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- PDB-8bqu: Molecular basis of ZP3/ZP1 heteropolymerization: crystal structur... -

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基本情報

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データベース: PDB / ID: 8bqu
タイトルMolecular basis of ZP3/ZP1 heteropolymerization: crystal structure of a native vertebrate egg coat filament
要素
  • (Choriogenin H) x 2
  • Zona pellucida sperm-binding protein 3
キーワードSTRUCTURAL PROTEIN / Cell adhesion / fertilization / egg-sperm interaction / gamete recognition / sperm receptor / extracellular matrix / egg coat / zona pellucida / vitelline envelope / fish chorion / glycoprotein / N-glycan / ZP module / ZP-N domain / ZP_C domain / trefoil domain / medaka / Japanese rice fish
機能・相同性
機能・相同性情報


egg coat formation / structural constituent of egg coat / egg coat / positive regulation of acrosome reaction / binding of sperm to zona pellucida / single fertilization / extracellular region / plasma membrane
類似検索 - 分子機能
: / : / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Zona pellucida domain, conserved site / ZP domain signature. ...: / : / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain
類似検索 - ドメイン・相同性
Zona pellucida sperm-binding protein 4 / Zona pellucida sperm-binding protein 3
類似検索 - 構成要素
生物種Oryzias latipes (ヒメダカ)
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. / de Sanctis, D. / Yasumasu, S. / Jovine, L.
資金援助 スウェーデン, 3件
組織認可番号国
Swedish Research Council2016-03999 スウェーデン
Swedish Research Council2020-04936 スウェーデン
Knut and Alice Wallenberg Foundation2018.0042 スウェーデン
引用
ジャーナル: Cell / 年: 2024
タイトル: ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat.
著者: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu / ...著者: Shunsuke Nishio / Chihiro Emori / Benjamin Wiseman / Dirk Fahrenkamp / Elisa Dioguardi / Sara Zamora-Caballero / Marcel Bokhove / Ling Han / Alena Stsiapanava / Blanca Algarra / Yonggang Lu / Mayo Kodani / Rachel E Bainbridge / Kayla M Komondor / Anne E Carlson / Michael Landreh / Daniele de Sanctis / Shigeki Yasumasu / Masahito Ikawa / Luca Jovine /
要旨: Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N- ...Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
#1: ジャーナル: J Mol Biol / 年: 1985
タイトル: Mouse egg extracellular coat is a matrix of interconnected filaments possessing a structural repeat.
著者: Greve, J.M. / Wassarman, P.M.
#2: ジャーナル: J Biochem / 年: 1989
タイトル: Purification and partial characterization of high choriolytic enzyme (HCE), a component of the hatching enzyme of the teleost, Oryzias latipes.
著者: Yasumasu, S. / Yamagami, K. / Iuchi, I.
#3: ジャーナル: J Biochem / 年: 1989
タイトル: Isolation and some properties of low choriolytic enzyme (LCE), a component of the hatching enzyme of the teleost, Oryzias latipes.
著者: Yasumasu, S. / Iuchi, I. / Yamagami, K.
#4: ジャーナル: Dev Biol / 年: 1992
タイトル: Isolation of cDNAs for LCE and HCE, two constituent proteases of the hatching enzyme of Oryzias latipes, and concurrent expression of their mRNAs during development.
著者: Yasumasu, S. / Yamada, K. / Akasaka, K. / Mitsunaga, K. / Iuchi, I. / Shimada, H. / Yamagami, K.
#5: ジャーナル: Proc Natl Acad Sci U S A / 年: 1997
タイトル: Cloning of cDNA and estrogen-induced hepatic gene expression for choriogenin H, a precursor protein of the fish egg envelope (chorion).
著者: Murata, K. / Sugiyama, H. / Yasumasu, S. / Iuchi, I. / Yasumasu, I. / Yamagami, K.
#6: ジャーナル: Dev Biol / 年: 1995
タイトル: Cloning of cDNAs for the precursor protein of a low-molecular-weight subunit of the inner layer of the egg envelope (chorion) of the fish Oryzias latipes.
著者: Murata, K. / Sasaki, T. / Yasumasu, S. / Iuchi, I. / Enami, J. / Yasumasu, I. / Yamagami, K.
#7: ジャーナル: Dev Growth Differ / 年: 1998
タイトル: The third egg envelope subunit in fish: cDNA cloning and analysis, and gene expression.
著者: Sugiyama, H. / Yasumasu, S. / Murata, K. / Iuchi, I. / Yamagami, K.
#8: ジャーナル: J Biochem / 年: 1999
タイトル: Formation of mature egg envelope subunit proteins from their precursors (choriogenins) in the fish, Oryzias latipes: loss of partial C-terminal sequences of the choriogenins.
著者: Sugiyama, H. / Murata, K. / Iuchi, I. / Nomura, K. / Yamagami, K.
#9: 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.
#10: ジャーナル: J Biochem / 年: 2010
タイトル: Mechanism of egg envelope digestion by hatching enzymes, HCE and LCE in medaka, Oryzias latipes.
著者: Yasumasu, S. / Kawaguchi, M. / Ouchi, S. / Sano, K. / Murata, K. / Sugiyama, H. / Akema, T. / Iuchi, I.
