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- PDB-6tqk: Cryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (... -

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データベース: PDB / ID: 6tqk
タイトルCryo-EM of native human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament.
要素Uromodulin
キーワードSTRUCTURAL PROTEIN (タンパク質) / ZP MODULE / ZP DOMAIN / ZP-N DOMAIN / ZP-C DOMAIN / INTERDOMAIN LINKER / EGF DOMAIN (EGF様ドメイン) / EXTRACELLULAR MATRIX (細胞外マトリックス) / GLYCOPROTEIN (糖タンパク質) / N-GLYCAN (N-結合型グリコシル化) / PROTEIN FILAMENT / PROTEIN POLYMERIZATION
機能・相同性
機能・相同性情報


citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / Asparagine N-linked glycosylation / protein transport into plasma membrane raft / urate transport / 排尿 / organ or tissue specific immune response ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / urea transmembrane transport / Asparagine N-linked glycosylation / protein transport into plasma membrane raft / urate transport / 排尿 / organ or tissue specific immune response / metanephric ascending thin limb development / antibacterial innate immune response / collecting duct development / protein localization to vacuole / renal urate salt excretion / regulation of protein transport / intracellular phosphate ion homeostasis / renal sodium ion absorption / intracellular chloride ion homeostasis / クレアチニンクリアランス / juxtaglomerular apparatus development / neutrophil migration / response to water deprivation / intracellular sodium ion homeostasis / potassium ion homeostasis / endoplasmic reticulum organization / regulation of urine volume / renal water homeostasis / IgG binding / ciliary membrane / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / extrinsic component of membrane / multicellular organismal response to stress / cellular response to unfolded protein / cellular defense response / side of membrane / chaperone-mediated protein folding / : / tumor necrosis factor-mediated signaling pathway / RNA splicing / apoptotic signaling pathway / 繊毛 / lipid metabolic process / intracellular calcium ion homeostasis / 血圧 / オートファジー / 紡錘体 / Golgi lumen / basolateral plasma membrane / defense response to Gram-negative bacterium / response to lipopolysaccharide / response to xenobiotic stimulus / 炎症 / apical plasma membrane / negative regulation of cell population proliferation / calcium ion binding / 細胞膜 / 小胞体 / extracellular space / extracellular exosome / 生体膜
類似検索 - 分子機能
: / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / EGF様ドメイン / Zona pellucida-like domain / Zona pellucida (ZP) domain / EGF様ドメイン / ZP domain profile. / Zona pellucida domain ...: / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / EGF様ドメイン / Zona pellucida-like domain / Zona pellucida (ZP) domain / EGF様ドメイン / ZP domain profile. / Zona pellucida domain / Calcium-binding EGF domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF様ドメイン
類似検索 - ドメイン・相同性
生物種Homo sapiens (ヒト)
手法電子顕微鏡法 / らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 3.35 Å
データ登録者Stsiapanava, A. / Xu, C. / Carroni, M. / Wu, B. / Jovine, L.
資金援助 スウェーデン, シンガポール, 4件
組織認可番号
Swedish Research Council2016-03999 スウェーデン
Knut and Alice Wallenberg Foundation2018.0042 スウェーデン
Ministry of Education (MoE, Singapore)2017-T1-001-168 シンガポール
Ministry of Education (MoE, Singapore)2016-T2-1-010 シンガポール
引用
ジャーナル: EMBO J / : 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.
#1: ジャーナル: Proc Soc Exp Biol Med / : 1950
タイトル: Characterization and separation of an inhibitor of viral hemagglutination present in urine.
#2: ジャーナル: Biol. Cellulaire / : 1980
タイトル: Etude chimique et ultrastructurale de la glycoproteine de Tamm et Horsfall ou uromucoide.
著者: Delain, E. / Thiery, J.P. / Coulard, D. / Joliviene, A. / Hartman, L.
#3: ジャーナル: Science / : 1987
タイトル: Identification of human uromodulin as the Tamm-Horsfall urinary glycoprotein.
