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- PDB-2vdp: Integrin AlphaIIbBeta3 Headpiece Bound to Fibrinogen Gamma chain ... -

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基本情報

登録情報
データベース: PDB / ID: 2vdp
タイトルIntegrin AlphaIIbBeta3 Headpiece Bound to Fibrinogen Gamma chain peptide,LGGAKQAGDV
要素
  • (MONOCLONAL ANTIBODY 10E5 ...) x 2
  • FIBRINOGEN
  • INTEGRIN ALPHA-IIB
  • INTEGRIN BETA-3
キーワードCELL ADHESION/IMMUNE SYSTEM / CELL ADHESION-IMMUNE SYSTEM COMPLEX / FIBRINOGEN BINDING / PLATELET INTEGRIN ALPHAIIBBETA3 / GLYCOPROTEIN / CELL ADHESION / MEMBRANE / INTEGRIN / RECEPTOR / ANTAGONIST / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION / DISEASE MUTATION / CLEAVAGE ON PAIR OF BASIC RESIDUES
機能・相同性
機能・相同性情報


platelet maturation / 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 / fibrinogen complex ...platelet maturation / 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 / fibrinogen complex / regulation of extracellular matrix organization / platelet alpha granule membrane / positive regulation of glomerular mesangial cell proliferation / Regulation of TLR by endogenous ligand / negative regulation of lipoprotein metabolic process / integrin alphav-beta3 complex / negative regulation of low-density lipoprotein receptor activity / fibrinogen binding / platelet alpha granule / 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 / cellular response to interleukin-6 / cell-substrate junction assembly / platelet-derived growth factor receptor binding / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / 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 / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / smooth muscle cell migration / cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / microvillus membrane / negative chemotaxis / Syndecan interactions / plasminogen activation / 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 peptide hormone secretion / positive regulation of osteoblast proliferation / cellular response to platelet-derived growth factor stimulus / TGF-beta receptor signaling activates SMADs / positive regulation of exocytosis / 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 / cellular response to interleukin-1 / protein polymerization / protein secretion / ECM proteoglycans / positive regulation of bone resorption / positive regulation of T cell migration / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / coreceptor activity / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of vasoconstriction / fibrinolysis / positive regulation of endothelial cell proliferation / embryo implantation / Integrin signaling / positive regulation of endothelial cell migration / cell-matrix adhesion / substrate adhesion-dependent cell spreading / platelet alpha granule lumen
類似検索 - 分子機能
ligand-binding face of the semaphorins, domain 2 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. ...ligand-binding face of the semaphorins, domain 2 / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / ligand-binding face of the semaphorins, domain 2 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / 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
Fibrinogen gamma chain / Integrin beta-3 / Integrin alpha-IIb / Fibrinogen gamma chain
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 / OTHER / 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
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: Advisory / 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 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / 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_database_status / 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 / _pdbx_database_status.status_code_sf / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年10月16日Group: Data collection / Database references / 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: FIBRINOGEN
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)151,27419
ポリマ－148,0155
非ポリマー3,25914
水10,034557
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 area11720 Å2
ΔGint-75.4 kcal/mol
Surface area72080 Å2
手法PQS
単位格子
Length a, b, c (Å)148.429, 148.429, 177.160
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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タンパク質・ペプチド , 1種, 1分子 C

#3: タンパク質・ペプチド FIBRINOGEN


分子量: 916.011 Da / 分子数: 1 / 断片: GAMMA CHAIN C-TERMINAL PEPTIDE, RESIDUES 428-437 / 由来タイプ: 合成 / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: Q53Y18, UniProt: P02679*PLUS

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抗体 , 2種, 2分子 HL

#4: 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
#5: 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

#6: 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
#7: 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
#10: 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: 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 , 4種, 566分子

#8: 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: 2 / 由来タイプ: 合成 / 式: C3H8O3
#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: 6 / 由来タイプ: 合成 / 式: Ca
#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: 1 / 由来タイプ: 合成 / 式: Mg
#12: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 557 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY
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. ACCORDING TO THE AUTHORS THE CORRECT CHAIN C SEQUENCE IS ANNOTATED IN NCBI ENTRY GI 70906437 WHICH CORRESPONDS TO THE UNIPROT ENTRY Q53Y18

