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- PDB-5hzv: Crystal structure of the zona pellucida module of human endoglin/CD105 -

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基本情報

登録情報
データベース: PDB / ID: 5hzv
タイトルCrystal structure of the zona pellucida module of human endoglin/CD105
要素Maltose-binding periplasmic protein,Endoglin
キーワードSIGNALING PROTEIN / ZONA PELLUCIDA DOMAIN / ANGIOGENESIS / GLYCOPROTEIN / RECEPTOR
機能・相同性
機能・相同性情報


atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development / atrial cardiac muscle tissue morphogenesis / central nervous system vasculogenesis ...atrioventricular canal morphogenesis / detection of hypoxia / endothelial microparticle / venous blood vessel morphogenesis / dorsal aorta morphogenesis / positive regulation of vascular associated smooth muscle cell differentiation / cell migration involved in endocardial cushion formation / vascular associated smooth muscle cell development / atrial cardiac muscle tissue morphogenesis / central nervous system vasculogenesis / epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / cardiac ventricle morphogenesis / regulation of transforming growth factor beta receptor signaling pathway / galactose binding / cardiac atrium morphogenesis / smooth muscle tissue development / type II transforming growth factor beta receptor binding / activin binding / regulation of phosphorylation / type I transforming growth factor beta receptor binding / ventricular trabecula myocardium morphogenesis / glycosaminoglycan binding / positive regulation of BMP signaling pathway / outflow tract septum morphogenesis / transforming growth factor beta binding / artery morphogenesis / endocardial cushion morphogenesis / branching involved in blood vessel morphogenesis / negative regulation of SMAD protein signal transduction / detection of maltose stimulus / heart looping / maltose transport complex / negative regulation of endothelial cell proliferation / positive regulation of systemic arterial blood pressure / carbohydrate transport / signaling receptor activator activity / positive regulation of SMAD protein signal transduction / extracellular matrix disassembly / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / BMP signaling pathway / vasculogenesis / regulation of cell adhesion / coreceptor activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / cell chemotaxis / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / wound healing / positive regulation of angiogenesis / transmembrane signaling receptor activity / cell migration / regulation of cell population proliferation / outer membrane-bounded periplasmic space / periplasmic space / response to hypoxia / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / nuclear body / negative regulation of gene expression / external side of plasma membrane / focal adhesion / DNA damage response / regulation of DNA-templated transcription / cell surface / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane
類似検索 - 分子機能
ZP-C domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Endoglin
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.7 Å
データ登録者Bokhove, M. / Saito, T. / Jovine, L.
資金援助 スウェーデン, 7件
組織認可番号国
Karolinska Institutet スウェーデン
Center for Biosciences スウェーデン
Swedish Research Council2012-5093 スウェーデン
Gustafsson Foundation for Research in Natural Sciences and Medicine スウェーデン
Sven and Ebba-Christina Hagberg foundation スウェーデン
European Molecular Biology Organization
European UnionERC 260759
引用
ジャーナル: Cell Rep / 年: 2017
タイトル: Structural Basis of the Human Endoglin-BMP9 Interaction: Insights into BMP Signaling and HHT1.
著者: Saito, T. / Bokhove, M. / Croci, R. / Zamora-Caballero, S. / Han, L. / Letarte, M. / de Sanctis, D. / Jovine, L.
#1: ジャーナル: J. Biol. Chem. / 年: 1990
タイトル: Primary structure of endoglin, an RGD-containing glycoprotein of human endothelial cells.
著者: Gougos, A. / Letarte, M.
#2: ジャーナル: FEBS Lett. / 年: 1992
タイトル: A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor.
著者: Bork, P. / Sander, C.
#3: ジャーナル: Annu Rev Biochem / 年: 2005
タイトル: Zona pellucida domain proteins.
著者: Luca Jovine / Costel C Darie / Eveline S Litscher / Paul M Wassarman /
要旨: Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to ...Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of approximately 260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.
#4: ジャーナル: Cell / 年: 2010
タイトル: Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
著者: Ling Han / Magnus Monné / Hiroki Okumura / Thomas Schwend / Amy L Cherry / David Flot / Tsukasa Matsuda / Luca Jovine /
要旨: ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization- ...ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.
#5: ジャーナル: Proc Natl Acad Sci U S A / 年: 2016
タイトル: A structured interdomain linker directs self-polymerization of human uromodulin.
著者: Marcel Bokhove / Kaoru Nishimura / Martina Brunati / Ling Han / Daniele de Sanctis / Luca Rampoldi / Luca Jovine /
要旨: Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite ...Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn's disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes.
履歴
登録2016年2月3日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02017年6月7日Provider: repository / タイプ: Initial release
改定 1.12017年6月14日Group: Database references / カテゴリ: citation
Item: _citation.country / _citation.page_last ..._citation.country / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
改定 1.22017年8月23日Group: Database references / Source and taxonomy / Structure summary
カテゴリ: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_mutation / _entity_src_gen.pdbx_end_seq_num ..._entity.pdbx_mutation / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
改定 1.32017年9月6日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_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] / _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_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type
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_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
改定 2.22024年10月23日Group: Structure summary
カテゴリ: 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: Maltose-binding periplasmic protein,Endoglin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,6633
ポリマ－68,2281
非ポリマー4342
水27015
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 area900 Å2
ΔGint2 kcal/mol
Surface area27770 Å2
手法PISA
単位格子
Length a, b, c (Å)125.160, 125.160, 88.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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要素

