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- PDB-5es4: RE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BE... -

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基本情報

登録情報
データベース: PDB / ID: 5es4
タイトルRE-REFINEMENT OF INTEGRIN ALPHAXBETA2 ECTODOMAIN IN THE CLOSED/BENT CONFORMATION
要素
  • Integrin alpha-X
  • Integrin beta-2
キーワードCELL ADHESION / Complement Receptor-4 alphaXbeta2
機能・相同性
機能・相同性情報


positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding ...positive regulation of endothelial tube morphogenesis / integrin alphaX-beta2 complex / cellular extravasation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / integrin alphaL-beta2 complex / ICAM-3 receptor activity / positive regulation of myelination / cell-cell adhesion via plasma-membrane adhesion molecules / complement component C3b binding / negative regulation of dopamine metabolic process / Toll Like Receptor 4 (TLR4) Cascade / neutrophil migration / leukocyte migration involved in inflammatory response / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / cellular response to low-density lipoprotein particle stimulus / ficolin-1-rich granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / ECM proteoglycans / Integrin cell surface interactions / endothelial cell migration / specific granule membrane / cell adhesion molecule binding / heat shock protein binding / neutrophil chemotaxis / receptor-mediated endocytosis / secretory granule membrane / positive regulation of superoxide anion generation / cell-matrix adhesion / animal organ morphogenesis / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / receptor tyrosine kinase binding / receptor internalization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / integrin binding / cell-cell signaling / extracellular vesicle / regulation of cell shape / signaling receptor activity / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / defense response to virus / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / external side of plasma membrane / focal adhesion / apoptotic process / positive regulation of cell population proliferation / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / cell surface / extracellular exosome / metal ion binding / membrane / plasma membrane
類似検索 - 分子機能
ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt ...ntegrin, alpha v. Chain A, domain 4 / Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / 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 / von Willebrand factor type A domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
Integrin beta-2 / Integrin alpha-X
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 3.3 Å
データ登録者Sen, M. / Springer, T.A.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI CA031798 米国
引用ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2016
タイトル: Leukocyte integrin alpha L beta 2 headpiece structures: The alpha I domain, the pocket for the internal ligand, and concerted movements of its loops.
著者: Sen, M. / Springer, T.A.
履歴
登録2015年11月16日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年3月2日Provider: repository / タイプ: Initial release
改定 1.12016年4月13日Group: Database references
改定 1.22016年5月11日Group: Database references
改定 2.02020年7月29日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_audit_support / 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_validate_close_contact / pdbx_validate_symm_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_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
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12022年3月23日Group: Database references / Structure summary / カテゴリ: chem_comp / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年11月6日Group: Data collection / Structure summary
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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-X
B: Integrin beta-2
C: Integrin alpha-X
D: Integrin beta-2
E: Integrin alpha-X
F: Integrin beta-2
G: Integrin alpha-X
H: Integrin beta-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)847,07169
ポリマ－824,9498
非ポリマー22,12261
水1,20767
1
A: Integrin alpha-X
B: Integrin beta-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)212,14118
ポリマ－206,2372
非ポリマー5,90416
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: Integrin alpha-X
D: Integrin beta-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,53016
ポリマ－206,2372
非ポリマー5,29314
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: Integrin alpha-X
F: Integrin beta-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,42717
ポリマ－206,2372
非ポリマー5,19015
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: Integrin alpha-X
H: Integrin beta-2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)211,97318
ポリマ－206,2372
非ポリマー5,73516
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)132.030, 163.480, 536.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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タンパク質 , 2種, 8分子 ACEGBDFH

#1: タンパク質
Integrin alpha-X / CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain ...CD11 antigen-like family member C / Leu M5 / Leukocyte adhesion glycoprotein p150 / 95 alpha chain / Leukocyte adhesion receptor p150 / 95


分子量: 125606.438 Da / 分子数: 4 / 断片: UNP residues 20-1103 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGAX, CD11C
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P20702
#2: タンパク質
Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


