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- PDB-4z7q: Integrin alphaIIbbeta3 in complex with AGDV-NH2 peptide -

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基本情報

登録情報
データベース: PDB / ID: 4z7q
タイトルIntegrin alphaIIbbeta3 in complex with AGDV-NH2 peptide
要素
  • (Monoclonal antibody 10E5 ...) x 2
  • Integrin alpha-IIb
  • Integrin beta-3
  • Tetrapeptide AGDV-NH2
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 / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane ...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 / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / fibrinogen binding / alphav-beta3 integrin-PKCalpha complex / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-HMGB1 complex / blood coagulation, fibrin clot formation / mesodermal cell differentiation / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / glycinergic synapse / angiogenesis involved in wound healing / Elastic fibre formation / regulation of release of sequestered calcium ion into cytosol / alphav-beta3 integrin-IGF-1-IGF1R complex / cell-substrate junction assembly / platelet-derived growth factor receptor binding / filopodium membrane / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of fibroblast migration / regulation of postsynaptic neurotransmitter receptor internalization / 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 / positive regulation of leukocyte migration / Molecules associated with elastic fibres / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / microvillus membrane / negative chemotaxis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / activation of protein kinase activity / p130Cas linkage to MAPK signaling for integrins / cell-substrate adhesion / protein disulfide isomerase activity / positive regulation of smooth muscle cell migration / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / 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 / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / coreceptor activity / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of endothelial cell proliferation / embryo implantation / Integrin signaling / positive regulation of endothelial cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / Signal transduction by L1 / integrin-mediated signaling pathway / response to activity / regulation of actin cytoskeleton organization / protein kinase C binding / positive regulation of smooth muscle cell proliferation / wound healing / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / MAP2K and MAPK activation / platelet activation / platelet aggregation / VEGFA-VEGFR2 Pathway / cell-cell adhesion / ruffle membrane / 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
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 / von Willebrand factor, type A domain / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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 / 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
alpha-D-mannopyranose / : / 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: 2.7 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 1.02015年12月16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: Advisory / Atomic model ...Advisory / 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 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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.occupancy / _atom_site.pdbx_formal_charge / _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 / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
改定 2.12024年10月30日Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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
G: Tetrapeptide AGDV-NH2
I: Tetrapeptide AGDV-NH2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)301,40140
ポリマ－296,98210
非ポリマー4,41930
水17,853991
1
A: Integrin alpha-IIb
B: Integrin beta-3
H: Monoclonal antibody 10E5 heavy chain
L: Monoclonal antibody 10E5 light chain
G: Tetrapeptide AGDV-NH2
I: Tetrapeptide AGDV-NH2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)151,20721
ポリマ－148,8496
非ポリマー2,35815
水1086
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)150,19319
ポリマ－148,1324
非ポリマー2,06115
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)259.440, 144.240, 104.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDモデル要素
11H-315-

HOH

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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: 49228.625 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: 51958.789 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 AGDV-NH2


分子量: 358.371 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: AGDV-NH2 / 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 heavy chain


分子量: 23612.305 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 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 , 5種, 7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 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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: 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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_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
#13: 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
#14: 糖 ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / α-D-マンノピラノ-ス


タイプ: D-saccharide, alpha linking / 分子量: 180.156 Da / 分子数: 1 / 由来タイプ: 組換発現 / 式: C6H12O6
識別子タイププログラム
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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非ポリマー , 6種, 1014分子

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


分子量: 96.063 Da / 分子数: 7 / 由来タイプ: 合成 / 式: SO4
#11: 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
#12: 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
#15: 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
#16: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 991 / 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: 3.3 Å3/Da / 溶媒含有率: 62.7 %
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 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2013年3月14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: 2.7→50 Å / Num. obs: 107768 / % possible obs: 99.6 % / 冗長度: 2.2 % / Net I/σ(I): 6.02