#1: タンパク質 Maltose-binding periplasmic protein,Endoglin / MBP / MMBP / Maltodextrin-binding protein


分子量: 68228.398 Da / 分子数: 1
変異: D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND ...変異: D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N,D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N
由来タイプ: 組換発現
詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 368-734 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS D449A, ...詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 368-734 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS D449A, K450A, E539A, N540A, A582H, K586H, K606A, A679V, I684V, E726A, E729A, D730A AND R734N (CORRESPONDING TO D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 738-981 ARE FROM HUMAN ENDOGLIN PROTEIN AND CORRESPOND TO RESIDUES 338-581 OF SWISS-PROT DATABASE ENTRY P17813. SUBTRACTING 400 FROM THE PDB ENTRY RESIDUE NUMBERING RESULTS IN THE NUMBERING ACCORDING TO UNIPROT ENTRY P17813.
由来: (組換発現) Escherichia coli (strain K12) (大腸菌), (組換発現) Homo sapiens (ヒト)
株: K12 / Cell: ENDOTHELIAL / 遺伝子: malE, b4034, JW3994, ENG, END / プラスミド: pHLsec / 細胞株 (発現宿主): HEK293T / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P0AEX9, UniProt: P17813
#2: 多糖 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


タイプ: oligosaccharide, Oligosaccharide / クラス: 栄養素 / 分子量: 342.297 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: oligosaccharide / 参照: alpha-maltose
記述子タイププログラム
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: 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: 1 / 由来タイプ: 合成 / 式: C3H8O3
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 15 / 由来タイプ: 天然 / 式: H2O
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: 2.94 Å3/Da / 溶媒含有率: 58.2 % / 解説: Hexagonal rod
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: 6.5
詳細: 11.5% equal mixture of MPD, PEG 1000 and PEG 3350 (1:1:1), MES/imidazole mix
PH範囲: 5.5-7.0

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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: ESRF / ビームライン: ID23-1 / 波長: 1 Å
検出器タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2015年9月25日
放射モノクロメーター: Si Single Crystal / 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 Å / 相対比: 1
反射解像度: 2.69→29.51 Å / Num. obs: 21583 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / 冗長度: 3.3 % / Biso Wilson estimate: 72.174 Å2 / Rsym value: 0.062 / Net I/σ(I): 9.43
反射 シェル解像度: 2.69→2.76 Å / 冗長度: 2.8 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 0.99 / % possible all: 85.4

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
XDS(Jun 17, 2015)データ削減
XSCALE(Jun 17, 2015)データスケーリング
PHASER(2.5.6)位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3SEX

3sex


解像度: 2.7→29.5037 Å / SU ML: 0.51 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 36.22 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.272 1138 5.31 %Random selection
Rwork0.2318 ---
obs0.234 21429 98.44 %-
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: 2.7→29.5037 Å
タンパク質核酸リガンド溶媒全体
原子数4582 0 29 15 4626
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0024719
X-RAY DIFFRACTIONf_angle_d0.5346414
X-RAY DIFFRACTIONf_dihedral_angle_d10.6332844
X-RAY DIFFRACTIONf_chiral_restr0.041727
X-RAY DIFFRACTIONf_plane_restr0.004823
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION

解像度 (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
2.7005-2.82340.44291254.780.4031249297
2.8234-2.97210.40351435.30.3637255399
2.9721-3.15810.36681495.550.3246253499
3.1581-3.40160.34061134.190.2837258299
3.4016-3.74330.28911575.880.2516251399
3.7433-4.28360.23651465.420.2187255099
4.2836-5.39150.21721525.70.1832251698
5.3915-29.50370.24831535.660.1829255197
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)詳細Origin x (Å)Origin y (Å)Origin z (Å)
11.2148-0.7364-1.09542.92131.80183.253-0.1450.1242-0.03730.2215-0.0513-0.07760.2670.1346-0.00390.8027-0.0504-0.01450.5983-0.00060.7139mMBP10.507883.751356.5438
21.481-0.7179-0.88371.50770.52891.26730.01580.25710.13530.094-0.15670.2022-0.6051-0.134-00.78460.1771-0.06160.97560.00670.7623ZP-N40.991150.116272.0674
30.4743-0.04590.05541.19650.46370.86320.05110.2044-0.43-0.41370.00810.72610.17890.1638-0.00010.98020.0858-0.00870.9352-0.0491.13ZP-C39.324415.256763.087
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 844:976)
2X-RAY DIFFRACTION2chain A and (resid 743:843)
3X-RAY DIFFRACTION3chain A and (resid 844:976)

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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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