246-0.0798-0.38070.06270.11150.0063-0.01880.0930.02080.097345.5391.15638.829
21.7983-0.1062-0.02370.87450.38160.9889-0.0151-0.0601-0.02270.1712-0.0750.2380.099-0.2620.09020.1108-0.01290.07150.07930.00280.122242.00295.48362.63
31.12720.563-0.22734.3203-0.01882.02670.0052-0.1472-0.13640.28390.0395-0.43130.16640.1514-0.04470.12070.0523-0.00280.04720.02510.089466.48286.11260.393
41.52880.14750.23452.40860.44491.6093-0.05050.0057-0.13650.08780.0957-0.14480.13340.0865-0.04520.10860.03550.04820.01630.01440.071462.67582.83145.052
57.30653.4987-0.56187.99840.542920.4155-0.4309-0.4759-1.39490.31530.0177-0.46211.89490.8260.41320.55130.4608-0.00020.8971-0.12730.6934117.74984.85437.138
69.8713-1.1401-2.82083.97841.5987.4353-0.184-0.23160.52210.120.9776-1.56180.46013.2698-0.79360.32020.3624-0.07372.0489-0.3760.9612126.51491.02134.437
75.4651-4.2968-4.04267.57027.19968.61670.1963-0.12140.8312-0.29650.6433-0.5552-0.35031.0157-0.83960.1523-0.05770.03730.6441-0.18970.6635103.718113.18551.674
84.00131.4921-0.07282.71390.57561.41190.0367-0.34980.31140.12240.015-0.1198-0.22150.0491-0.05170.18680.02640.03960.0487-0.0160.144366.376123.02966.223
90.93790.69050.26292.5530.77151.3835-0.0153-0.03130.1056-0.01350.1094-0.1932-0.1230.1081-0.09410.10340.00960.0430.022-0.00280.121668.671116.07261.92
105.6166-0.98351.08375.91183.034314.1401-0.2167-0.2775-0.02520.67460.2820.18670.82290.9027-0.06530.19340.08540.0480.2895-0.02160.44798.881101.71857.386
113.7586-2.5965-3.33033.64324.73989.3908-0.11810.0651-0.14980.21470.16590.06280.32050.4981-0.04780.14030.0233-0.02220.4096-0.06480.450499.308104.78650.806
128.9120.83850.28881.5651-1.022415.0908-0.20170.27110.2249-0.24920.4248-0.24080.24361.1079-0.22310.23020.16060.09070.7523-0.02870.5872115.99788.54319.206
133.41220.6674-0.78071.8398-0.59983.2922-0.049-0.39990.11880.1329-0.0347-0.2733-0.0960.59390.08380.0877-0.01360.02110.3573-0.07190.131388.80695.168130.208
141.95010.55610.00461.1475-0.0871.2238-0.06810.117-0.0402-0.20080.0095-0.24010.17490.50020.05860.14940.0380.11050.2888-0.00220.119291.96189.763106.678
152.9155-1.89930.07323.7696-0.62023.3858-0.07510.0883-0.5233-0.14090.01890.18010.5204-0.03890.05620.2253-0.03520.05920.0386-0.01710.129671.22875.833114.608
162.73480.24850.13881.8903-0.11582.4722-0.0253-0.2804-0.3915-0.01380.0276-0.08610.43290.1906-0.00230.18490.04270.0620.15820.03560.086575.33680.371129.41
177.2185-2.174-3.358911.11725.586514.8679-0.21060.0546-1.16130.1127-0.3101-0.27091.7333-0.21250.52060.6905-0.33490.09180.51960.03860.475321.90768.585139.408
184.1918-1.1716-4.54256.1559-1.946416.0777-0.40130.2205-0.1430.2550.26961.04021.1969-2.26180.13170.3918-0.47410.07320.9015-0.03740.579911.20671.557140.351
192.40132.1587-2.90666.4555-7.285415.75560.2520.21540.27590.41520.260.26-0.8639-0.8008-0.5120.11760.02190.0360.4740.02640.229726.50995.776113.446
201.27410.144-0.27950.8109-0.56152.2242-0.04090.35080.2523-0.05950.06470.0714-0.0198-0.3251-0.02380.1994-0.02620.0350.15840.02680.099554.317100.93298.911
212.052-0.34630.73350.9116-0.2512.5049-0.06370.03030.243-0.05360.05270.0221-0.1443-0.16030.0110.1586-0.02320.0470.08050.01770.070460.754100.615101.18
224.17740.05990.79323.0294-0.792314.153-0.16120.1808-0.4332-0.2711-0.0301-0.17541.06890.0750.19130.1935-0.05450.08290.21310.03410.239136.181.49112.557
