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- PDB-5osq: ZP-N domain of mammalian sperm receptor ZP3 (crystal form II, pro... -

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基本情報

登録情報
データベース: PDB / ID: 5osq
タイトルZP-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in P21221)
要素Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
キーワードCELL ADHESION / FERTILIZATION / OOCYTE / EGG COAT / ZONA PELLUCIDA / VITELLINE ENVELOPE / ZP DOMAIN / EGG-SPERM INTERACTION / SPECIES-SPECIFIC GAMETE RECOGNITION / SPECIATION / BIODIVERSITY / INFERTILITY / EXTRACELLULAR MATRIX / IMMUNOGLOBULIN-LIKE FOLD / GLYCOPROTEIN / RECEPTOR / SECRETED / TRANSMEMBRANE
機能・相同性
機能・相同性情報


positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / egg coat formation / positive regulation of humoral immune response / Interaction With Cumulus Cells And The Zona Pellucida / structural constituent of egg coat / egg coat / positive regulation of acrosome reaction / positive regulation of ovarian follicle development ...positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / egg coat formation / positive regulation of humoral immune response / Interaction With Cumulus Cells And The Zona Pellucida / structural constituent of egg coat / egg coat / positive regulation of acrosome reaction / positive regulation of ovarian follicle development / humoral immune response mediated by circulating immunoglobulin / regulation of signaling receptor activity / binding of sperm to zona pellucida / oocyte development / blastocyst formation / positive regulation of leukocyte migration / detection of maltose stimulus / positive regulation of interleukin-4 production / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / positive regulation of T cell proliferation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of type II interferon production / positive regulation of inflammatory response / : / outer membrane-bounded periplasmic space / carbohydrate binding / periplasmic space / receptor ligand activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / extracellular space / membrane / plasma membrane
類似検索 - 分子機能
: / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. ...: / Zona pellucida domain, conserved site / ZP domain signature. / : / : / ZP-N domain / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida 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 / TRIETHYLENE GLYCOL / Maltose/maltodextrin-binding periplasmic protein / Zona pellucida sperm-binding protein 3
類似検索 - 構成要素
生物種Escherichia coli K-12 (大腸菌)
Mus musculus (ハツカネズミ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 Å
データ登録者Jovine, L. / Monne, M.
資金援助 スウェーデン, 2件
組織認可番号国
Swedish Research CouncilProject grant 2005-5102 スウェーデン
European UnionMarie Curie ERG 31055
引用
ジャーナル: Nature / 年: 2008
タイトル: Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats
著者: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
#1: ジャーナル: Cell(Cambridge,Mass.) / 年: 1980
タイトル: Mammalian Sperm-Egg Interaction: Identification of a Glycoprotein in Mouse Egg Zonae Pellucidae Possessing Receptor Activity for Sperm
著者: Bleil, J.D. / Wassarman, P.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: Nat Cell Biol / 年: 2002
タイトル: The ZP domain is a conserved module for polymerization of extracellular proteins.
著者: Luca Jovine / Huayu Qi / Zev Williams / Eveline Litscher / Paul M Wassarman /
要旨: Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian ...Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian egg coat proteins, Tamm-Horsfall protein (THP), glycoprotein-2 (GP-2), alpha- and beta-tectorins, transforming growth factor (TGF)-beta receptor III and endoglin, DMBT-1 (deleted in malignant brain tumour-1), NompA (no-mechanoreceptor-potential-A), Dumpy and cuticlin-1 (refs 1,2). Here, we report that the ZP domain of ZP2, ZP3 and THP is responsible for polymerization of these proteins into filaments of similar supramolecular structure. Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors. Our results demonstrate that the C-terminal transmembrane domain and short cytoplasmic tail of ZP2 and ZP3 are not required for secretion, but are essential for assembly. Finally, we suggest a molecular basis for dominant human hearing disorders caused by point mutations within the ZP domain of alpha-tectorin.
#4: ジャーナル: Proc Natl Acad Sci U S A / 年: 2004
タイトル: A duplicated motif controls assembly of zona pellucida domain proteins.
著者: Luca Jovine / Huayu Qi / Zev Williams / Eveline S Litscher / Paul M Wassarman /
要旨: Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) ...Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) domains. ZP domain proteins are synthesized as precursors containing C-terminal propeptides that are cleaved at conserved sites. However, the consequences of this processing and the mechanism by which nascent proteins assemble are unclear. By microinjection of mutated DNA constructs into growing oocytes and mammalian cell transfection, we have identified a conserved duplicated motif [EHP (external hydrophobic patch)/IHP (internal hydrophobic patch)] regulating the assembly of mouse ZP proteins. Whereas the transmembrane domain (TMD) of ZP3 can be functionally replaced by an unrelated TMD, mutations in either EHP or IHP do not hinder secretion of full-length ZP3 but completely abolish its assembly. Because mutants truncated before the TMD are not processed, we conclude that the conserved TMD of mammalian ZP proteins does not engage them in specific interactions but is essential for C-terminal processing. Cleavage of ZP precursors results in loss of the EHP, thereby activating secreted polypeptides to assemble by using the IHP within the ZP domain. Taken together, these findings suggest a general mechanism for assembly of ZP domain proteins.
#5: 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.
#6: ジャーナル: BMC Biochem. / 年: 2006
タイトル: The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation
著者: Jovine, L. / Janssen, W.G. / Litscher, E.S. / Wassarman, P.M.
#7: 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.
#8: ジャーナル: Biol. Reprod. / 年: 2011
タイトル: A structural view of egg coat architecture and function in fertilization
著者: Monne, M. / Jovine, L.
履歴
登録2017年8月18日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02017年9月6日Provider: repository / タイプ: Initial release
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 / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.pdbx_formal_charge / _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.id / _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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年1月17日Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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,Zona pellucida sperm-binding protein 3
B: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)106,97311
ポリマ－105,8982
非ポリマー1,0759
水5,567309
1
A: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,4115
ポリマ－52,9491
非ポリマー4634
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)53,5626
ポリマ－52,9491
非ポリマー6135
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)91.340, 92.160, 140.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))
21(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA33
12LYSLYSLYSLYS(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA4343
13THRTHRTHRTHR(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA346346
21THRTHRTHRTHR(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB33
22LYSLYSLYSLYS(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB4343
23THRTHRTHRTHR(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB346346

