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- PDB-2vdk: Re-refinement of Integrin AlphaIIbBeta3 Headpiece -

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基本情報

登録情報
データベース: PDB / ID: 2vdk
タイトルRe-refinement of Integrin AlphaIIbBeta3 Headpiece
要素
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • INTEGRIN ALPHA-IIB
  • INTEGRIN BETA-3
キーワードCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / PHOSPHORYLATION
機能・相同性
機能・相同性情報


regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / 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 / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization ...regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / 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 / maintenance of postsynaptic specialization structure / 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 / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / mesodermal cell differentiation / glycinergic synapse / extracellular matrix binding / filopodium membrane / regulation of release of sequestered calcium ion into cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell adhesion mediated by integrin / apolipoprotein A-I-mediated signaling pathway / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / positive regulation of leukocyte migration / wound healing, spreading of epidermal cells / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / cell adhesion mediated by integrin / smooth muscle cell migration / heterotypic cell-cell adhesion / Molecules associated with elastic fibres / positive regulation of smooth muscle cell migration / negative chemotaxis / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / positive regulation of cell-matrix adhesion / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / protein disulfide isomerase activity / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / coreceptor activity / cellular response to platelet-derived growth factor stimulus / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / embryo implantation / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein kinase C binding / cell-matrix adhesion / response to activity / Signal transduction by L1 / integrin-mediated signaling pathway / regulation of actin cytoskeleton organization / wound healing / cellular response to mechanical stimulus / Signaling by high-kinase activity BRAF mutants / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / cell-cell adhesion / MAP2K and MAPK activation / platelet activation / VEGFA-VEGFR2 Pathway / platelet aggregation / integrin binding / cellular response to xenobiotic stimulus / positive regulation of fibroblast proliferation / ruffle membrane
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 alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / 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 alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / 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) / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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
CACODYLATE ION / 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: 2.8 Å
データ登録者Springer, T.A. / Zhu, J. / Xiao, T.
引用
ジャーナル: J.Cell Biol. / 年: 2008
タイトル: Structural Basis for Distinctive Recognition of Fibrinogen Gammac Peptide by the Platelet Integrin Alphaiibbeta3.
著者: Springer, T.A. / Zhu, J. / Xiao, T.
#1: ジャーナル: Nature / 年: 2004
タイトル: Structural Basis for Allostery in Integrins and Binding to Fibrinogen-Mimetic Therapeutics
著者: Xiao, T. / Takagi, J. / Coller, B.S. / Wang, J.-H. / Springer, T.A.
履歴
登録2007年10月10日登録サイト: PDBE / 処理サイト: PDBE
置き換え2008年9月2日ID: 1TY3
改定 1.02008年9月2日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Refinement description / Version format compliance
改定 1.22019年1月30日Group: Data collection / Experimental preparation / Other
カテゴリ: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
改定 1.32019年2月6日Group: Data collection / Experimental preparation / カテゴリ: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
改定 1.42019年11月20日Group: Advisory / Derived calculations / Other
カテゴリ: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf
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_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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12023年12月13日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_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
改定 2.22024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
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)150,49519
ポリマ－147,0994
非ポリマー3,39615
水11,025612
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-70.7 kcal/mol
Surface area71610 Å2
手法PISA
単位格子
Length a, b, c (Å)148.869, 148.869, 176.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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要素

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タンパク質 , 2種, 2分子 AB

#1: タンパク質 INTEGRIN ALPHA-IIB / PLATELET MEMBRANE GLYCOPROTEIN IIB / GPALPHA IIB / GPIIB / INTEGRIN ALPHA-IIB HEAVY CHAIN


分子量: 49030.367 Da / 分子数: 1 / 断片: HEADPIECE, RESIDUES 32-483 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 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 ANTIGEN


分子量: 50969.664 Da / 分子数: 1 / 断片: HEADPIECE, RESIDUES 27-487 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 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, 2分子 HL

#3: 抗体 MONOCLONAL ANTIBODY 10E5 HEAVY CHAIN


分子量: 23766.473 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) MUS MUSCULUS (ハツカネズミ) / 細胞株: 10E5 HYBRIDOMA / 株: BALB/C
#4: 抗体 MONOCLONAL ANTIBODY 10E5 LIGHT CHAIN