231.37540.348-1.55331.5444-1.819410.7579-0.1497-0.0034-0.1563-0.0377-0.0123-0.13070.5029-0.38520.1620.1375-0.07890.01540.27990.02150.193433.22886.016119.299
2413.61342.1181-1.04346.31514.79145.7472-0.0621-0.5614-0.24570.1347-0.16480.23390.4225-0.48360.2270.2066-0.14220.08180.1992-0.01370.218521.25679.357155.424
257.0473-3.9841-1.75717.0426-1.84136.3586-0.14890.504-1.0838-1.2615-0.281-0.10461.8576-0.01930.42990.8949-0.09160.23360.658-0.17930.4725115.55583.41686.172
265.5617-1.54632.58366.02020.67923.56780.24240.56470.3448-0.8975-0.3096-0.34490.35330.24150.06720.4977-0.0330.28220.60270.02210.2677114.53996.07985.703
275.0754-1.6493-1.14142.06590.27775.10730.19180.558-0.2263-1.1457-0.1956-0.28780.69340.05860.00380.8965-0.04030.30390.5976-0.04760.4264114.83789.88487.168
2813.1808-0.93361.3472.34313.27785.98080.46941.4765-0.57330.0201-0.1497-0.6087-0.28340.3701-0.31960.90880.04520.1180.69420.28671.1397149.51986.40576.128
297.1384-3.5521-3.71115.92463.84143.37960.4233-0.5207-0.7275-0.5386-0.4339-1.12290.0858-0.59430.01061.1217-0.19270.30521.18260.35461.4926147.33580.24683.838
308.26372.716111.76266.87487.537319.2779-0.99760.56870.644-0.660.1354-0.5555-1.43910.44450.86220.4721-0.02070.40090.919-0.08881.0173143.4789.47978.292
319.953.25713.293510.24432.44911.4262-0.29940.4432-0.2461-0.96570.1153-1.05120.07420.23640.18411.21210.15680.51451.49390.32862.0502157.54679.01279.305
328.8368-2.02254.95897.3534-1.72914.0285-0.526-0.55822.37740.1594-0.4667-1.8319-0.26690.35160.99270.3135-0.13790.02731.0993-0.08331.3404130.309104.795101.409
336.3495-1.3387-0.26356.0006-1.53724.4816-0.2463-0.34720.21540.2289-0.2145-0.84490.07140.50010.46080.1326-0.0830.12280.6446-0.00540.5106122.63798.01104.468
347.3458-2.12043.76554.9615-2.20886.10760.11430.30310.1959-0.277-0.3825-0.99860.29750.83050.26810.2-0.05830.26270.58560.06210.5284125.00699.15197.284
354.7729-0.6448-1.67712.88932.783814.1616-0.05060.08350.1119-0.97910.0554-0.1527-0.43620.7617-0.00480.6052-0.0280.22470.80770.28271.1422153.53598.31582.219
365.3162-2.8918-3.20285.92354.98754.3775-0.10910.2323-0.1549-0.72470.0938-0.1504-0.4169-0.04130.01530.69770.00480.36171.12720.30561.2476149.28695.41580.712
371.39580.3513-0.05536.03-2.13010.7594-0.2207-0.38570.5428-1.0653-0.3512-1.68410.34690.06420.57191.0097-0.41040.47661.66190.35261.7196158.336104.90581.403
3844.143-21.925917.848813.6955-11.22439.21152.31920.565-0.6625-1.1311-1.17211.42260.95291.0966-1.14711.04560.02120.35251.4972-0.13571.0203166.30496.91570.807
398.4421-2.2063-4.40834.90742.59349.490.0006-0.6526-0.61411.3577-0.04810.12290.8025-0.42730.04750.723-0.08190.05730.48350.08360.277418.44290.47686.48
403.50581.23790.45475.84140.88784.7140.2772-0.36640.30540.7872-0.26690.24450.0234-0.2016-0.01030.2573-0.03890.12510.2711-0.07560.189618.621101.60779.302
413.42280.3805-1.40333.1673-0.36494.31510.1169-0.62940.10441.1309-0.16060.17370.1264-0.28410.04370.4876-0.06740.11750.3933-0.05410.26218.76596.45681.074
425.10890.8922-1.44392.19771.5517.8077-0.2221-1.024-1.6111-0.0861-0.11570.38330.36820.15690.33780.51390.1050.30210.42280.22781.1514-13.57786.39694.347