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要素

#1: タンパク質 Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3 / MBP / MMBP / Maltodextrin-binding protein / Sperm receptor / Zona pellucida glycoprotein 3 / Zp-3 / ...MBP / MMBP / Maltodextrin-binding protein / Sperm receptor / Zona pellucida glycoprotein 3 / Zp-3 / Zona pellucida protein C


分子量: 52948.945 Da / 分子数: 2
断片: UNP RESIDUES 27-393,ZP3 ZP-N domain, UNP residues 42-143
変異: I28T, E385A, K388A, D389A, R393N / 由来タイプ: 組換発現
詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 2-368 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3T, E360A, ...詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 2-368 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I3T, E360A, K363A, D364A, R368N (CORRESPONDING TO I28T, E385A, K388A, D389A AND R393N IN P0AEX9). RESIDUES 372-473 ARE FROM MOUSE ZP3 PROTEIN AND CORRESPOND TO RESIDUES 42-143 OF SWISS-PROT DATABASE ENTRY P10761.
由来: (組換発現) Escherichia coli K-12 (大腸菌), (組換発現) Mus musculus (ハツカネズミ)
細胞内の位置: EXTRACELLULAR MATRIX / 遺伝子: malE, b4034, JW3994, Zp3, Zp-3, Zpc / プラスミド: PLJMBP4C, PLJDIS1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Origami B / 参照: UniProt: P0AEX9, UniProt: P10761
#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: 2 / 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-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Ca
#4: 化合物 ChemComp-PGE / TRIETHYLENE GLYCOL / トリエチレングリコ-ル


分子量: 150.173 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C6H14O4
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 309 / 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: 2.8 Å3/Da / 溶媒含有率: 56.17 %
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: 7
詳細: SAMPLE: 15MG/ML PROTEIN IN 0.05M SODIUM CHLORIDE, 0.01M TRIS-HCL, PH7.2, 0.001M MALTOSE. RESERVOIR: 10% PEG6000, 0.2M CALCIUM CHLORIDE, 0.1M TRIS-HCL, PH7.0. SAMPLE TO RESERVOIR RATIO IN DROP: ...詳細: SAMPLE: 15MG/ML PROTEIN IN 0.05M SODIUM CHLORIDE, 0.01M TRIS-HCL, PH7.2, 0.001M MALTOSE. RESERVOIR: 10% PEG6000, 0.2M CALCIUM CHLORIDE, 0.1M TRIS-HCL, PH7.0. SAMPLE TO RESERVOIR RATIO IN DROP: 1:1, PH7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K
PH範囲: 7