要旨: The primary structure of human uromodulin, a 616-amino acid, 85-kilodalton glycoprotein with in vitro immunosuppressive properties, was determined through isolation and characterization of ...The primary structure of human uromodulin, a 616-amino acid, 85-kilodalton glycoprotein with in vitro immunosuppressive properties, was determined through isolation and characterization of complementary DNA and genomic clones. The amino acid sequence encoded by one of the exons of the uromodulin gene has homology to the low-density-lipoprotein receptor and the epidermal growth factor precursor. Northern hybridization analyses demonstrate that uromodulin is synthesized by the kidney. Evidence is provided that uromodulin is identical to the previously characterized Tamm-Horsfall glycoprotein, the most abundant protein in normal human urine.
#4: ジャーナル: Nat Cell Biol / : 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.
#5: ジャーナル: Am J Kidney Dis / : 2003
タイトル: Tamm-Horsfall glycoprotein: biology and clinical relevance.
著者: Franca Serafini-Cessi / Nadia Malagolini / Daniela Cavallone /
要旨: Tamm-Horsfall glycoprotein (THP) is the most abundant urinary protein in mammals. Urinary excretion occurs by proteolytic cleavage of the large ectodomain of the glycosyl phosphatidylinositol- ...Tamm-Horsfall glycoprotein (THP) is the most abundant urinary protein in mammals. Urinary excretion occurs by proteolytic cleavage of the large ectodomain of the glycosyl phosphatidylinositol-anchored counterpart exposed at the luminal cell surface of the thick ascending limb of Henle's loop. We describe the physical-chemical structure of human THP and its biosynthesis and interaction with other proteins and leukocytes. The clinical relevance of THP reported here includes: (1) involvement in the pathogenesis of cast nephropathy, urolithiasis, and tubulointerstitial nephritis; (2) abnormalities in urinary excretion in renal diseases; and (3) the recent finding that familial juvenile hyperuricemic nephropathy and autosomal dominant medullary cystic kidney disease 2 arise from mutations of the THP gene. We critically examine the literature on the physiological role and mechanism(s) that promote urinary excretion of THP. Some lines of research deal with the in vitro immunoregulatory activity of THP, termed uromodulin when isolated from urine of pregnant women. However, an immunoregulatory function in vivo has not yet been established. In the most recent literature, there is renewed interest in the capacity of urinary THP to compete efficiently with urothelial cell receptors, such as uroplakins, in adhering to type 1 fimbriated Escherichia coli. This property supports the notion that abundant THP excretion in urine is promoted in the host by selective pressure to obtain an efficient defense against urinary tract infections caused by uropathogenic bacteria.
#6: ジャーナル: Proc Natl Acad Sci U S A / : 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.
#7: ジャーナル: Annu Rev Biochem / : 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.
#8: ジャーナル: Mol Biol Cell / : 2009
タイトル: Analysis of uromodulin polymerization provides new insights into the mechanisms regulating ZP domain-mediated protein assembly.
著者: Céline Schaeffer / Sara Santambrogio / Simone Perucca / Giorgio Casari / Luca Rampoldi /
要旨: Uromodulin is the most abundant protein secreted in urine, in which it is found as a high-molecular-weight polymer. Polymerization occurs via its zona pellucida (ZP) domain, a conserved module shared ...Uromodulin is the most abundant protein secreted in urine, in which it is found as a high-molecular-weight polymer. Polymerization occurs via its zona pellucida (ZP) domain, a conserved module shared by many extracellular eukaryotic proteins that are able to assemble into matrices. In this work, we identified two motifs in uromodulin, mapping in the linker region of the ZP domain and in between protein cleavage and glycosylphosphatidylinositol (GPI)-anchoring sites, which regulate its polymerization. Indeed, mutations in either module led to premature intracellular polymerization of a soluble uromodulin isoform, demonstrating the inhibitory role of these motifs for ZP domain-mediated protein assembly. Proteolytic cleavage separating the external motif from the mature monomer is necessary to release the inhibitory function and allow protein polymerization. Moreover, we report absent or abnormal assembly into filaments of GPI-anchored uromodulin mutated in either the internal or the external motif. This effect is due to altered processing on the plasma membrane, demonstrating that the presence of the two modules has not only an inhibitory function but also can positively regulate protein polymerization. Our data expand previous knowledge on the control of ZP domain function and suggest a common mechanism regulating polymerization of ZP domain proteins.
#9: ジャーナル: Cell / : 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.
#10: ジャーナル: Kidney Int / : 2011
タイトル: The rediscovery of uromodulin (Tamm-Horsfall protein): from tubulointerstitial nephropathy to chronic kidney disease.