#11: 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.
#12: ジャーナル: Curr Top Dev Biol / 年: 2018
タイトル: Structure of Zona Pellucida Module Proteins.
著者: Marcel Bokhove / Luca Jovine /
要旨: The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common ...The egg coat, an extracellular matrix made up of glycoprotein filaments, plays a key role in animal fertilization by acting as a gatekeeper for sperm. Egg coat components polymerize using a common zona pellucida (ZP) "domain" module that consists of two related immunoglobulin-like domains, called ZP-N and ZP-C. The ZP module has also been recognized in a large number of other secreted proteins with different biological functions, whose mutations are linked to severe human diseases. During the last decade, tremendous progress has been made toward understanding the atomic architecture of the ZP module and the structural basis of its polymerization. Moreover, sperm-binding regions at the N-terminus of mollusk and mammalian egg coat subunits were found to consist of domain repeats that also adopt a ZP-N fold. This discovery revealed an unexpected link between invertebrate and vertebrate fertilization and led to the first structure of an egg coat-sperm protein recognition complex. In this review we summarize these exciting findings, discuss their functional implications, and outline future challenges that must be addressed in order to develop a comprehensive view of this family of biomedically important extracellular molecules.
#13: ジャーナル: EMBO J / 年: 2020
タイトル: Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.
著者: Alena Stsiapanava / Chenrui Xu / Martina Brunati / Sara Zamora-Caballero / Céline Schaeffer / Marcel Bokhove / Ling Han / Hans Hebert / Marta Carroni / Shigeki Yasumasu / Luca Rampoldi / Bin ...著者: Alena Stsiapanava / Chenrui Xu / Martina Brunati / Sara Zamora-Caballero / Céline Schaeffer / Marcel Bokhove / Ling Han / Hans Hebert / Marta Carroni / Shigeki Yasumasu / Luca Rampoldi / Bin Wu / Luca Jovine /
要旨: Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous ...Assembly of extracellular filaments and matrices mediating fundamental biological processes such as morphogenesis, hearing, fertilization, and antibacterial defense is driven by a ubiquitous polymerization module known as zona pellucida (ZP) "domain". Despite the conservation of this element from hydra to humans, no detailed information is available on the filamentous conformation of any ZP module protein. Here, we report a cryo-electron microscopy study of uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant protein in human urine and an archetypal ZP module-containing molecule, in its mature homopolymeric state. UMOD forms a one-start helix with an unprecedented 180-degree twist between subunits enfolded by interdomain linkers that have completely reorganized as a result of propeptide dissociation. Lateral interaction between filaments in the urine generates sheets exposing a checkerboard of binding sites to capture uropathogenic bacteria, and UMOD-based models of heteromeric vertebrate egg coat filaments identify a common sperm-binding region at the interface between subunits.
#14: ジャーナル: Zoological Lett / 年: 2022
タイトル: Targeted deletion of liver-expressed Choriogenin L results in the production of soft eggs and infertility in medaka, Oryzias latipes.
著者: Murata, K. / Kinoshita, M.
履歴
登録2022年11月21日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02024年3月13日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / Structure summary / カテゴリ: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _struct.title
改定 1.22024年11月6日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Zona pellucida sperm-binding protein 3
B: Choriogenin H
C: Choriogenin H
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)72,7604
ポリマ－71,4843
非ポリマー1,2761
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: 電子顕微鏡法, Fragments belonging to adjacent asymmetric units pack head-to-tail to reconstitute the native heteropolymeric state of their components, generating pseudo-infinite ...根拠: 電子顕微鏡法, Fragments belonging to adjacent asymmetric units pack head-to-tail to reconstitute the native heteropolymeric state of their components, generating pseudo-infinite filaments that run parallel to the long c axis of the crystal unit cells.
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)59.059, 59.059, 473.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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要素

