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- PDB-3d4g: ZP-N domain of mammalian sperm receptor ZP3 (crystal form II) -

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基本情報

登録情報
データベース: PDB / ID: 3d4g
タイトルZP-N domain of mammalian sperm receptor ZP3 (crystal form II)
要素Maltose-binding periplasmic protein, LINKER, Zona pellucida 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 / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / egg coat / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction ...positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / egg coat / structural constituent of egg coat / acrosin binding / positive regulation of acrosome reaction / positive regulation of ovarian follicle development / binding of sperm to zona pellucida / humoral immune response mediated by circulating immunoglobulin / oocyte development / blastocyst formation / regulation of signaling receptor activity / 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 / extracellular matrix / positive regulation of inflammatory response / positive regulation of type II interferon production / outer membrane-bounded periplasmic space / carbohydrate binding / collagen-containing extracellular matrix / 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, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Zona pellucida, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like 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 / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
類似検索 - ドメイン・相同性
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Zona pellucida sperm-binding protein 3
類似検索 - 構成要素
生物種Escherichia coli (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: 2.3 Å
データ登録者Jovine, L. / Monne, M.
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.
履歴
登録2008年5月14日登録サイト: RCSB / 処理サイト: PDBJ
改定 1.02008年12月2日Provider: repository / タイプ: Initial release
改定 1.12011年7月13日Group: Version format compliance
改定 1.22017年6月28日Group: Source and taxonomy / カテゴリ: entity_src_gen
改定 1.32017年8月23日Group: Data collection / カテゴリ: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_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 / _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_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_asym.entity_id / _struct_ref_seq_dif.details
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12021年11月10日Group: Database references / Structure summary / カテゴリ: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
改定 2.22023年11月1日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED
Remark 40MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V.B.CHEN, R.M.IMMORMINO, J.J.HEADD,W.B.ARENDALL,J.M.WORD AUTHORS: I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE: MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE VALIDATION FOR PROTEINS AND NUCLEIC ACIDS NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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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, LINKER, Zona pellucida protein 3
B: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
C: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
D: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
E: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
F: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
G: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
H: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)427,29240
ポリマ－423,5928
非ポリマー3,70032
水34,8411934
1
A: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
2
B: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
3
C: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
4
D: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
5
E: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
6
F: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
7
G: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
8
H: Maltose-binding periplasmic protein, LINKER, Zona pellucida 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
手法PISA
単位格子
Length a, b, c (Å)91.050, 91.960, 140.480
Angle α, β, γ (deg.)89.99, 90.18, 89.98
Int Tables number1
Space group name H-MP1

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要素

#1: タンパク質
Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3 / Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm ...Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm receptor / Zona pellucida protein C


分子量: 52948.945 Da / 分子数: 8
断片: ZP3 ZP-N domain, UNP residues 27-393, UNP residues 42-143
変異: I3T, E360A, K363A, D364A, R368N / 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 (strain K12) (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: Zp3, Zp-3, Zpc / プラスミド: PLJMBP4C, PLJDIS1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): Origami B (DE3) / 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: 8 / 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: 24 / 由来タイプ: 合成 / 式: Ca
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1934 / 由来タイプ: 天然 / 式: H2O

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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: 2.76 Å3/Da / 溶媒含有率: 55.48 %
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

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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 / 波長: 0.9535 Å
検出器タイプ: MAR CCD 165 mm / 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: 2.3→500 Å / Num. all: 202456 / Num. obs: 193240 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 2 % / Biso Wilson estimate: 48.357 Å2 / Rsym value: 0.05 / Net I/σ(I): 11
反射 シェル解像度: 2.3→2.35 Å / 冗長度: 2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 12935 / Rsym value: 0.529 / % possible all: 95.7