4312.02989.01995.296111.00248.60858.4779-0.46340.4561-1.63081.23590.6632-0.38021.97231.5274-0.19980.83670.48640.21351.0006-0.06681.8325-7.57578.80191.011
4415.96376.64497.69452.98291.679915.3038-0.31520.1509-0.0891-0.09650.01170.021-0.1250.4580.30340.12580.08480.22040.2331-0.0250.6491-9.64688.79389.426
458.51460.85625.61614.1876-0.016611.8299-0.6136-0.9507-2.24690.5743-0.17210.00022.8046-0.30330.78571.55380.16110.90880.63130.2282.2721-17.96975.98894.842
463.4143-3.0312-1.85676.33420.93991.17360.10341.0981-0.6141-0.0828-0.35661.6337-0.0641-0.80120.25330.11090.0983-0.00470.9721-0.41761.09590.90198.90962.983
475.0210.2183-0.02244.44760.67063.24070.01410.2329-0.2732-0.062-0.34740.60080.1106-0.68330.33340.0264-0.00650.05280.42-0.12790.351710.32394.15562.466
488.46613.81220.74846.3782.68913.69120.0996-0.1175-0.1480.3958-0.51780.85180.222-0.70330.41820.08230.01530.14640.4548-0.14190.38297.08797.17468.661
498.93690.0206-1.07533.20430.91420.3946-0.51040.6409-2.17630.50730.13940.35520.2171-0.07070.3710.2215-0.08830.31270.4457-0.18861.3103-20.54887.86685.618
504.2898-2.1659-0.99693.48063.64275.2664-0.09230.5072-0.8182-0.0632-0.05160.3048-0.3547-0.25890.14380.1286-0.00770.08930.4965-0.08560.7063-21.33795.74683.245
515.3016-1.518-3.61143.01252.70510.7474-0.38160.3285-0.93630.1765-0.03940.3482-0.0577-0.31910.42110.082-0.05110.10640.334-0.0380.7181-21.12594.22985.258
5276.2091120.085623.8164191.526234.22212.21544.0626-1.7034-3.49244.2853-3.5156-5.83074.45280.4618-0.5472.55650.04460.471.527-0.34870.9033-34.4591.15597.278
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 73
2X-RAY DIFFRACTION2A74 - 274
3X-RAY DIFFRACTION3A275 - 334
4X-RAY DIFFRACTION4A335 - 454
5X-RAY DIFFRACTION5B1 - 25
6X-RAY DIFFRACTION6B26 - 60
7X-RAY DIFFRACTION7B61 - 108
8X-RAY DIFFRACTION8B109 - 177
9X-RAY DIFFRACTION9B178 - 354
10X-RAY DIFFRACTION10B355 - 383
11X-RAY DIFFRACTION11B384 - 432
12X-RAY DIFFRACTION12B433 - 466
13X-RAY DIFFRACTION13C1 - 73
14X-RAY DIFFRACTION14C74 - 274
15X-RAY DIFFRACTION15C275 - 334
16X-RAY DIFFRACTION16C335 - 453
17X-RAY DIFFRACTION17D1 - 25
18X-RAY DIFFRACTION18D26 - 59
19X-RAY DIFFRACTION19D60 - 91
20X-RAY DIFFRACTION20D92 - 176
21X-RAY DIFFRACTION21D177 - 353
22X-RAY DIFFRACTION22D354 - 383
23X-RAY DIFFRACTION23D384 - 436
24X-RAY DIFFRACTION24D437 - 468
25X-RAY DIFFRACTION25E1 - 33
26X-RAY DIFFRACTION26E34 - 64
27X-RAY DIFFRACTION27E65 - 113
28X-RAY DIFFRACTION28E114 - 151
29X-RAY DIFFRACTION29E152 - 170
30X-RAY DIFFRACTION30E171 - 187
31X-RAY DIFFRACTION31E188 - 221
32X-RAY DIFFRACTION32F1 - 24
33X-RAY DIFFRACTION33F25 - 79
34X-RAY DIFFRACTION34F80 - 105
35X-RAY DIFFRACTION35F106 - 156
36X-RAY DIFFRACTION36F157 - 187
37X-RAY DIFFRACTION37F188 - 207
38X-RAY DIFFRACTION38F208 - 214
39X-RAY DIFFRACTION39H1 - 29
40X-RAY DIFFRACTION40H30 - 64
41X-RAY DIFFRACTION41H65 - 113
42X-RAY DIFFRACTION42H114 - 151
43X-RAY DIFFRACTION43H152 - 167
44X-RAY DIFFRACTION44H168 - 187
45X-RAY DIFFRACTION45H188 - 221
46X-RAY DIFFRACTION46L1 - 24
47X-RAY DIFFRACTION47L25 - 79
48X-RAY DIFFRACTION48L80 - 105
49X-RAY DIFFRACTION49L106 - 128
50X-RAY DIFFRACTION50L129 - 155
51X-RAY DIFFRACTION51L156 - 209
52X-RAY DIFFRACTION52L210 - 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://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