#1: タンパク質 Zona pellucida sperm-binding protein 3


分子量: 34873.172 Da / 分子数: 1 / 由来タイプ: 天然 / 詳細: ZP-N domain + interdomain linker + ZP-C domain / 由来: (天然) Oryzias latipes (ヒメダカ) / 参照: UniProt: Q91184
#2: タンパク質 Choriogenin H


分子量: 18734.260 Da / 分子数: 1 / 由来タイプ: 天然
詳細: C-terminal half of the ZP-N/ZP-C interdomain linker + ZP-C domain
由来: (天然) Oryzias latipes (ヒメダカ) / 参照: UniProt: P79817
#3: タンパク質 Choriogenin H


分子量: 17876.166 Da / 分子数: 1 / 由来タイプ: 天然
詳細: Trefoil domain + ZP-N domain + N-terminal half of the ZP-N/ZP-C interdomain linker
由来: (天然) Oryzias latipes (ヒメダカ) / Plasmid details: Egg vitelline envelope / 参照: UniProt: P79817
#4: 多糖 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharide / 分子量: 1276.157 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
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
研究の焦点であるリガンドがあるかY
Has protein modificationY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 3.46 Å3/Da / 溶媒含有率: 64.16 % / 解説: Bipyramidal prismatic
結晶化温度: 277.15 K / 手法: 蒸気拡散法 / pH: 8
詳細: 22% (w/v) PEG 3350, 0.2 M sodium/potassium phosphate, 0.1 M Tris-HCl pH 8.0