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解析

ソフトウェア
名称バージョン分類
PHASER位相決定
REFMAC5.3.0038精密化
MxCuBEデータ収集
XDSデータ削減
XDSデータスケーリング
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: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.285 / SU ML: 0.196 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.215 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor反射数%反射Selection details
Rfree0.2265 2139 1.1 %RANDOM
Rwork0.2014 ---
obs0.2017 193225 95.45 %-
all-202438 --
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK
原子変位パラメータBiso mean: 50.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0.06 Å2-0.65 Å2
2--0.97 Å2-0.08 Å2
3---0.26 Å2
精密化ステップサイクル: LAST / 解像度: 2.3→50 Å
タンパク質核酸リガンド溶媒全体
原子数29088 0 208 1934 31230
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02230000
X-RAY DIFFRACTIONr_bond_other_d00.0220125
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.97840741
X-RAY DIFFRACTIONr_angle_other_deg4.2073.00249185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52553759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35725.2721286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.755154960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.97415112
X-RAY DIFFRACTIONr_chiral_restr0.0510.24584
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0233225
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025655
X-RAY DIFFRACTIONr_nbd_refined0.1770.26182
X-RAY DIFFRACTIONr_nbd_other0.2170.219936
X-RAY DIFFRACTIONr_nbtor_refined0.1690.214731
X-RAY DIFFRACTIONr_nbtor_other0.1270.213175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.21880
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.292
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.273
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_mcbond_it0.4251.518811
X-RAY DIFFRACTIONr_mcbond_other01.57590
X-RAY DIFFRACTIONr_mcangle_it0.778230174
X-RAY DIFFRACTIONr_scbond_it0.779311189
X-RAY DIFFRACTIONr_scangle_it1.3534.510567
LS精密化 シェル解像度: 2.3→2.36 Å / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.35 174 -
Rwork0.317 14156 -
obs-14330 95.6 %
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)
13.2916-1.95090.37263.6828-0.51432.33440.17210.2019-0.2461-0.5382-0.1210.31970.10110.0515-0.0511-0.10820.0387-0.0053-0.18360.0492-0.2231-38.2227-25.910615.6214
22.85570.40350.57473.3368-1.02571.0943-0.0939-0.1834-0.23780.0237-0.2678-0.63150.03660.44060.3617-0.31560.05350.0057-0.07020.178-0.1759-20.1399-21.964423.634
32.6376-0.7806-0.0352.8283-0.64850.6969-0.0045-0.31970.09550.3605-0.2712-0.3079-0.42220.42540.2757-0.0896-0.0387-0.1272-0.01010.0608-0.1158-23.2823-7.789124.0125
46.9732-2.8859-2.56645.47481.99186.09380.1078-0.00790.2560.0395-0.1254-0.042-0.27840.11280.0175-0.0073-0.02210.0129-0.10010.0017-0.1099-35.78554.550214.7875
56.2957-0.25991.528425.135417.887719.86180.0992-0.84081.05260.74410.2063-1.0458-0.55180.0439-0.30540.1435-0.0879-0.06710.08230.00250.1825-28.66698.991819.432
66.53761.9738-1.80522.9372-0.72781.3162-0.2408-0.1354-1.3631-0.02690.0539-0.40370.208-0.04560.18690.1362-0.1049-0.0433-0.16810.00740.1747-9.6-71.737953.3944
74.47450.2641-0.60462.8036-0.68731.4116-0.33020.782-0.8567-0.49030.49060.37220.5918-0.5523-0.16040.0137-0.3232-0.16320.06330.0373-0.0156-28.1575-67.524546.6485
85.56551.64240.06162.2826-0.67741.0222-0.05290.69590.0986-0.29070.43750.22960.2851-0.5877-0.3846-0.0323-0.1753-0.11820.15640.2013-0.116-25.018-53.348946.6
94.67352.5979-1.75384.5219-1.86144.85510.08710.10870.18350.08640.08740.15520.0866-0.2469-0.1745-0.05020.00220.0219-0.06950.0491-0.0925-11.9714-41.32555.4415
105.1497-1.2391.961725.509-18.712821.07760.02120.70980.85450.00810.4530.747-0.515-0.7679-0.4741-0.05840.02180.0230.13330.15380.0829-19.4166-37.055351.1843
