[日本語] English
万見
- PDB-4wrl: Structure of the human CSF-1:CSF-1R complex -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 4wrl
タイトルStructure of the human CSF-1:CSF-1R complex
要素(Macrophage colony-stimulating factor ...) x 2
キーワードCYTOKINE/CYTOKINE RECEPTOR / cytokine-cytokine receptor complex
機能・相同性
機能・相同性情報


regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction ...regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / monocyte homeostasis / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / positive regulation of macrophage migration / osteoclast proliferation / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / forebrain neuron differentiation / macrophage colony-stimulating factor receptor activity / CSF1-CSF1R complex / monocyte activation / macrophage colony-stimulating factor signaling pathway / regulation of macrophage migration / positive regulation of microglial cell migration / mammary duct terminal end bud growth / cellular response to macrophage colony-stimulating factor stimulus / cell-cell junction maintenance / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of mononuclear cell proliferation / olfactory bulb development / mammary gland duct morphogenesis / myeloid leukocyte migration / host-mediated activation of viral process / neutrophil homeostasis / ruffle organization / positive regulation of monocyte differentiation / positive regulation of multicellular organism growth / positive regulation of osteoclast differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of macrophage proliferation / branching involved in mammary gland duct morphogenesis / positive regulation of Ras protein signal transduction / regulation of bone resorption / positive regulation of cell motility / positive regulation of tyrosine phosphorylation of STAT protein / Other interleukin signaling / positive regulation of cell-matrix adhesion / growth factor binding / positive regulation of protein tyrosine kinase activity / positive regulation of macrophage chemotaxis / cytokine binding / cellular response to cytokine stimulus / positive regulation of protein metabolic process / Interleukin-10 signaling / monocyte differentiation / hemopoiesis / regulation of MAPK cascade / Transcriptional Regulation by VENTX / macrophage differentiation / regulation of ossification / positive regulation of chemokine production / Transcriptional and post-translational regulation of MITF-M expression and activity / homeostasis of number of cells within a tissue / axon guidance / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / peptidyl-tyrosine phosphorylation / response to ischemia / cytokine activity / regulation of actin cytoskeleton organization / Post-translational protein phosphorylation / growth factor activity / receptor protein-tyrosine kinase / Signaling by CSF1 (M-CSF) in myeloid cells / positive regulation of protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cytokine-mediated signaling pathway / cell migration / regulation of cell shape / protein autophosphorylation / protein tyrosine kinase activity / protein phosphatase binding / Ras protein signal transduction / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / endoplasmic reticulum lumen / negative regulation of cell population proliferation / innate immune response / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular region / nucleoplasm / ATP binding / identical protein binding
類似検索 - 分子機能
Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Macrophage colony-stimulating factor 1 receptor / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin ...Macrophage colony stimulating factor-1 / Macrophage colony stimulating factor-1 (CSF-1) / Macrophage colony-stimulating factor 1 receptor / Platelet-derived growth factor receptor Ig-like domain 4 / Tyrosine-protein kinase, receptor class III, conserved site / Receptor tyrosine kinase class III signature. / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Immunoglobulin / Immunoglobulin domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
3'-sialyl-N-acetyllactosamine / N-acetyl-alpha-neuraminic acid / Macrophage colony-stimulating factor 1 receptor / Macrophage colony-stimulating factor 1
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: 2.802 Å
データ登録者Felix, J. / De Munck, S. / Elegheert, J. / Savvides, S.N.
引用ジャーナル: Structure / 年: 2015
タイトル: Structure and Assembly Mechanism of the Signaling Complex Mediated by Human CSF-1.
著者: Jan Felix / Steven De Munck / Kenneth Verstraete / Leander Meuris / Nico Callewaert / Jonathan Elegheert / Savvas N Savvides /
要旨: Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). Despite ever- ...Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). Despite ever-growing insights into the central role of hCSF-1R signaling in innate and adaptive immunity, inflammatory diseases, and cancer, the structural basis of the functional dichotomy of hCSF-1R has remained elusive. Here, we report crystal structures of ternary complexes between hCSF-1 and hCSF-1R, including their complete extracellular assembly, and propose a mechanism for the cooperative human CSF-1:CSF-1R complex that relies on the adoption by dimeric hCSF-1 of an active conformational state and homotypic receptor interactions. Furthermore, we trace the cytokine-binding duality of hCSF-1R to a limited set of conserved interactions mediated by functionally equivalent residues on CSF-1 and IL-34 that play into the geometric requirements of hCSF-1R activation, and map the possible mechanistic consequences of somatic mutations in hCSF-1R associated with cancer.
履歴
登録2014年10月24日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02015年8月12日Provider: repository / タイプ: Initial release
改定 1.12015年9月9日Group: Database references
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_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 / _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] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年1月10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6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

-
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

-
集合体

登録構造単位
A: Macrophage colony-stimulating factor 1 receptor
C: Macrophage colony-stimulating factor 1 receptor
B: Macrophage colony-stimulating factor 1
D: Macrophage colony-stimulating factor 1
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)107,02913
ポリマ－102,6824
非ポリマー4,3479
水00
1