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解析

ソフトウェア
名称バージョン分類
PHENIX1.9_1692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: 2.7→48.94 Å / SU ML: 0.36 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.236 1078 1 %
Rwork0.188 --
obs0.188 107750 99.5 %
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: 2.7→48.94 Å
タンパク質核酸リガンド溶媒全体
原子数20765 0 251 991 22007
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00421749
X-RAY DIFFRACTIONf_angle_d0.64629419
X-RAY DIFFRACTIONf_dihedral_angle_d10.657831
X-RAY DIFFRACTIONf_chiral_restr0.0283273
X-RAY DIFFRACTIONf_plane_restr0.0033824
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82280.33411330.320113229X-RAY DIFFRACTION100
2.8228-2.97160.34491340.290613225X-RAY DIFFRACTION100
2.9716-3.15780.29271340.264913253X-RAY DIFFRACTION100
3.1578-3.40150.29611340.229913235X-RAY DIFFRACTION100
3.4015-3.74370.25861340.19613282X-RAY DIFFRACTION99
3.7437-4.28520.18271340.159813212X-RAY DIFFRACTION99
4.2852-5.39780.20811350.135513401X-RAY DIFFRACTION99
5.3978-48.94630.20621400.166713835X-RAY DIFFRACTION100
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)
17.2738-1.4802-1.87554.76571.44285.1391-0.1730.3757-0.0186-0.36780.17770.13040.2345-0.2406-0.02640.3372-0.0301-0.01380.28460.05820.258948.894288.066938.77
25.1458-0.168-1.17965.06974.35275.43830.4110.23930.3317-1.1209-0.60180.537-0.9583-0.6170.12870.55480.1327-0.02570.4910.09440.370940.5595.37438.8818
32.5861-0.11380.14491.04990.21921.10360.0433-0.1659-0.02530.2973-0.10220.28960.0687-0.24650.06260.4617-0.0380.11850.39680.01040.397742.229294.780162.5452
42.38641.57950.05597.40440.535.29040.085-0.1103-0.1950.43920.026-0.36590.27590.1422-0.06310.34880.08680.0110.2780.05790.306866.480585.60560.1531
52.26530.4939-0.1051.81520.32472.3766-0.1066-0.1348-0.35560.14860.1388-0.16450.2718-0.0105-0.03440.44430.1040.05250.31290.0460.317162.678582.924945.5832
66.0935-5.41756.25854.8775-5.48946.50431.07672.21930.9541-1.4685-2.0337-2.32991.42360.43720.49850.75380.12750.13830.32770.03490.633360.076972.865833.1655
79.2724-3.2771-3.53392.57241.39034.1569-0.54690.2204-0.62490.12540.2443-1.0490.82552.45030.18270.93570.4229-0.04812.1326-0.17711.4148122.859789.095835.6764
84.3445-1.0397-2.53829.32917.23759.05110.1392-0.44881.14660.28180.8332-1.0199-0.15771.1855-1.07240.5204-0.10680.01771.1091-0.13550.9394103.506113.304652.3917
92.52360.7410.32782.75420.55261.25310.0802-0.29640.320.2198-0.0014-0.1507-0.35110.0531-0.06960.5285-0.01330.05590.3076-0.0020.413667.8109117.988363.5025
107.3117-5.2275-6.4697.38886.02237.6336-0.2573-0.0755-0.15180.57570.4128-0.061.21051.0121-0.09360.67230.0948-0.10240.8103-0.0070.905797.2821103.941760.5564
113.7860.1193-1.43755.05275.54399.3592-0.05310.14080.01520.51730.0691-0.29690.99020.5913-0.00910.66570.1163-0.15470.901-0.03030.8859100.5001104.325348.2377
122.48783.006-0.93336.0948-4.22514.8013-0.3579-1.5707-0.6254-0.76060.2203-1.00870.03571.6830.09460.86090.11960.17541.9794-0.19411.0803116.289488.472719.2271
