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- PDB-4mmx: Integrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibr... -

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基本情報

登録情報
データベース: PDB / ID: 4mmx
タイトルIntegrin AlphaVBeta3 ectodomain bound to the tenth domain of Fibronectin
要素
  • Fibronectin
  • Integrin alpha-V
  • Integrin beta-3
キーワードCELL ADHESION / integrin / A domain / hybrid domain / PSI / EGF repeats / beta TA thigh / beta propeller / RGD motif / fibronectin / vitronectin
機能・相同性
機能・相同性情報


negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / Extracellular matrix organization ...negative regulation of monocyte activation / negative regulation of transforming growth factor beta production / integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / extracellular matrix protein binding / opsonin binding / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / neural crest cell migration involved in autonomic nervous system development / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / peptidase activator activity / 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 / fibrinogen complex / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / peptide cross-linking / maintenance of postsynaptic specialization structure / alphav-beta3 integrin-vitronectin complex / regulation of extracellular matrix organization / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / platelet alpha granule membrane / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-PKCalpha complex / integrin activation / fibrinogen binding / negative regulation of low-density lipoprotein particle clearance / blood coagulation, fibrin clot formation / alphav-beta3 integrin-HMGB1 complex / ALK mutants bind TKIs / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / positive regulation of vascular endothelial growth factor signaling pathway / regulation of phagocytosis / regulation of release of sequestered calcium ion into cytosol / Elastic fibre formation / glycinergic synapse / mesodermal cell differentiation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / platelet-derived growth factor receptor binding / transforming growth factor beta binding / positive regulation of small GTPase mediated signal transduction / filopodium membrane / extracellular matrix binding / regulation of protein phosphorylation / angiogenesis involved in wound healing / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of bone resorption / proteoglycan binding / apolipoprotein A-I-mediated signaling pathway / positive regulation of cell adhesion mediated by integrin / apoptotic cell clearance / integrin complex / wound healing, spreading of epidermal cells / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / extracellular matrix structural constituent / biological process involved in interaction with symbiont / positive regulation of smooth muscle cell migration / smooth muscle cell migration / Molecules associated with elastic fibres / MET activates PTK2 signaling / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / positive regulation of cell-matrix adhesion / negative chemotaxis / cellular response to insulin-like growth factor stimulus / cell adhesion mediated by integrin / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / positive regulation of osteoblast proliferation / microvillus membrane / regulation of postsynaptic neurotransmitter receptor internalization / protein disulfide isomerase activity / response to muscle activity / cell-substrate adhesion / endodermal cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / TGF-beta receptor signaling activates SMADs / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of intracellular signal transduction / lamellipodium membrane / fibronectin binding / positive regulation of bone resorption / negative regulation of macrophage derived foam cell differentiation
類似検索 - 分子機能
Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Hormone receptor fold / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. ...Hormone receptor fold - #30 / ntegrin, alpha v. Chain A, domain 4 / Integrin domains. Chain A, domain 2 / ntegrin, alpha v. Chain A, domain 3 / Integrin alpha, N-terminal / Hormone receptor fold / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / : / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin beta tail domain / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / 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) / 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 alpha, N-terminal / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Laminin / Laminin / Kringle-like fold / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / Fibronectin type 3 domain / 7 Propeller / Methylamine Dehydrogenase; Chain H / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Ribbon / Few Secondary Structures / Irregular / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
: / Fibronectin / Integrin beta-3 / Integrin alpha-V
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 / 分子置換 / 解像度: 3.32 Å
データ登録者van Agthoven, J. / Xiong, J. / Arnaout, M.A.
資金援助 米国, 4件
組織認可番号国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK088327 米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK48549 米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK096334 米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK007540 米国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2014
タイトル: Structural basis for pure antagonism of integrin alpha V beta 3 by a high-affinity form of fibronectin.
著者: Van Agthoven, J.F. / Xiong, J.P. / Alonso, J.L. / Rui, X. / Adair, B.D. / Goodman, S.L. / Arnaout, M.A.
履歴
登録2013年9月9日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02014年3月26日Provider: repository / タイプ: Initial release
改定 1.12014年4月9日Group: Database references
改定 1.22014年4月30日Group: Database references
改定 1.32017年11月15日Group: Refinement description / カテゴリ: software
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
カテゴリ: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_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 / _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_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年11月6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 / _database_2.pdbx_database_accession
改定 3.02025年3月26日Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn / entity_name_com / entity_src_gen / pdbx_audit_support / pdbx_branch_scheme / pdbx_contact_author / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_refine_tls / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
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_seq_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _diffrn.pdbx_serial_crystal_experiment / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entry_details.has_ligand_of_interest / _pdbx_modification_feature.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly_prop.value / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_all / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _reflns.number_all / _reflns.observed_criterion_sigma_I / _reflns_shell.number_unique_obs / _software.classification / _software.name / _software.version / _struct.pdbx_CASP_flag / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_sheet.id / _struct_sheet.number_strands
解説: Ligand geometry / Provider: author / タイプ: Coordinate replacement