112.93411.688-0.23534.1901-0.45872.14010.1203-0.21070.27910.5318-0.0990.2983-0.05010.1237-0.0212-0.1237-0.03720.0512-0.17210.0333-0.19677.2463-21.323753.7743
122.7616-0.4904-0.64423.3699-0.91811.1622-0.09320.17210.2683-0.0412-0.2694-0.6599-0.03530.47310.3626-0.3186-0.0420.041-0.04590.1928-0.160525.3525-25.261545.7948
133.20550.56190.41163.2921-1.13190.7518-0.04810.2834-0.1318-0.3694-0.2949-0.40610.36330.34920.3429-0.08550.05560.18380.01260.0748-0.114422.0645-39.777145.4762
147.19973.22332.92085.2192.0866.0720.1531-0.0165-0.22030.029-0.1902-0.03960.33310.14490.0371-0.01090.04250.0386-0.08260.0061-0.09789.6364-51.774854.6051
157.072-1.859-1.765127.17318.231320.11050.09750.8705-1.2292-0.65980.2376-0.58230.68220.3892-0.3350.11510.09820.070.0876-0.02150.218916.7286-56.253650.051
1611.82285.1218-0.0596.8102-1.67550.59320.0502-1.27791.90810.1691-0.51180.0219-0.4740.72730.46160.1964-0.1079-0.03120.1563-0.02680.453735.4689-59.321113.0084
1711.9214-1.65030.79152.4784-0.71141.5452-0.1856-0.09230.9030.04560.1911-0.0748-0.2253-0.2388-0.00550.10890.12540.0794-0.1542-0.0447-0.04735.8579-74.98418.8999
184.6243-0.38070.50142.7948-0.83561.397-0.3948-0.76090.85830.55090.51640.399-0.669-0.4529-0.12160.03820.28610.15490.12230.0641-0.018417.3977-71.646222.7059
195.1644-1.61150.36912.9314-0.23710.8683-0.1055-0.6689-0.13020.29210.45280.3135-0.2504-0.5792-0.3473-0.06410.17210.18780.19230.2059-0.123920.6722-86.163622.6881
205.4549-2.70362.35694.7163-2.04585.54210.0933-0.0494-0.0947-0.06190.0940.1542-0.0291-0.2747-0.1873-0.0458-0.00580.0193-0.0790.0609-0.085533.6194-97.85613.9435
216.63681.2061-1.486121.709-16.417419.89770.1127-0.9472-0.95990.03140.53110.92410.6322-0.5165-0.6439-0.0340.00580.0180.15980.19470.09526.08-102.116318.1504
223.45821.73380.39373.71340.34252.05930.1442-0.1626-0.26270.5483-0.1353-0.29370.0562-0.0852-0.0088-0.1066-0.0458-0.0071-0.1907-0.0309-0.209437.0236-25.9217-16.4488
232.7644-0.33250.60933.51031.00731.2774-0.08650.2061-0.2236-0.0293-0.28150.66590.0664-0.48560.368-0.3223-0.06110.0023-0.075-0.171-0.170818.952-21.9812-24.4595
242.0310.5273-0.1753.02851.03480.63560.00560.35010.095-0.3956-0.32320.4273-0.4146-0.42280.3176-0.09060.0474-0.12450.0032-0.0535-0.082622.096-7.8093-24.85
256.85012.7739-2.67655.4429-2.23266.22240.1121-0.07160.2362-0.021-0.13720.0928-0.3013-0.08660.0251-0.01070.01830.0069-0.0980.0092-0.103434.59754.5287-15.6263
267.1631-0.7211.024731.2542-21.598220.87250.25170.73371.2484-0.88330.04310.9022-0.1014-0.261-0.29480.06910.1051-0.03160.05490.02610.117427.55478.2866-19.4704
273.0816-2.0218-0.2914.93620.36242.02430.11610.1910.3025-0.5577-0.138-0.2901-0.0604-0.06720.0219-0.11990.02860.0446-0.1571-0.0223-0.201-8.8894-21.319285.8194
282.8830.3805-0.4953.34310.97811.1722-0.1297-0.25440.30010.001-0.26820.6643-0.0372-0.46870.3979-0.31090.0470.0272-0.0514-0.1795-0.1586-26.989-25.255993.8122
292.4517-0.36920.15793.68521.43471.4462-0.0067-0.4531-0.06940.2789-0.32180.42520.3832-0.39250.3285-0.0984-0.05760.16930.0282-0.0525-0.1019-23.7118-39.766694.1391
307.1581-3.12182.80755.2074-1.84986.24250.1820.0715-0.230.0368-0.1790.09630.3263-0.0739-0.0030.0136-0.03740.027-0.09930.0137-0.1049-11.2931-51.767885.0078
317.9596-1.53060.57922.2294-16.805320.60020.276-0.9763-1.21020.27440.42721.25690.7906-0.4074-0.70320.0724-0.0830.04010.09180.02240.1478-18.5612-55.436288.7733
326.28982.32152.0772.99870.82131.0551-0.3465-0.18091.3422-0.10520.09080.4048-0.19420.02850.25570.1193-0.11060.0426-0.1658-0.02050.1721-37.2052-67.4765-16.7994
335.03430.14510.77962.73830.65391.2393-0.3960.76230.9036-0.48610.5458-0.4068-0.57750.5879-0.14980.0036-0.34140.18190.0818-0.0439-0.0202-18.6482-71.6957-23.5127