分子量: 80630.695 Da / 分子数: 4 / 断片: UNP residues 23-696 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGB2, CD18, MFI7
発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ)
参照: UniProt: P05107

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糖 , 13種, 44分子

#3: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-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
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 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
DManpa1-6DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e6-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#5: 多糖 alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / 分子数: 3 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: 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
#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: 1 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 多糖 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 748.682 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 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
DManpa1-2DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1_f2-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]{[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#10: 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
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 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: 3 / 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
#12: 多糖 alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1072.964 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
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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: 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
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#14: 多糖 alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 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
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#17: 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: 27 / 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 , 3種, 84分子

#15: 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: 16 / 由来タイプ: 合成 / 式: Ca
#16: 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
#18: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 67 / 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: 3.51 Å3/Da / 溶媒含有率: 64.96 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.55M TRI-SODIUM CITRATE, 0.1M IMIDAZOLE, PH 6.5, EVAPORATION, 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: 0.97926 Å
検出器タイプ: MARMOSAIC 300 mm CCD / 検出器: CCD / 日付: 2006年12月1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: 0.97926 Å / 相対比: 1
反射解像度: 3.15→50 Å / Num. obs: 198644 / % possible obs: 98.6 % / 冗長度: 7.2 % / Rmerge(I) obs: 0.205 / Net I/σ(I): 9.46
反射 シェル最高解像度: 3.15 Å