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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-V
B: Integrin beta-3
C: Fibronectin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)199,90825
ポリマ－192,9213
非ポリマー6,98722
水362
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 area16220 Å2
ΔGint56 kcal/mol
Surface area80080 Å2
手法PISA
単位格子
Length a, b, c (Å)129.859, 129.859, 305.831
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 , 3種, 3分子 ABC

#1: タンパク質 Integrin alpha-V / Vitronectin receptor / Vitronectin receptor subunit alpha


分子量: 106048.359 Da / 分子数: 1 / 断片: Extracellular domain (UNP residues 31-989) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ITGAV, MSK8, VNRA, VTNR
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
株 (発現宿主): Hi5 / 参照: UniProt: P06756
#2: タンパク質 Integrin beta-3 / Platelet membrane glycoprotein IIIa / GPIIIa


分子量: 76523.125 Da / 分子数: 1 / 断片: Extracellular domain (UNP residues 27-718) / 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: Spodoptera frugiperda (ツマジロクサヨトウ)
株 (発現宿主): Hi5 / 参照: UniProt: P05106
#3: タンパク質 Fibronectin / FN / Cold-insoluble globulin / CIG


分子量: 10349.573 Da / 分子数: 1
断片: Fibronectin type-III domain 10 (UNP residues 1448-1540)
由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: FN1, FN / プラスミド: pET / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P02751

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糖 , 5種, 14分子

#4: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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: 4 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 多糖 alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-beta-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
DManpa1-4DManpb1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-2-3/a4-b1_b4-c1_c3-d1_c6-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{[(4+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#8: 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: 5 / 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 , 2種, 10分子

#9: 化合物
ChemComp-MN / MANGANESE (II) ION


分子量: 54.938 Da / 分子数: 8 / 由来タイプ: 合成 / 式: Mn
#10: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 2 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかN
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: 3.85 Å3/Da / 溶媒含有率: 68.05 %
結晶化温度: 277.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.5
詳細: 12% PEG3350, 0.8 M sodium chloride, 0.1 M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
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: 0.97921 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2012年10月13日
放射モノクロメーター: sagitally focused 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: 0.97921 Å / 相対比: 1
反射解像度: 3.32→75.49 Å / Num. obs: 39593 / % possible obs: 88 % / Observed criterion σ(F): 5.3 / 冗長度: 6.2 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 13.9
反射 シェル解像度: 3.32→3.41 Å / 冗長度: 6.4 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3003 / Rsym value: 0.676 / % possible all: 88

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.20.1_4487: ???)精密化
DENZOデータ削減
SCALEPACKデータスケーリング
PHASER位相決定
HKL-2000データ削減
HKL-2000データスケーリング
精密化構造決定の手法: 分子置換 / 解像度: 3.32→42.51 Å / SU ML: 0.43 / 交差検証法: FREE R-VALUE / σ(F): 1.38 / 位相誤差: 26.53 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2694 1942 4.91 %
Rwork0.2204 --
obs0.2227 39586 88 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 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: 3.32→42.51 Å
タンパク質核酸リガンド溶媒全体
原子数13184 0 440 2 13626
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00313884
X-RAY DIFFRACTIONf_angle_d0.66118818
X-RAY DIFFRACTIONf_dihedral_angle_d14.1445221
X-RAY DIFFRACTIONf_chiral_restr0.0462172
X-RAY DIFFRACTIONf_plane_restr0.0052431
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.32-3.40.33941470.29123003X-RAY DIFFRACTION100
3.4-3.490.3401850.30421356X-RAY DIFFRACTION46
3.5-3.60.34981660.28042984X-RAY DIFFRACTION100
3.6-3.710.3307470.26621222X-RAY DIFFRACTION40
3.71-3.850.28761270.25923018X-RAY DIFFRACTION100
3.85-40.3405820.24711431X-RAY DIFFRACTION47
4-4.180.25551520.23633046X-RAY DIFFRACTION100
4.18-4.40.22261380.20553033X-RAY DIFFRACTION100
4.4-4.680.22721730.17953029X-RAY DIFFRACTION100
4.68-5.040.23521750.18453027X-RAY DIFFRACTION100
5.04-5.540.2641840.20233037X-RAY DIFFRACTION100
5.55-6.340.27591590.23433077X-RAY DIFFRACTION100
6.35-7.980.29961680.23813125X-RAY DIFFRACTION100
7.99-42.510.25231390.19663256X-RAY DIFFRACTION99
精密化 TLS