  • 登録構造と同一
  • 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 area8190 Å2
ΔGint21 kcal/mol
Surface area44790 Å2
手法PISA
単位格子
Length a, b, c (Å)142.997, 142.997, 138.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

-
要素

-
Macrophage colony-stimulating factor ... , 2種, 4分子 ACBD

#1: タンパク質 Macrophage colony-stimulating factor 1 receptor / CSF-1 receptor / M-CSF-R / Proto-oncogene c-Fms


分子量: 31583.867 Da / 分子数: 2 / 断片: UNP residues 20-296 / 変異: N240Q / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CSF1R, FMS / 細胞株 (発現宿主): HEK-293S / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P07333, receptor protein-tyrosine kinase
#2: タンパク質 Macrophage colony-stimulating factor 1 / MCSF / Lanimostim


分子量: 19757.314 Da / 分子数: 2 / 断片: UNP residues 33-181 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CSF1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P09603

-
糖 , 5種, 9分子

#3: 多糖 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 820.744 Da / 分子数: 2 / 由来タイプ: 合成
記述子タイププログラム
DNeup5Aca2-3DGalpb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-2-3-4/a4-b1_a6-d1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 多糖 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 383.349 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
DGalpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#5: 多糖 N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine


タイプ: oligosaccharide, Oligosaccharide / クラス: 基質類似体 / 分子量: 674.604 Da / 分子数: 2 / 由来タイプ: 合成 / 詳細: oligosaccharide / 参照: 3'-sialyl-N-acetyllactosamine
記述子タイププログラム
DNeup5Aca2-3DGalpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#6: 糖 ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / N-アセチル-α-ノイラミン酸


タイプ: D-saccharide, alpha linking / 分子量: 309.270 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C11H19NO9
識別子タイププログラム
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: 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: 合成 / 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

-
詳細

Has protein modificationY

-
実験情報

-
実験

実験手法: X線回折

-
試料調製

結晶マシュー密度: 3.44 Å3/Da / 溶媒含有率: 64.28 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 0.2 M Lithium sulfate monohydrate, 0.1 M Tris pH 8.5 and 28% w/v PEG 3350

-
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: ESRF / ビームライン: ID23-1 / 波長: 0.97625 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2014年4月25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: 0.97625 Å / 相対比: 1
反射解像度: 2.8→49.71 Å / Num. obs: 34125 / % possible obs: 99.8 % / 冗長度: 6.9 % / Biso Wilson estimate: 82.26 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.73
反射 シェル解像度: 2.8→2.97 Å / 冗長度: 6.8 % / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 2.32 / % possible all: 99.2