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10_2155: ???)精密化
XDSデータ削減
XSCALEデータスケーリング
精密化構造決定の手法: 多波長異常分散 / 解像度: 3.3→49.51 Å / SU ML: 0.66 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 39.97 / 立体化学のターゲット値: MLHL
Rfactor反射数%反射Selection details
Rfree0.307 1819 1.04 %Random selection
Rwork0.257 ---
obs0.258 174325 99.6 %-
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: 3.3→49.51 Å
タンパク質核酸リガンド溶媒全体
原子数49499 0 1432 67 50998
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00752369
X-RAY DIFFRACTIONf_angle_d1.18371193
X-RAY DIFFRACTIONf_dihedral_angle_d10.66231783
X-RAY DIFFRACTIONf_chiral_restr0.0688134
X-RAY DIFFRACTIONf_plane_restr0.0069200
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.38920.43751370.449712994X-RAY DIFFRACTION98
3.3892-3.48890.43331390.403813054X-RAY DIFFRACTION99
3.4889-3.60150.43231440.374813110X-RAY DIFFRACTION100
3.6015-3.73020.39781290.341213152X-RAY DIFFRACTION100
3.7302-3.87950.3711330.315413187X-RAY DIFFRACTION99
3.8795-4.0560.3471350.292913120X-RAY DIFFRACTION99
4.056-4.26970.30891400.274413243X-RAY DIFFRACTION100
4.2697-4.5370.28521560.236613235X-RAY DIFFRACTION100
4.537-4.8870.27641480.215213264X-RAY DIFFRACTION100
4.887-5.37830.29831390.224213305X-RAY DIFFRACTION100
5.3783-6.15530.31221260.247413411X-RAY DIFFRACTION100
6.1553-7.75020.31191570.272113539X-RAY DIFFRACTION100
7.7502-49.51230.25481360.214413892X-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)
10.535-0.02810.424-0.0194-0.01361.97360.0710.28770.15360.53120.082-0.11480.2526-0.2792-0.00071.09070.1686-0.18970.88940.05831.0174-23.847519.0553-13.0643
20.0742-0.29790.43790.6161-0.36621.38610.2080.1018-0.0881-0.567-0.3229-0.00150.69080.663201.1710.0772-0.05840.99720.0620.9151-21.838713.132233.4337
31.80.9671-1.45030.7717-0.85561.0714-0.24470.2449-0.0668-0.22380.1569-0.07960.1134-0.114500.8846-0.085-0.00630.61250.0210.9151-2.902424.348149.6324
41.20290.4320.09392.42270.3704-0.20990.50140.27-0.3386-1.2947-0.2348-0.3760.70220.7436-0.03343.06120.97270.32940.7163-0.21491.4059-10.1912-17.461219.782
50.87521.2471.03250.04730.22680.7341-0.3774-0.0308-0.1027-1.25140.37980.10591.4433-0.08080.05893.15640.51090.38061.02460.01110.932-13.7293-10.01449.5107
60.74940.36790.25020.38350.40060.18260.41710.1674-0.6883-0.18160.2605-0.26811.2230.1080.00013.09610.59340.32711.74950.01361.9777-4.1412-22.648133.4044
70.2008-0.0336-0.04960.04020.0939-0.0507-0.1815-0.9226-0.05231.2020.1714-0.62470.49450.2607-0.00672.40390.07710.07551.09230.25451.5191-14.3511-20.87375.9306
80.01680.3339-0.22930.37440.02671.04130.16180.0115-0.0533-0.1410.033-0.0297-0.0560.37440.00011.60110.12520.10331.36440.19481.23663.56258.569731.4036
90.27910.01770.1562-0.04430.33312.10450.1392-0.5806-0.05720.33250.0623-0.29930.4669-0.42540.00131.0714-0.2065-0.34271.69710.12771.030424.254352.2123103.5674
101.27281.2282-0.6991.1934-0.4859-0.76760.228-0.7463-0.23080.4537-0.4739-0.2659-0.14660.4522-0.00010.9046-0.14-0.06081.11360.15250.97017.662626.929784.6488
111.8622-0.2240.83190.80540.32440.23550.0515-0.4489-0.31190.87120.2873-1.92680.5190.20020.4022.2710.5055-0.73951.50640.10062.541353.016819.136384.0506
120.53750.44540.19020.54660.82630.88050.2875-0.5803-0.10370.90770.1172-0.60850.5389-0.0545-0.00012.6140.2874-0.7392.4190.29781.948548.355728.003113.6542
130.06510.34420.16430.37160.25560.0550.2933-1.0831-1.39640.6804-0.40220.3491-0.3445-0.26460.00011.3118-0.13580.04361.87250.30051.673138.146637.382165.584
140.9561-0.340.4030.14250.14460.62290.02360.7308-0.6598-0.09150.9432-0.02751.2925-1.89160.00022.4834-0.2761-0.32432.31110.39561.808120.789610.3725111.4364
151.63970.2250.95170.38881.16923.2576-0.0589-0.93370.02940.3804-0.01450.02390.4358-0.2393-0.00030.8609-0.0844-0.0871.46740.02560.8845-32.977833.6309114.0189
160.24920.2898-0.13910.21420.11060.33930.1475-0.2997-0.02020.2743-0.14530.0107-0.01420.084300.7691-0.1658-0.19930.9888-0.05650.9558-23.232357.037187.2665
171.3326-0.2167-0.24691.89150.87520.5562-0.0904-0.81060.04660.04970.03630.80370.1534-1.15580.02011.50410.65850.07961.8722-0.56741.6818-68.345760.3004109.968
180.11430.2355-0.2831.4565-0.5176-0.0402-0.1709-1.1006-0.09440.1576-0.0144-0.0098-0.0501-0.332101.43490.198-0.10883.1606-0.4681.1526-50.623647.4628142.2594