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.93531.08960.91333.124-0.41912.0635-0.36710.24140.246-0.21560.2242-0.0011-0.45120.13380.09810.6824-0.1872-0.0180.33780.00410.42747.670656.020522.336
24.54890.31071.8522-0.3864-0.06920.9806-0.12340.60090.193-0.2240.09190.2896-0.0275-0.01970.05390.9761-0.2907-0.21760.73140.12970.8911-27.351248.12751.3008
32.6108-0.38650.20532.5723-0.96914.531-0.1856-0.23390.0492-0.08840.15950.33810.20290.29360.04130.8022-0.0806-0.2010.64720.06730.7692-51.825242.506521.8485
44.7384-2.16742.99342.9277-2.69036.3691-0.0716-0.4505-0.10620.43350.08160.0008-0.00460.03380.06320.88370.24350.02660.4834-0.05280.6194-26.153336.538771.6902
58.2535-2.1775.73562.6451-2.29815.8901-0.09650.5244-0.9267-0.58140.39970.55390.0905-0.4742-0.73311.3352-0.3177-0.12240.7499-0.02591.2916-33.11742.377911.7887
62.36991.1957-0.05923.3805-0.83370.51950.1608-0.0393-1.13250.4558-0.1073-0.96550.21610.1661-0.01480.8483-0.0538-0.0490.41230.02930.81136.778215.519534.8642
70.76530.3219-0.36094.5054-1.33432.70170.08030.1331-0.8934-0.2080.2003-0.95180.28850.4473-0.21510.6773-0.0670.0050.4115-0.02791.079318.395427.14731.7515
83.59012.98920.35443.75490.7369-0.0741-0.0299-0.1628-0.37630.0335-0.1381-0.2870.2355-0.02470.15030.944-0.04880.01340.41130.07230.723-3.829818.647333.7537
95.8538-3.72053.69883.3047-3.28245.3050.6732.4297-0.17-1.7056-0.60390.23351.68710.27890.02621.8464-0.4379-0.17341.722-0.08540.939-30.55037.849-2.353
105.12410.04473.60871.96151.62214.7627-0.56380.57060.8659-0.7812-0.15250.96770.15540.170.8441.2245-0.2435-0.23480.90040.08391.3334-38.519424.392215.1967
115.534-6.56375.38877.559-6.1555.0272-0.1634-0.4913-0.0321-0.35920.2479-1.38480.1364-0.5099-0.11490.758-0.07390.09380.5601-0.04880.8977-18.562917.327658.9447
123.17992.2231.06181.76821.80046.0442-0.07940.2966-0.16880.10230.0651-0.4660.0820.6844-0.09961.23350.2758-0.08290.63830.08261.1463-7.555515.248968.4749
131.921-1.0069-1.35313.82573.62553.64450.7245-0.01210.34721.3589-0.2620.102-0.24130.6473-0.2692.41940.6952-0.91441.7061-0.47741.619627.267347.124461.9343
140.4740.35-0.21441.7762-2.5193.83870.1676-1.95431.4191.1427-1.55832.4025-1.62431.33870.91185.43161.3814-0.64733.7554-1.49642.481415.799546.26978.4372
155.2872-4.18426.54486.7594-6.40458.612-0.2782-1.31850.85781.7857-1.0161-0.83473.07030.54921.37262.0922-0.0127-0.05651.5862-0.06261.059918.506346.661260.1757
165.5659-1.42033.48112.86732.09045.7229-1.15471.75673.8551-1.3711-1.8971-0.3919-2.80920.43692.80862.61580.2557-0.38461.72110.29722.675716.124428.802468.508
176.644-5.4933-1.44895.19483.41037.80750.288-1.57-0.46192.4407-1.9082.67331.59182.01621.16041.7824-0.29860.45251.383-0.0381.010313.13848.271862.6543
188.20545.655-2.40614.0184-2.07052.12560.6342-0.61210.1349-1.1519-1.2851-1.5433.97022.76111.06452.07030.52460.42882.86481.01271.838714.430536.195376.3503
199.233-5.0404-7.40932.75094.04175.953-0.0594-3.44790.10832.82320.4587-0.93753.57160.2465-0.64732.9074-0.9684-0.12842.5225-0.47061.096319.500140.129461.7429
207.9706-4.9366-5.81824.76835.64756.6953-0.3368-1.4031.18961.31190.1868-2.8793.52591.04220.56421.4105-0.114-0.49420.83270.22771.096220.746941.653248.3364
210.61710.29960.00870.13980.0046-0.00171.9952-2.3012-0.32831.32460.42110.1357-5.48710.7547-2.02712.43690.15650.70323.36610.52051.539323.701238.732173.1529
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 320 )
2X-RAY DIFFRACTION2chain 'A' and (resid 321 through 590 )
3X-RAY DIFFRACTION3chain 'A' and (resid 591 through 729 )
4X-RAY DIFFRACTION4chain 'A' and (resid 730 through 956 )
5X-RAY DIFFRACTION5chain 'B' and (resid 5 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 169 )
7X-RAY DIFFRACTION7chain 'B' and (resid 170 through 278 )
8X-RAY DIFFRACTION8chain 'B' and (resid 279 through 423 )
9X-RAY DIFFRACTION9chain 'B' and (resid 424 through 462 )
10X-RAY DIFFRACTION10chain 'B' and (resid 463 through 588 )
11X-RAY DIFFRACTION11chain 'B' and (resid 589 through 630 )
12X-RAY DIFFRACTION12chain 'B' and (resid 631 through 690 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1417 through 1425 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1426 through 1433 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1434 through 1452 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1453 through 1461 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1462 through 1473 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1474 through 1483 )
19X-RAY DIFFRACTION19chain 'C' and (resid 1484 through 1490 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1491 through 1502 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1503 through 1509 )

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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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