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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: 3.8 Å3/Da / 溶媒含有率: 67.2 % / 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: 1.07223
検出器タイプ: CUSTOM (SBC2 3K) / 検出器: CCD / 日付: 2004年12月15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: 1.07223 Å / 相対比: 1
反射解像度: 2.8→50 Å / Num. obs: 55536 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / 冗長度: 6.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.2
反射 シェル解像度: 2.7→2.8 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.8 / % possible all: 99.6

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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
CNS位相決定
精密化構造決定の手法: OTHER
開始モデル: NONE

解像度: 2.8→46.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.932 / SU B: 19.036 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.579 / ESU R Free: 0.274 / 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
Rfree0.204 2747 5.1 %RANDOM
Rwork0.156 ---
obs0.158 51563 97.3 %-
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: 48.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20.66 Å20 Å2
2--1.32 Å20 Å2
3----1.99 Å2
精密化ステップサイクル: LAST / 解像度: 2.8→46.23 Å
タンパク質核酸リガンド溶媒全体
原子数10337 0 205 557 11099
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02210930
X-RAY DIFFRACTIONr_bond_other_d0.0010.027321
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.97914918
X-RAY DIFFRACTIONr_angle_other_deg0.773.00417798
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.46851375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4524.367474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.317151709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9211559
X-RAY DIFFRACTIONr_chiral_restr0.0610.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212178
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022152
X-RAY DIFFRACTIONr_nbd_refined0.1810.22025
X-RAY DIFFRACTIONr_nbd_other0.1740.27483
X-RAY DIFFRACTIONr_nbtor_refined0.1710.25356
X-RAY DIFFRACTIONr_nbtor_other0.080.25726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2521
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1650.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.67757014
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.7021010928
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.56754553
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.486103977
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→2.88 Å / Total num. of bins used: 20 /
Rfactor反射数
Rfree0.347 190
Rwork0.276 3556
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.375-2.36240.04958.64832.20852.87850.10020.0363-0.67190.9044-0.4605-1.27060.52670.84820.3604-0.17850.1509-0.04540.05040.3930.036133.06912.1678.497
23.86740.5323-0.49773.54170.46673.3466-0.0923-0.0516-0.1278-0.0728-0.1415-0.40170.12150.39620.2338-0.18590.04410.0150.02730.2365-0.1243129.12721.58369.085
31.4535-0.6441-0.15261.3791-1.06471.7087-0.0081-0.07920.09140.089-0.1625-0.37840.04190.32970.1706-0.1027-0.0561-0.016-0.02030.1459-0.0304118.62433.45164.529
44.4836-0.1897-2.09721.4638-0.23112.61040.074-0.0332-0.12540.0758-0.20230.2321-0.0665-0.06860.1284-0.0843-0.1092-0.0308-0.00870.0871-0.1198107.03535.99663.777
50.633-0.2184-0.61971.5137-1.00922.99320.03520.2279-0.12230.0101-0.1510.0540.2412-0.22790.1158-0.0762-0.08890.0044-0.04750.0586-0.0419106.00224.36564.122
62.4465-0.9347-0.30583.79540.96025.1675-0.05570.1869-0.3731-0.0922-0.15330.09950.1491-0.27060.209-0.0044-0.16850.0695-0.17180.0688-0.053499.64713.00372.544
73.9057-1.2266-2.08525.26812.46534.9168-0.1696-0.2839-0.42640.5635-0.060.14270.8740.04990.22960.0223-0.10260.0496-0.28590.19-0.0845107.7377.09984.564
83.12750.42090.10072.59210.38093.4108-0.18370.012-0.36480.017-0.23260.03770.9074-0.03940.41630.1553-0.03790.08-0.27890.1978-0.0902110.4342.81278.892