137.09060.394-2.09623.3737-0.14056.1077-0.0397-0.2289-0.0430.0092-0.0673-0.46020.09511.29760.15310.42570.00410.06280.6842-0.09220.378687.948794.5243131.805
142.89430.30590.20080.99930.10621.3361-0.09880.6674-0.0299-0.3778-0.0277-0.26620.17290.62120.14020.61290.03630.18490.8998-0.00650.510792.376589.6973107.4968
154.97-2.444-0.41625.50950.24985.7364-0.08480.5994-0.8177-0.48930.00110.10220.90280.00990.10810.772-0.08930.17640.5077-0.11660.525471.731175.538115.3055
163.9696-0.46692.40653.77550.0373.6741-0.2506-0.1545-0.6153-0.02460.3043-0.17510.7138-0.04990.00220.65260.03820.20910.4729-0.02850.470373.108176.3126.1439
178.3371-0.34650.85246.30880.09076.2393-0.37450.4151-0.57090.25760.2141-0.2750.6995-0.10390.15180.4330.03570.08190.5150.01340.342175.750284.7978132.3587
186.7859-4.61773.49646.483-7.03128.6929-0.2841-0.9-0.03061.08840.2665-0.068-0.1908-0.0678-0.18730.57960.02830.0960.7471-0.08820.397182.176885.699136.7016
197.81223.7259-3.91916.3818-1.64464.2736-1.17150.3314-1.3317-0.3748-0.26790.89871.9138-1.25491.25361.3149-0.68960.28871.598-0.22841.18715.950768.8586141.1402
203.05721.1876-1.54281.5094-1.06912.9162-0.06350.79150.5509-0.20840.27450.42180.1526-0.9832-0.19410.7325-0.1758-0.06240.98420.07030.488144.564697.9408104.9548
212.7429-0.00341.30860.92470.14183.9924-0.13090.4960.2376-0.34790.08920.0073-0.1351-0.25910.01870.56-0.11040.02270.74110.10190.414760.8319100.3359101.3021
225.6910.2032-3.48052.1843-1.01032.7442-0.36630.3671-0.3725-0.1479-0.04180.03210.6706-0.34440.46510.8188-0.3037-0.03710.90740.07890.608533.371484.0688118.3769
234.91044.81435.09085.80714.21085.8347-0.4191-0.5744-0.3670.092-0.29620.45190.9013-1.4720.70640.8967-0.23930.27931.3564-0.14790.893320.352178.9031156.972
242.17622.29892.08522.49912.24242.0232-0.30782.1566-3.85190.25080.40883.14792.6186-2.99250.00411.8615-0.31480.02311.5153-0.04292.634629.801172.324158.6919
256.5677-2.7915-1.12365.5183.30012.0311-0.75340.4574-0.6845-1.7266-0.3348-0.81553.38172.1681.2061.45110.25960.22721.1001-0.06980.9692121.072682.553984.0723
265.12073.2544-4.0669.12250.52494.64320.660.6464-0.0082-1.128-1.7035-0.0478-0.0211.11240.9931.82380.11590.27031.8602-0.26480.9565116.378184.811578.5268
275.428-3.48822.59014.74651.99166.5850.2638-0.12110.2071-0.9756-0.5007-0.16191.05040.11340.20091.0268-0.14850.33271.3217-0.00110.7528112.726692.695188.0129
283.545-0.9337-2.44252.12752.68168.18680.11841.18020.0011-0.7176-0.3881-0.38110.9267-0.39940.1541.1970.0410.47281.5782-0.00660.8566116.085989.545185.8281
294.22170.12991.66333.57872.70892.53480.24471.10080.0921-0.7-0.2219-1.2763-0.16550.781-0.00441.44260.22330.36171.66610.36461.499150.304783.113579.767
301.962-0.4711-1.52673.86782.66252.81120.69851.017-0.4532-0.3886-0.5437-0.94711.21651.3068-0.111.58260.63270.39462.29960.07571.6142152.373182.135379.706
316.104-5.11627.34544.3687-5.94819.4072-1.04271.25161.0169-0.35830.0163-2.0182-0.05960.45960.93090.9666-0.20620.2230.99560.2141.4784126.9011107.011295.9895