分子量: 23332.686 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) MUS MUSCULUS (ハツカネズミ) / 細胞株: 10E5 HYBRIDOMA / 株: BALB/C

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糖 , 3種, 5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 alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 1235.105 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]DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#9: 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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 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, 622分子

#7: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#8: 化合物
ChemComp-CA / CALCIUM ION


分子量: 40.078 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Ca
#10: 化合物 ChemComp-CAC / CACODYLATE ION / dimethylarsinate


分子量: 136.989 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C2H6AsO2
#11: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Mg
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 612 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
非ポリマーの詳細CACODYLATE ION (CAC): CACODYLATE IS FOUND IN THE LIGAND BINDING SITE. BASED ON IMPURITIES IN ...CACODYLATE ION (CAC): CACODYLATE IS FOUND IN THE LIGAND BINDING SITE. BASED ON IMPURITIES IN CACODYLATE AND HYDROGEN BOND DONORS NEAR THE CACODYLATE, IT IS POSSIBLE THAT ONE OR TWO METHYL GROUPS HAVE BEEN LOST.
配列の詳細ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH ...ACCORDING TO THE AUTHORS THE CORRECT CHAIN A SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 88758615 WHICH SHOULD BE USED IN PLACE OF P08514.

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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: 3.7 Å3/Da / 溶媒含有率: 66.8 % / 解説: NONE
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: 6.5
詳細: 11% PEG 3350, 0.7 M MAGNESIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5, 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: 19-ID / 波長: 0.9793
検出器タイプ: CUSTOM (SBC2 3K) / 検出器: CCD / 日付: 2003年8月5日 / 詳細: MIRROR
放射モノクロメーター: SI(111) / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.9793 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 55875 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / 冗長度: 7.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 14
反射 シェル解像度: 2.8→2.9 Å / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
REFMAC5.3.0037精密化
HKL-2000データ削減
SCALEPACKデータスケーリング
AMoRE位相決定
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 1TXV