345.14851.01810.06843.0963-0.1180.8994-0.10110.7046-0.1067-0.34360.4782-0.3967-0.26390.6008-0.3771-0.0403-0.18620.18020.1911-0.1905-0.1056-21.804-85.8727-23.5722
355.63833.0412.99244.67251.84125.90250.13660.045-0.09850.09680.0332-0.13750.0290.3264-0.1698-0.07340.01760.0277-0.0617-0.0445-0.0757-34.8797-97.8859-14.7712
365.7703-2.2572-1.944716.664612.095817.02020.09450.5778-0.7170.03740.4424-0.55990.69570.7775-0.5369-0.04530.01360.02050.1731-0.13790.0858-27.5552-101.2934-18.3342
378.37292.4729-2.98764.07160.23391.439-0.391-0.0279-1.837-0.1371-0.1950.04590.4521-0.40740.5860.20520.0172-0.0215-0.0297-0.11040.48348.4218-79.843983.2563
3811.5134-2.7829-0.09482.4010.60161.0568-0.105-0.0371-0.72120.02750.18420.10380.21210.154-0.07920.12490.1045-0.0451-0.14810.0678-0.06318.0453-64.180389.1426
394.3962-0.3564-0.51292.69810.85621.5483-0.377-0.7812-0.81850.54710.4974-0.36250.65020.4509-0.12050.04690.2894-0.15510.1049-0.0422-0.024426.4874-67.524292.9546
404.8335-1.1012-0.49682.95720.77640.5512-0.103-0.65990.05250.45610.4469-0.40730.23240.5874-0.344-0.02610.1865-0.15270.1968-0.1836-0.093123.3574-53.338493.0103
415.4683-2.9112-2.5865.62262.36766.0230.1158-0.06460.1649-0.10430.1035-0.1760.08220.2831-0.2194-0.0771-0.01410.0195-0.0513-0.029-0.107210.3195-41.310884.1695
425.4609-0.1051.22324.985320.104522.419-0.2119-0.62870.9606-0.03041.0041-1.0757-0.57491.0645-0.79230.0043-0.0150.00110.147-0.14180.141717.8477-37.126588.4651
精密化 TLSグループ
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 793 - 79
2X-RAY DIFFRACTION1AI4821
3X-RAY DIFFRACTION2AA80 - 32080 - 320
4X-RAY DIFFRACTION3AA321 - 370321 - 370
5X-RAY DIFFRACTION4AA371 - 449371 - 449
6X-RAY DIFFRACTION5AA450 - 473450 - 473
7X-RAY DIFFRACTION6BB3 - 793 - 79
8X-RAY DIFFRACTION6BJ4821
9X-RAY DIFFRACTION7BB80 - 32080 - 320
10X-RAY DIFFRACTION8BB321 - 370321 - 370
11X-RAY DIFFRACTION9BB371 - 449371 - 449
12X-RAY DIFFRACTION10BB450 - 473450 - 473
13X-RAY DIFFRACTION11CC3 - 793 - 79
14X-RAY DIFFRACTION11CK4821
15X-RAY DIFFRACTION12CC80 - 32180 - 321
16X-RAY DIFFRACTION13CC322 - 370322 - 370
17X-RAY DIFFRACTION14CC371 - 449371 - 449
18X-RAY DIFFRACTION15CC450 - 473450 - 473
19X-RAY DIFFRACTION16DD5 - 415 - 41
20X-RAY DIFFRACTION17DD42 - 7942 - 79
21X-RAY DIFFRACTION17DL4821
22X-RAY DIFFRACTION18DD80 - 32180 - 321
23X-RAY DIFFRACTION19DD322 - 370322 - 370
24X-RAY DIFFRACTION20DD371 - 449371 - 449
25X-RAY DIFFRACTION21DD450 - 473450 - 473
26X-RAY DIFFRACTION22EE3 - 793 - 79
27X-RAY DIFFRACTION22EM4821
28X-RAY DIFFRACTION23EE80 - 32080 - 320
29X-RAY DIFFRACTION24EE321 - 370321 - 370
30X-RAY DIFFRACTION25EE371 - 449371 - 449
31X-RAY DIFFRACTION26EE450 - 474450 - 474
32X-RAY DIFFRACTION27FF3 - 793 - 79
33X-RAY DIFFRACTION27FN4821
34X-RAY DIFFRACTION28FF80 - 32180 - 321
35X-RAY DIFFRACTION29FF322 - 370322 - 370
36X-RAY DIFFRACTION30FF371 - 449371 - 449
37X-RAY DIFFRACTION31FF450 - 474450 - 474
38X-RAY DIFFRACTION32GG3 - 793 - 79
39X-RAY DIFFRACTION32GO4821
40X-RAY DIFFRACTION33GG80 - 32080 - 320
41X-RAY DIFFRACTION34GG321 - 370321 - 370
42X-RAY DIFFRACTION35GG371 - 449371 - 449
43X-RAY DIFFRACTION36GG450 - 474450 - 474
44X-RAY DIFFRACTION37HH5 - 415 - 41
45X-RAY DIFFRACTION38HH42 - 7942 - 79
46X-RAY DIFFRACTION38HP4821
47X-RAY DIFFRACTION39HH80 - 32080 - 320
48X-RAY DIFFRACTION40HH321 - 370321 - 370
49X-RAY DIFFRACTION41HH371 - 449371 - 449
50X-RAY DIFFRACTION42HH450 - 473450 - 473

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万見について

-
お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

-
2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.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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