321.0782-1.40942.69882.6769-3.05827.07990.54360.58671.67620.2727-0.7993-0.50570.68090.47530.04370.6178-0.12520.02062.03360.20921.293133.6846102.57106.6447
334.4396-0.25320.94582.4849-0.62353.8302-0.23160.36440.4714-0.0511-0.2265-0.83640.07121.17580.40720.6086-0.13260.2091.48330.09260.9947122.775398.5022102.3556
341.9537-2.1549-0.21353.81180.41520.0459-0.0210.58690.2036-1.1352-1.126-0.84610.56780.81321.00810.95860.26580.50872.80360.33491.8728150.820497.555195.0302
352.18181.3836-0.15531.2999-0.72093.6060.40430.23610.4392-0.74610.3706-0.1174-0.55810.5957-0.84071.5470.25150.70391.85010.31341.6788152.388998.161178.8582
365.22291.3601-3.03211.22930.16554.60680.0620.2489-0.5487-0.8042-0.2352-1.2081-0.32711.62040.18821.31090.02430.53942.02680.53981.9904156.426698.743780.0273
375.058-5.6661-5.29216.59695.92025.562-0.9353-1.8589-0.23511.83370.81150.74922.160.3796-0.00591.14930.13080.19761.30040.10860.780119.575689.85585.4862
383.62353.16753.5117.06420.18736.80910.0087-0.28620.31820.3695-0.02670.5615-0.4827-0.3033-0.06640.54790.10090.1950.6478-0.01520.488518.0444101.677679.7694
397.04930.6769-4.1482.0991-0.20972.6296-0.2127-1.17930.04891.07530.07590.37010.36680.15890.07350.7580.05630.14860.8107-0.0890.558617.414496.013583.0659
406.39685.3615.66484.45624.81045.020.2406-1.0304-1.98030.8039-0.20310.54870.97620.2246-0.05070.97120.06710.18861.23890.37861.8686-17.084983.854994.3397
417.585.01594.53086.31251.074.0087-0.3956-0.9884-2.45660.03880.44530.33950.63970.1377-0.03470.64080.2660.37231.39310.41292.1743-8.483982.59889.934
423.2755-0.3915-0.65360.21220.95985.3642-0.0584-0.0349-2.30.42270.24760.04411.6252-0.1118-0.09180.84290.03330.32041.29840.71952.634-15.746977.569693.8844
433.67323.09160.70719.89841.2290.53980.04450.42020.7310.1722-0.02711.42610.0591-0.6759-0.01210.49970.10.09031.1447-0.16311.07921.915399.991863.1919
446.11360.816-0.50586.63770.10324.9704-0.08420.594-0.6421-0.05510.09011.07590.464-1.1448-0.02780.3735-0.09570.03490.8759-0.17060.740211.900493.950163.1506
457.25125.56411.48455.54971.62633.2060.18710.4878-0.15270.4068-0.45191.24720.3522-1.31810.2590.4590.00070.14261.1451-0.25831.02875.995194.976666.4675
466.2374-0.507-3.22813.21162.34639.637-0.70760.1884-1.84020.2987-0.03590.48830.86370.21260.70010.54090.08170.28671.18640.10961.4085-19.979489.110484.0805
475.9368-1.9659-0.47113.25831.91076.8572-0.436-0.6473-1.51890.12550.25530.3813-0.11080.47070.17310.4829-0.00860.23181.05480.31261.3911-17.604994.363984.4745
486.59162.3522-2.90313.94561.04397.3881-0.1001-0.1992-1.16850.5737-0.57050.7818-0.3928-2.74760.50730.64380.19560.32541.25250.05681.4209-28.811995.171989.1441
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 1:62)
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 1:50)
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

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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