-
解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4DKD, 3UF2

4dkd

3uf2


解像度: 2.802→49.71 Å / SU ML: 0.52 / 交差検証法: FREE R-VALUE / σ(F): 1.36 / 位相誤差: 30.59 / 立体化学のターゲット値: ML
詳細: Galactose 403 and Galactose 408 on chain C failed to be fitted in the exo-anomeric conformation of their glycosidic bond
Rfactor反射数%反射
Rfree0.2613 1706 5 %
Rwork0.2231 --
obs0.225 34117 99.83 %
溶媒の処理減衰半径: 1 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.802→49.71 Å
タンパク質核酸リガンド溶媒全体
原子数6370 0 287 0 6657
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0066827
X-RAY DIFFRACTIONf_angle_d1.0949324
X-RAY DIFFRACTIONf_dihedral_angle_d13.4462424
X-RAY DIFFRACTIONf_chiral_restr0.0521125
X-RAY DIFFRACTIONf_plane_restr0.0141181
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8016-2.88410.521380.38952638X-RAY DIFFRACTION98
2.8841-2.97710.40031420.34352709X-RAY DIFFRACTION100
2.9771-3.08350.36061420.30312686X-RAY DIFFRACTION100
3.0835-3.2070.31141420.2772710X-RAY DIFFRACTION100
3.207-3.35290.35311400.2812660X-RAY DIFFRACTION100
3.3529-3.52960.31821440.24362722X-RAY DIFFRACTION100
3.5296-3.75070.32641430.24862712X-RAY DIFFRACTION100
3.7507-4.04020.23041410.21392683X-RAY DIFFRACTION100
4.0402-4.44650.21861430.19212720X-RAY DIFFRACTION100
4.4465-5.08940.2241420.18322707X-RAY DIFFRACTION100
5.0894-6.40990.23161430.20672713X-RAY DIFFRACTION100
6.4099-49.7180.2281460.2042751X-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)
12.04951.12660.67514.57181.35782.8965-0.26510.2951-0.2415-0.26350.3831-0.3601-0.01590.13650.00240.4579-0.19280.0810.6725-0.01880.49999.93840.3851-31.0206
20.6902-1.54610.52593.70090.33671.8101-0.12740.7808-1.2759-0.13850.3654-0.3956-0.10690.14990.04330.5787-0.1620.12040.7533-0.30070.74285.2551-17.6289-37.1975
30.6052-0.3862-0.11370.3652-0.50860.4428-0.1698-0.0323-0.43910.48250.28040.4974-0.00670.084101.3968-0.19380.45081.1787-0.23961.599-20.0162-41.5512-32.524
41.9839-0.7686-0.4444.53841.73753.4121-0.3053-0.38790.19350.2490.3642-0.2645-0.00040.21990.00220.46650.2062-0.08630.6569-0.01190.53389.9514-71.8339-93.0482
50.5320.5857-0.23612.26852.01912.2243-0.0595-0.76690.2964-0.41350.3784-0.2014-0.570.25850.02410.73320.3196-0.20890.9233-0.13910.6914.7987-54.159-85.9649
60.4720.58610.31360.32590.469-0.1453-0.54060.24920.4013-0.01190.43650.2238-0.2084-0.2765-01.25990.1868-0.28161.3673-0.191.4065-23.8003-30.7563-86.8703
70.38620.3680.08130.17290.08550.0115-0.47690.30120.6201-1.3439-0.86780.1882-0.6276-1.3306-0.01391.56260.1902-0.34511.0267-0.13550.785-0.7174-33.0247-80.5741
80.98020.04020.24131.46431.130.6458-0.22310.55140.0911-1.04070.235-0.5656-0.72130.9547-01.0645-0.17350.13921.0965-0.01150.777916.297-33.4447-78.218
91.9611-0.7519-0.05631.90391.14610.7378-0.191-0.045-0.1112-0.2786-0.21460.3517-0.17510.264700.63460.0704-0.04730.5137-0.14450.69683.8785-42.4387-74.8677
100.38250.3704-0.00311.5379-0.05250.7067-0.03010.82840.7001-1.99210.1378-0.8437-2.02430.86870.01721.3736-0.16610.10031.0359-0.08090.698612.5449-31.5687-81.6448
110.25850.2494-0.23010.78660.14360.51150.40430.7234-0.0023-2.0307-0.161-1.0221-0.9860.2719-0.14023.5515-0.42140.87581.47610.2643-0.307712.9308-31.2862-95.9154
120.6197-0.34440.04420.4053-0.18070.19640.1298-0.738-0.79631.2805-0.11490.70360.4185-1.5855-01.3166-0.05340.28370.9408-0.03050.84990.0795-38.1582-42.8784
131.85240.3964-0.54891.25380.90710.5504-0.1097-0.8076-0.19481.01180.1947-0.59450.7521.176800.99660.244-0.09931.08720.03430.809516.7402-37.9355-46.1865
141.1551-0.252-0.43641.5120.78040.5878-0.20630.09540.16010.3755-0.09810.401-0.1272-0.124500.669-0.06040.04180.5633-0.10740.67093.9359-29.0358-50.3681
150.6006-0.43830.06832.0638-0.27991.0246-0.0116-0.923-0.51331.84050.2061-0.55961.9731.33480.02491.31550.10520.01450.95310.00230.754312.9626-39.456-42.1615
160.1040.302-0.0291.863-0.10750.03230.1599-1.22260.22372.8827-0.51450.10871.39111.21990.07582.52510.1621-0.27341.87870.03040.710614.5039-40.3146-28.2403
170.1509-0.1636-0.24721.55170.8832-0.4553-0.1745-0.63770.06790.2839-0.0622-0.0098-0.3868-0.21840.0011.36210.3863-0.00571.5109-0.02331.4183-0.7765-61.0911-97.5169
180.03710.5298-0.89930.78740.64591.1836-0.2504-0.00330.1011-0.42890.0810.16920.1767-0.42870.00011.5058-0.1573-0.28581.69230.10191.33860.1541-9.2536-29.8537
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 174 )
2X-RAY DIFFRACTION2chain 'A' and (resid 175 through 208 )
3X-RAY DIFFRACTION3chain 'A' and (resid 209 through 296 )
4X-RAY DIFFRACTION4chain 'C' and (resid 20 through 174 )
5X-RAY DIFFRACTION5chain 'C' and (resid 175 through 208 )
6X-RAY DIFFRACTION6chain 'C' and (resid 209 through 296)
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 24 )
8X-RAY DIFFRACTION8chain 'B' and (resid 25 through 63 )
9X-RAY DIFFRACTION9chain 'B' and (resid 64 through 89 )
10X-RAY DIFFRACTION10chain 'B' and (resid 90 through 130 )
11X-RAY DIFFRACTION11chain 'B' and (resid 131 through 146 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 24 )
13X-RAY DIFFRACTION13chain 'D' and (resid 25 through 63 )
14X-RAY DIFFRACTION14chain 'D' and (resid 64 through 87 )
15X-RAY DIFFRACTION15chain 'D' and (resid 88 through 130 )
16X-RAY DIFFRACTION16chain 'D' and (resid 131 through 146 )
17X-RAY DIFFRACTION17chain 'C' and (resid 401 through 409)
18X-RAY DIFFRACTION18chain 'A' and (resid 401 through 411)

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る