1txv
PDB 未公開エントリ


解像度: 2.8→42.64 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.783 / SU ML: 0.187 / TLS residual ADP flag: UNVERIFIED / 交差検証法: THROUGHOUT / ESU R: 0.648 / ESU R Free: 0.279 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY3. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT ...詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THESE ARE RE-REFINED COORDINATES OF THE PREVIOUS WWPDB SUBMISSION 1TY3. THE STARTING MODEL WAS A 2.4 ANGSTROM STRUCTURE WITH A DIFFERENT BOUND LIGAND. THE MODEL IS REFINED TO LOWER RFREE. ONE SEQUENCE MISTAKE IN THE AIIB SUBUNIT IS CORRECTED. MORE OF BETA SUBUNIT DOMAIN I-EGF1 IS BUILT. MISTAKES IN CARBOHYDRATE ANOMERIC LINKAGES ARE ALSO CORRECTED.
Rfactor反射数%反射Selection details
Rfree0.205 2713 5.1 %RANDOM
Rwork0.161 ---
obs0.164 50725 95.5 %-
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: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 17.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.61 Å20 Å2
2--1.21 Å20 Å2
3----1.82 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→42.64 Å
タンパク質核酸リガンド溶媒全体
原子数10285 0 210 612 11107
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210895
X-RAY DIFFRACTIONr_bond_other_d0.0010.027298
X-RAY DIFFRACTIONr_angle_refined_deg0.9361.97914875
X-RAY DIFFRACTIONr_angle_other_deg0.7583.00417733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.26451368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.21124.271473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.618151698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4721560
X-RAY DIFFRACTIONr_chiral_restr0.0580.21675
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212134
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022157
X-RAY DIFFRACTIONr_nbd_refined0.1790.22003
X-RAY DIFFRACTIONr_nbd_other0.1710.27610
X-RAY DIFFRACTIONr_nbtor_refined0.1710.25306
X-RAY DIFFRACTIONr_nbtor_other0.0780.25668
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2591
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.39156993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2221010878
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.29354552
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.093103985
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS精密化 シェル解像度: 2.8→2.87 Å / Total num. of bins used: 20 /
Rfactor反射数
Rfree0.34 198
Rwork0.252 3343
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)
19.8542-1.79072.37840.3473-0.07296.46960.03390.1518-0.7180.5668-0.2769-1.06071.00891.08140.243-0.10290.09830.02170.0070.3594-0.058133.40412.42978.164
22.7069-0.2144-0.00183.141-0.35321.84-0.0892-0.1503-0.1357-0.1263-0.0455-0.48890.19040.36690.1348-0.14180.04890.0390.02770.2387-0.024129.40422.02268.755
30.9099-0.5198-0.66781.4825-0.43231.3487-0.0027-0.1389-0.02520.1927-0.1496-0.3490.01710.3760.1523-0.0928-0.065-0.03430.00680.15210.0256118.91633.75764.167
43.9776-0.5619-1.49561.9144-0.28282.28690.0639-0.0628-0.19760.0128-0.22060.1439-0.01670.05160.1567-0.0715-0.0901-0.0449-0.03510.0855-0.0909107.33336.30763.449
50.8671-0.0029-0.60241.5963-0.8381.72220.06490.1272-0.0975-0.0069-0.1357-0.05220.2522-0.07760.0708-0.0285-0.0715-0.0026-0.05240.0657-0.0262106.27824.63463.706
61.6649-0.5156-0.12592.91090.27423.6359-0.09580.0898-0.3031-0.0647-0.12890.10130.2493-0.15060.22470.0021-0.11550.0785-0.13280.0565-0.0048100.02713.19872.022
73.71260.0138-0.34756.39292.16075.1977-0.028-0.2419-0.4280.36740.07430.03890.57350.0404-0.0463-0.0424-0.05580.0679-0.26350.2231-0.0313108.0467.31184.041
82.84360.3144-0.39633.56641.31513.982-0.10090.0651-0.3432-0.1734-0.2519-0.03390.6679-0.03010.35280.13810.01150.0688-0.26070.2061-0.0731110.8022.97278.364
92.73910.0386-0.36561.7804-0.50982.407-0.0189-0.1973-0.37180.233-0.2935-0.48860.57470.5560.31240.02380.10470.0371-0.12710.25810.0063124.5517.76279.845
104.4435-2.38962.71823.4148-3.02057.2168-0.2317-0.7806-0.03121.13650.3983-0.2074-1.0758-0.7251-0.16660.48430.0725-0.1775-0.376-0.1157-0.3563106.85821.119168.773
119.1334-5.966518.445611.8711-16.446639.6766-1.2-0.96430.50651.49110.6796-0.6431-3.3078-2.04320.52040.5630.178-0.0396-0.15050.0256-0.1705103.11130.087148.75