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I02 / 波長: 0.97938 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年11月29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: 0.97938 Å / 相対比: 1
反射解像度: 2.419→51.147 Å / Num. obs: 14348 / % possible obs: 89.9 % / 冗長度: 4.39 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.994 / CC1/2 anomalous: 0.026 / Rmerge(I) obs: 0.1987 / Rpim(I) all: 0.1024 / Rrim(I) all: 0.2248 / AbsDiff over sigma anomalous: 0.803 / Baniso tensor eigenvalue 1: 124.6775 Å2 / Baniso tensor eigenvalue 2: 124.6775 Å2 / Baniso tensor eigenvalue 3: 0 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 3.96 Å / Aniso diffraction limit 2: 3.96 Å / Aniso diffraction limit 3: 2.257 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 6.17 / Num. measured all: 63019 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 88.6 / % possible ellipsoidal: 89.9 / % possible ellipsoidal anomalous: 88.6 / % possible spherical: 37.3 / % possible spherical anomalous: 33 / Redundancy anomalous: 2.61 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
9.658-51.1473.780.046918.05271027107167160.9980.2790.02520.05380.77199.49799.49799.42.8497
7.56-9.6584.70.08113.63337533757187180.996-0.0570.03990.09070.79610098.610098.61002.9298.6
6.543-7.564.240.15217.9304130417187180.989-0.0790.07910.17250.76699.899.299.899.299.82.699.2
5.917-6.5434.380.20096.38315731577207200.987-0.0050.10460.22760.83199.298.599.298.599.22.6298.5
5.479-5.9174.890.19636.71348734877137130.992-0.0350.09580.21960.79399.898.399.898.399.82.8898.3
5.138-5.4794.90.18336.99352635267207200.993-0.0290.09010.20520.75798.89998.89998.82.899
4.866-5.1384.820.19696.47345434547167160.993-0.0190.09770.22110.81299.199.299.199.299.12.8899.2
4.647-4.8664.730.24735.55339233927177170.9920.0750.12410.27780.83210099.410099.41002.6699.4
4.464-4.6474.320.22095.54310931097197190.9900.11490.250.79199.899.699.899.699.82.5199.6
4.303-4.4644.650.28754.95333633367177170.991-0.0320.14620.32380.8199.899.499.899.499.82.699.4
4.163-4.3034.80.34454.24344434447177170.9860.0070.17060.38640.79299.598.299.598.299.52.7798.2
4.015-4.1634.960.32744.76354935497167160.9830.0240.15860.36510.78580.281.280.281.280.22.7881.2
3.839-4.0154.640.32384.91334333437207200.976-0.0550.16410.36450.80568.171.968.158.155.82.6771.9
3.663-3.8394.560.32414.75326632667167160.976-0.0210.16690.36620.76476.97976.950.846.92.6179
3.492-3.6634.50.3624.35324032407207200.980.0020.1860.40890.83783.284.983.241.838.52.684.9
3.319-3.4924.240.31534.66302530257137130.9820.0620.16710.35880.84183.386.783.33430.42.4886.7
3.136-3.3194.090.35834.29294229427207200.963-0.0020.19230.40880.81584.285.484.226.222.92.3985.4
2.945-3.1363.930.37544.04281328137167160.970.0450.20430.430.84383.384.783.319.9172.3484.7
2.745-2.9453.650.49933.11261226127167160.8670.1010.28380.57830.83985.588.785.514.511.52.288.7
2.419-2.7453.050.61482.17219821987207200.720.0060.38890.73370.75461.97061.96.14.11.9270

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解析

ソフトウェア
名称バージョン分類
autoPROC1.0.5 20220608data processing
XDSJan 10, 2022データ削減
Aimless0.7.9データスケーリング
PHASER2.8.3位相決定
PHENIXdev_4742精密化
STARANISO2.3.87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: Ensemble derived from PDB ID 7ZBM