93.11970.1586-0.12032.3491-0.50552.8387-0.0731-0.2664-0.46620.2293-0.2609-0.40380.57590.59830.33390.00440.07890.0232-0.10940.2756-0.0525124.3127.38480.229
104.1347-1.65652.16913.1839-1.5746.3418-0.1645-0.9077-0.04821.04470.4577-0.2323-0.6025-0.7964-0.29320.32640.1316-0.137-0.3717-0.1472-0.374106.41521.385169.626
118.499-5.004916.445510.5134-16.719838.3639-0.7776-0.75720.32651.19270.6227-0.6324-2.8502-1.57840.15490.59380.30050.0271-0.1017-0.01-0.2527102.84930.339149.466
120.2858-0.25020.25270.3609-0.72241.9942-0.0194-0.14430.0050.40690.0092-0.0162-0.46530.050.01020.2698-0.19160.0765-0.03110.0206-0.111997.46838.193104.568
131.6648-0.5337-0.91181.64360.06232.34860.0554-0.33950.07960.4529-0.0567-0.0784-0.13010.20860.00120.0616-0.18550.0258-0.07710.0579-0.1866102.94234.26996.271
142.7817-1.80317.63093.2226-4.16921.22780.63760.6941-0.5921-0.17730.3031-0.04031.07320.7841-0.94070.1223-0.07820.1566-0.08950.0112-0.1368100.19622.655131.283
155.1708-1.87397.35232.1877-2.061120.4062-0.42020.85890.2560.76760.4524-0.5348-1.87521.6414-0.03220.2681-0.0832-0.0198-0.4009-0.0295-0.2949109.33128.248149.479
163.3604-0.2296-4.59380.01570.31386.2798-1.5493-1.80970.572-0.1441-0.2731-0.6768-2.67113.27831.82231.6845-0.0647-0.76790.7793-0.03240.6585119.20831.4183.595
177.3175-4.75246.05288.3579-8.204610.47250.15070.4785-0.6326-0.6786-0.06840.36541.05-0.2618-0.0823-0.0172-0.1955-0.13870.05010.0263-0.127889.73136.56733.436
183.6793-0.61810.58162.388-0.06422.8221-0.0116-0.0921-0.00130.09630.11190.20240.2083-0.3511-0.1003-0.1957-0.0497-0.0161-0.00930.0877-0.076993.93741.90741.465
193.4141-0.51711.68281.5081-1.1663.6057-0.0835-0.12480.1779-0.03780.04880.09740.1721-0.19460.0347-0.1959-0.06150.01690.00850.0916-0.057293.76342.79643.702
202.7787-2.0125-0.9341.93031.90063.4840.13840.1929-0.45380.04180.00250.0133-0.5796-1.0782-0.1409-0.2719-0.1559-0.12120.12910.0679-0.004786.15747.46213.175
218.16730.7462-6.61271.50660.825114.91470.24050.1712-0.4571-0.1950.0166-0.13181.3225-0.2606-0.2571-0.17250.078-0.1611-0.13510.0649-0.167192.28844.5374.88
225.5771.1195-2.07821.33090.0714.69150.3327-0.3330.14-0.47810.00590.1540.56290.3316-0.3386-0.15240.0947-0.0659-0.15460.0576-0.267294.30347.3039.427
238.597-0.1422-1.60851.33511.23564.32980.69150.0794-1.5153-0.7848-0.57880.07040.81121.2039-0.11270.49750.3075-0.14170.0628-0.1007-0.063493.66140.319-3.512
2411.94636.4023-17.441511.0363-6.755626.3478-0.6070.6738-0.6419-1.46010.47880.59992.1393-1.72960.1282-0.2611-0.011-0.34870.1164-0.0377-0.151285.90643.993-2.281
251.61730.5313-0.1080.73140.45392.47510.12240.15030.2079-0.0825-0.0736-0.0461-0.20680.2741-0.0488-0.14480.04870.04840.02750.16570.0038114.11149.92435.341
265.73691.430.02992.2959-1.50424.04590.03810.3908-0.3509-0.18190.047-0.05210.78050.228-0.0851-0.11090.0530-0.01530.0381-0.0673113.38538.97636.411
274.6233-0.5726-2.26351.81360.43886.5969-0.0520.3054-0.0968-0.0765-0.03710.0860.3511-0.01370.0891-0.14840.0151-0.0583-0.04280.1187-0.0533112.20745.49735.819
281.8825-2.00813.38153.0048-2.93526.59790.52670.2634-0.3226-0.4485-0.2840.1670.71470.2319-0.2426-0.14650.08240.01710.2390.0899-0.0864100.25952.9538.339
296.7928-4.74252.89147.7301-2.10682.48740.003-0.20650.57810.078-0.2879-0.446-0.0240.29470.2849-0.22530.0376-0.01480.24410.0669-0.2343101.47459.569.022
309.0169-3.61924.40363.7924-2.14245.9187-0.00980.24260.2185-0.2741-0.1478-0.0086-0.03310.14720.1577-0.25680.04060.02960.10910.0185-0.19995.02559.9233.164
3117.6041-6.62746.11286.7983-4.52035.61050.50041.4644-0.1356-0.5864-0.5404-0.1399-0.05771.05250.04-0.25160.13330.08010.20850.1488-0.2139102.91662.288-1.901
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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