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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: BM14 / 波長: 0.9535 Å
検出器タイプ: MARRESEARCH / 検出器: CCD / 日付: 2006年12月7日
放射モノクロメーター: SI(111) MONOCHROMATOR / 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: 0.9535 Å / 相対比: 1
反射解像度: 2.05→50 Å / Num. obs: 75254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / 冗長度: 7.43 % / CC1/2: 0.999 / Rsym value: 0.106 / Net I/σ(I): 13.09
反射 シェル解像度: 2.05→2.1 Å / 冗長度: 7.51 % / Mean I/σ(I) obs: 0.67 / Num. unique obs: 5501 / CC1/2: 0.188 / Rsym value: 0.3863 / % possible all: 99.9

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解析

ソフトウェア
名称バージョン分類
XDSJun 1, 2017 BUILT=20170720データ削減
XDSJun 1, 2017 BUILT=20170720データスケーリング
PHASER2.6.0位相決定
PHENIX1.12-2829精密化
精密化構造決定の手法: 分子置換
開始モデル: PDB ENTRY 3D4C

3d4c


解像度: 2.05→32.898 Å / SU ML: 0.34 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 29.84
Rfactor反射数%反射Selection details
Rfree0.2411 1857 2.47 %RANDOM
Rwork0.2091 ---
obs0.2099 75143 99.83 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso mean: 66 Å2
精密化ステップサイクル: LAST / 解像度: 2.05→32.898 Å
タンパク質核酸リガンド溶媒全体
原子数7291 0 62 309 7662
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0117580
X-RAY DIFFRACTIONf_angle_d0.78310266
X-RAY DIFFRACTIONf_dihedral_angle_d12.5532795
X-RAY DIFFRACTIONf_chiral_restr0.0461152
X-RAY DIFFRACTIONf_plane_restr0.0061327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A5614X-RAY DIFFRACTION5.185TORSIONAL
12B5614X-RAY DIFFRACTION5.185TORSIONAL
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.38081800.36537210X-RAY DIFFRACTION100
2.1233-2.20830.36271810.34997250X-RAY DIFFRACTION100
2.2083-2.30870.37871870.33187261X-RAY DIFFRACTION100
2.3087-2.43040.31111800.2897266X-RAY DIFFRACTION100
2.4304-2.58260.2971860.26657265X-RAY DIFFRACTION100
2.5826-2.78190.25741840.25387303X-RAY DIFFRACTION100
2.7819-3.06170.27911910.23857335X-RAY DIFFRACTION100
3.0617-3.50430.24921870.21627353X-RAY DIFFRACTION100
3.5043-4.41340.20181860.16287418X-RAY DIFFRACTION100
4.4134-32.90240.18811950.16077625X-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)
13.16510.63910.95581.43890.25510.8479-0.33680.5470.6031-0.29280.4286-0.1648-0.38350.48130.01890.595-0.24240.09540.5401-0.00980.4903114.30889.001148.8151
20.94470.2452-0.18160.43580.0550.38460.06630.0577-0.13950.11970.0523-0.04610.00840.0359-00.4673-0.0032-0.030.4618-0.08320.426104.441562.953155.1983
32.0187-0.1042-0.08832.46341.10431.3493-0.0841-0.16290.216-0.0794-0.19470.3039-0.0599-0.3228-0.07620.32070.0448-0.00450.4338-0.09910.3355115.331143.297522.3083
40.8995-0.2313-0.34270.50630.07660.40110.10520.0376-0.1603-0.0767-0.1222-0.00980.2210.007500.5076-0.0328-0.01810.39360.0350.3931124.852116.689716.2748
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESI 3:371 OR RESI 900)
2X-RAY DIFFRACTION2CHAIN A AND RESI 372:474
3X-RAY DIFFRACTION3CHAIN B AND (RESI 2:371 OR RESI 900)
4X-RAY DIFFRACTION4CHAIN B AND RESI 372:473

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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

他の情報も見る