191.0604-1.4932-0.85121.48760.61180.4418-0.2156-0.22590.26360.06590.174-0.0708-1.3949-0.3270.02460.74180.0958-0.17811.6206-0.37311.104-68.254556.4141100.2052
201.66070.9404-0.28520.1483-0.3347-0.04550.2429-0.5480.3130.2832-0.27510.2845-0.1578-0.4788-01.1586-0.183-0.05561.436-0.35061.1849-35.650866.5325106.0644
211.67840.34570.41591.08070.92571.45910.09630.27380.0629-1.0693-0.19380.1216-0.6160.255-01.48470.1494-0.1690.7402-0.02291.0635-2.557571.484516.2816
221.97840.24741.58111.06321.03930.35390.0148-0.04850.14880.0034-0.1111-0.0742-0.0987-0.4240.00020.6675-0.0137-0.0620.5679-0.01570.89164.087474.965366.7027
230.97060.59570.51620.77271.47442.3246-0.10920.4143-0.0448-0.25860.1849-0.1019-0.2487-0.0071-00.7835-0.0169-0.11880.94420.00421.0062-34.07353.807144.2472
240.17020.03330.16810.3981-0.2580.19830.2828-0.46660.3192-0.4477-0.04980.24220.1035-0.2548-02.27340.2301-0.30361.3884-0.25111.8285-16.576108.422664.322
251.2741-0.0348-1.16570.8021-0.93430.50410.2330.74840.29-0.87640.29010.32290.18910.03760.00013.09050.5616-0.53421.42280.16431.887-16.9773104.00764.3038
260.15340.4307-0.41710.03450.250.3869-0.3587-0.2886-0.2148-2.5386-0.01110.0209-1.4447-0.10860.00583.21110.5228-1.04671.3136-0.00261.3701-15.773998.14859.1884
270.44940.1389-0.15090.1504-0.38850.477-0.1498-1.256-0.09221.11450.04111.284-2.2460.4997-0.02052.61340.8671-0.35761.7754-0.44842.5923-23.373107.87729.2268
280.09490.2947-0.01510.2749-0.16710.0503-0.15030.06080.5736-0.163-0.2782-0.5553-1.0971-0.51520.00023.113-0.3613-0.43361.4163-0.02092.3566-4.8792116.58959.0051
290.7893-0.42640.1760.313-0.28250.1212-0.0216-0.4311-0.76570.26480.5813-0.2499-1.38440.27470.0391.9555-0.3163-0.07171.0582-0.24191.0899-3.665499.428477.1453
300.6602-0.1488-0.46820.12-0.12560.6020.39690.3452-0.00670.4741-0.0094-0.05420.4028-0.323301.4919-0.0186-0.2150.98550.03771.3437-29.302979.238137.6724
31-0.0784-0.0442-0.03730.0976-0.14130.16370.30580.943-0.21640.33790.6075-0.2494-0.07030.6374-0.00021.56220.0051-0.18391.0187-0.05721.3418-46.768863.546415.9661
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 356 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 357 THROUGH 639 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 640 THROUGH 1080 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 1 THROUGH 213 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 214 THROUGH 360 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 361 THROUGH 431 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 432 THROUGH 482 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 483 THROUGH 674 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 1 THROUGH 691 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 692 THROUGH 1080 )
11X-RAY DIFFRACTION11CHAIN 'D' AND (RESID 1 THROUGH 114 )
12X-RAY DIFFRACTION12CHAIN 'D' AND (RESID 115 THROUGH 464 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 465 THROUGH 552 )
14X-RAY DIFFRACTION14CHAIN 'D' AND (RESID 553 THROUGH 674 )
15X-RAY DIFFRACTION15CHAIN 'E' AND (RESID 1 THROUGH 662 )
16X-RAY DIFFRACTION16CHAIN 'E' AND (RESID 663 THROUGH 1080 )
17X-RAY DIFFRACTION17CHAIN 'F' AND (RESID 1 THROUGH 138 )
18X-RAY DIFFRACTION18CHAIN 'F' AND (RESID 139 THROUGH 329 )
19X-RAY DIFFRACTION19CHAIN 'F' AND (RESID 330 THROUGH 482 )
20X-RAY DIFFRACTION20CHAIN 'F' AND (RESID 483 THROUGH 674 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 1 THROUGH 595 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 596 THROUGH 805 )
23X-RAY DIFFRACTION23CHAIN 'G' AND (RESID 806 THROUGH 1080 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 1 THROUGH 55 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 56 THROUGH 213 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 214 THROUGH 363 )
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 364 THROUGH 413 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 414 THROUGH 452 )
29X-RAY DIFFRACTION29CHAIN 'H' AND (RESID 453 THROUGH 497 )
30X-RAY DIFFRACTION30CHAIN 'H' AND (RESID 498 THROUGH 637 )
31X-RAY DIFFRACTION31CHAIN 'H' AND (RESID 638 THROUGH 674 )

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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

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