120.5361-0.1732-0.17690.4293-1.00293.0679-0.0258-0.1035-0.02770.3452-0.0588-0.0048-0.43150.01710.08460.1784-0.17770.0296-0.06960.0347-0.094697.638.216104.055
131.7751-0.3811-0.98421.1894-0.09412.00080.0064-0.26740.02830.3356-0.0664-0.1425-0.05140.15590.06010.0409-0.1402-0.0124-0.07340.0631-0.1158103.11134.33395.809
143.3791-1.6528.93653.1517-4.790323.70940.70510.4028-0.5122-0.11370.1055-0.04591.49740.4634-0.81060.0767-0.02180.0455-0.19050.0128-0.1888100.26122.557130.597
154.5806-1.12627.37882.1046-1.35219.7418-0.29470.74250.08970.730.4744-0.7443-1.84931.2909-0.17970.3225-0.1077-0.0805-0.39780.0332-0.2316109.48428.084148.683
160.96763.6215-2.974313.5549-11.13249.1428-0.6064-2.16290.83261.6236-0.1915-1.1158-3.08343.13760.79791.8135-0.2024-0.8420.5504-0.2340.483119.46831.109182.654
177.2173-5.15075.89434.8143-5.265910.83330.37020.5788-0.737-0.6322-0.11150.2980.84210.1383-0.2587-0.0643-0.2048-0.0610.01360.03910.052490.04936.87133.247
183.4314-0.40561.19682.5418-0.80313.0549-0.0082-0.1078-0.13080.0984-0.05880.06040.2327-0.10150.067-0.1649-0.044-0.0016-0.01730.0377-0.056594.2642.22441.192
193.5601-0.73271.4731.3828-1.38243.4154-0.068-0.1130.12710.0080.01360.06220.1607-0.18660.0545-0.1406-0.07260.0036-0.04590.0467-0.031894.0843.09243.411
201.3523-0.936-0.45681.32471.26593.57010.05220.229-0.0788-0.1586-0.09620.0927-0.1893-0.5180.044-0.2089-0.0759-0.07320.10140.05240.032586.47147.77412.757
215.5062-0.3213-4.15381.23831.293412.940.16540.3948-0.4307-0.1370.0601-0.23441.2814-0.1713-0.2254-0.16080.0553-0.0825-0.08820.0011-0.111892.58744.8464.726
226.38130.2307-1.4833.40210.51813.21270.2216-0.04280.0009-0.2578-0.11020.33310.54950.1618-0.1114-0.15710.1001-0.0247-0.17750.057-0.15694.59547.6169.229
239.6159-2.1416-3.28422.274.30778.25440.45650.4901-1.5845-0.1981-1.0473-0.2150.09620.44630.59080.62280.2667-0.01450.0237-0.0992-0.044493.97440.618-3.656
2412.12798.3666-13.69399.6128-6.403824.7977-0.31140.9509-0.4901-1.19360.38810.89331.5849-1.477-0.0768-0.11620.037-0.25220.1289-0.057-0.236386.20944.228-2.419
251.01390.6109-0.36120.6984-0.57260.51010.04960.14010.0766-0.1047-0.0864-0.0197-0.0230.13150.0369-0.11890.02320.00280.04310.12840.0581114.36550.3335.074
263.8357-0.0739-0.24061.4014-1.74592.20410.10340.4733-0.2887-0.16260.039-0.03930.60290.2706-0.1424-0.05130.0151-0.00650.0310.03830.0104113.70539.41836.136
274.68790.1199-2.27180.6861-0.48414.2853-0.09250.255-0.1202-0.0392-0.0480.07480.26670.09280.1406-0.13380.0048-0.0446-0.02670.0868-0.0288112.46445.90535.52
281.6319-1.63043.25442.1707-2.50147.52840.51450.2071-0.2084-0.3897-0.30580.14120.72170.2342-0.2087-0.13230.06010.02120.14240.0559-0.017100.45853.2978.181
295.4667-5.41483.2567.7987-1.9852.5708-0.1138-0.12980.51890.1965-0.0814-0.3896-0.04360.42650.1953-0.21830.0129-0.00810.22430.0596-0.1287101.62659.8928.821
307.5391-3.36572.87443.8034-1.433.8771-0.08180.34580.0266-0.2967-0.0848-0.00510.03260.08730.1666-0.21950.03390.00680.09430.0477-0.153495.14560.2462.972
312.2961-1.4101-1.74556.0706-2.97274.4701-0.09661.52870.2088-0.3934-0.5259-0.2768-0.33591.22190.6225-0.21540.12440.07260.24620.1676-0.1136102.97262.671-2.037
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 62
3X-RAY DIFFRACTION3A63 - 115
4X-RAY DIFFRACTION4A116 - 167
5X-RAY DIFFRACTION5A168 - 243
6X-RAY DIFFRACTION6A244 - 290
7X-RAY DIFFRACTION7A291 - 326
8X-RAY DIFFRACTION8A327 - 372
9X-RAY DIFFRACTION9A373 - 452
10X-RAY DIFFRACTION10B1 - 72
11X-RAY DIFFRACTION11B79 - 98
12X-RAY DIFFRACTION12B99 - 172
13X-RAY DIFFRACTION13B173 - 338
14X-RAY DIFFRACTION14B339 - 393
15X-RAY DIFFRACTION15B394 - 437
16X-RAY DIFFRACTION16B438 - 461
17X-RAY DIFFRACTION17H1 - 13
18X-RAY DIFFRACTION18H14 - 54
19X-RAY DIFFRACTION19H55 - 110
20X-RAY DIFFRACTION20H111 - 134
21X-RAY DIFFRACTION21H137 - 164
22X-RAY DIFFRACTION22H165 - 189
23X-RAY DIFFRACTION23H190 - 206
24X-RAY DIFFRACTION24H207 - 221
25X-RAY DIFFRACTION25L1 - 38
26X-RAY DIFFRACTION26L39 - 69
27X-RAY DIFFRACTION27L70 - 97
28X-RAY DIFFRACTION28L98 - 135
29X-RAY DIFFRACTION29L136 - 167
30X-RAY DIFFRACTION30L168 - 197
31X-RAY DIFFRACTION31L198 - 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

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