7zbm
PDB 未公開エントリ


解像度: 2.7→51.147 Å / SU ML: 0.3019 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 24.9194
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.307 646 4.69 %
Rwork0.2473 13141 -
obs0.25 13787 49.46 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 25.55 Å2
精密化ステップサイクル: LAST / 解像度: 2.7→51.147 Å
タンパク質核酸リガンド溶媒全体
原子数4766 0 86 0 4852
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00324978
X-RAY DIFFRACTIONf_angle_d0.60356800
X-RAY DIFFRACTIONf_chiral_restr0.0461790
X-RAY DIFFRACTIONf_plane_restr0.006877
X-RAY DIFFRACTIONf_dihedral_angle_d11.0631803
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.970.4926500.3343936X-RAY DIFFRACTION14.61
2.97-3.40.3742790.30071595X-RAY DIFFRACTION24.5
3.4-4.290.32021460.24973734X-RAY DIFFRACTION55.87
4.29-51.1470.27643710.23066876X-RAY DIFFRACTION98.79
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)
1-0.0019168707210.00600642813723-0.003540535822720.0106199164748-0.003088899631190.00457009150290.003890428141880.0118791545469-0.007038348370640.0002297912593730.001702884803030.0133077920582-0.015996918023-0.008072809352284.82178806033E-90.267197921707-0.05806951024990.1083005623940.04471782766960.02312054090590.031410660595725.5161767554-19.1597344069-5.76830899184
20.001260286963490.0117597698194-0.003698759925690.00157817185278-8.25725494654E-50.0032742923515-0.008711124573490.05700300631990.00477439059358-0.0596459981276-0.0210607365670.003560135144010.00416126361157-0.0115598217881-7.90064981524E-10-0.106426619898-0.193279432517-0.0691447016627-0.122144022768-0.0514484901039-0.10540655384230.5103314531-20.7940964223-45.3016360698
30.000440768985925-0.0003899135339550.0001245924794990.000106084797618-9.46589044384E-58.12105202252E-50.001561874248570.000985025742157-0.00234892999653-0.001916978978810.000402092910813-0.000946135439334-0.00531467631431-0.000162916802477-3.87549680502E-70.2721278445750.0103626260727-0.01398216778440.261917188694-0.01368120820980.28775488432940.1023670793-5.36900410377-49.2231777627
40.0004301300499390.001540748627960.001136456900150.000846993266259-0.0001131022520970.000382756463219-0.003557284771960.005969288260340.00605975008842-0.00302156998383-0.003758926482380.00191020724422-0.00296735593623-0.00531750230853-5.31532243085E-90.328033094816-0.0942653923056-0.09955926026270.31457147440.01773212443440.3178356825743.0735893028-3.11953579398-87.1656681534
50.001483168828290.01822088381360.002679783317210.003338172243585.76829506209E-50.00197701549898-0.0124269797073-0.0152719148199-0.0291198485969-0.00243151832562-0.008737329321150.01032676782420.0055426855610.00464801449891-5.32162204053E-90.0662952723004-0.251805451872-0.1240215573180.0590240904617-0.03136642687280.094327484547834.0729064612-20.4974291489-84.1785176739
60.01151219909510.0173572842444-0.001524998648010.007711286104910.001464258720530.003667658405890.01296371663190.00648837111953-0.007474862855580.02694982724870.0185455691929-0.054030537555-0.003292675986680.00441042987072-6.94767419448E-10-0.109566891918-0.0504356528196-0.04538876647080.206930371018-0.009357556234390.060587217626333.6043746177-21.3123163558-125.282336729
70.000316080220929-0.000335045296069-0.0002464735442526.23935195871E-50.001118140873660.00110242509524-0.00170030357988-0.00292521422593-0.00381799070348-0.00251462016990.002047865052373.82382866704E-50.00199002431852-0.001095902761633.18668976164E-60.338540606779-0.0022072061129-0.01778399492140.352897806630.006676376591760.35758890908323.4827577547-28.5804141622-156.237713862
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resi 77:181)AA77 - 181
2X-RAY DIFFRACTION2(chain B and resi 398:405)BB398 - 405
3X-RAY DIFFRACTION3(chain B and resi 406:423)BB406 - 423
4X-RAY DIFFRACTION4(chain C and resi 229:269)CC229 - 269
5X-RAY DIFFRACTION5(chain C and resi 270:373)CC270 - 373
6X-RAY DIFFRACTION6(chain A and resi 207:363)AA207 - 363
7X-RAY DIFFRACTION7(chain A and resi 364:374)AA364 - 374
8X-RAY DIFFRACTION1(chain B and resi 388:397)BB388 - 397
9X-RAY DIFFRACTION2(chain B and resi 424:552)BB424 - 552
10X-RAY DIFFRACTION5(chain A and resi 194:206)AA194 - 206
11X-RAY DIFFRACTION5(chain C and resi 374:387)CC374 - 387
12X-RAY DIFFRACTION2(chain A and resi 182:193)AA182 - 193

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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