著者: Luca Rampoldi / Francesco Scolari / Antonio Amoroso / Gianmarco Ghiggeri / Olivier Devuyst /
要旨: Uromodulin (Tamm-Horsfall protein) is the most abundant protein excreted in the urine under physiological conditions. It is exclusively produced in the kidney and secreted into the urine via ...Uromodulin (Tamm-Horsfall protein) is the most abundant protein excreted in the urine under physiological conditions. It is exclusively produced in the kidney and secreted into the urine via proteolytic cleavage. Its biological function is still not fully understood. Uromodulin has been linked to water/electrolyte balance and to kidney innate immunity. Also, studies in knockout mice demonstrated that it has a protective role against urinary tract infections and renal stone formation. Mutations in the gene encoding uromodulin lead to rare autosomal dominant diseases, collectively referred to as uromodulin-associated kidney diseases. They are characterized by progressive tubulointerstitial damage, impaired urinary concentrating ability, hyperuricemia, renal cysts, and progressive renal failure. Novel in vivo studies point at intracellular accumulation of mutant uromodulin as a key primary event in the disease pathogenesis. Recently, genome-wide association studies identified uromodulin as a risk factor for chronic kidney disease (CKD) and hypertension, and suggested that the level of uromodulin in the urine could represent a useful biomarker for the development of CKD. In this review, we summarize these recent investigations, ranging from invalidation studies in mouse to Mendelian disorders and genome-wide associations, which led to a rediscovery of uromodulin and boosted the scientific and clinical interest for this long discovered molecule.
#11: ジャーナル: Elife / : 2015
タイトル: The serine protease hepsin mediates urinary secretion and polymerisation of Zona Pellucida domain protein uromodulin.
著者: Martina Brunati / Simone Perucca / Ling Han / Angela Cattaneo / Francesco Consolato / Annapaola Andolfo / Céline Schaeffer / Eric Olinger / Jianhao Peng / Sara Santambrogio / Romain Perrier ...著者: Martina Brunati / Simone Perucca / Ling Han / Angela Cattaneo / Francesco Consolato / Annapaola Andolfo / Céline Schaeffer / Eric Olinger / Jianhao Peng / Sara Santambrogio / Romain Perrier / Shuo Li / Marcel Bokhove / Angela Bachi / Edith Hummler / Olivier Devuyst / Qingyu Wu / Luca Jovine / Luca Rampoldi /
要旨: Uromodulin is the most abundant protein in the urine. It is exclusively produced by renal epithelial cells and it plays key roles in kidney function and disease. Uromodulin mainly exerts its function ...Uromodulin is the most abundant protein in the urine. It is exclusively produced by renal epithelial cells and it plays key roles in kidney function and disease. Uromodulin mainly exerts its function as an extracellular matrix whose assembly depends on a conserved, specific proteolytic cleavage leading to conformational activation of a Zona Pellucida (ZP) polymerisation domain. Through a comprehensive approach, including extensive characterisation of uromodulin processing in cellular models and in specific knock-out mice, we demonstrate that the membrane-bound serine protease hepsin is the enzyme responsible for the physiological cleavage of uromodulin. Our findings define a key aspect of uromodulin biology and identify the first in vivo substrate of hepsin. The identification of hepsin as the first protease involved in the release of a ZP domain protein is likely relevant for other members of this protein family, including several extracellular proteins, as egg coat proteins and inner ear tectorins.
#12: ジャーナル: Proc Natl Acad Sci U S A / : 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.
#13: ジャーナル: Curr Top Dev Biol / : 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.
#14: ジャーナル: bioRxiv / : 2020
タイトル: Cryo-EM structure of native human uromodulin, a zona pellucida module polymer.
著者: Stsiapanava, A. / Xu, C. / Brunati, M. / Zamora-Caballero, S. / Schaeffer, C. / Han, L. / Carroni, M. / Yasumasu, S. / Rampoldi, L. / Wu, B. / Jovine, L.
履歴
登録2019年12月16日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年11月4日Provider: repository / タイプ: Initial release
改定 1.12020年12月2日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
改定 1.22020年12月9日Group: Structure summary / カテゴリ: struct / Item: _struct.title
改定 1.32020年12月16日Group: Database references / カテゴリ: pdbx_database_related / Item: _pdbx_database_related.details
改定 1.42021年3月3日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume

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構造ビューア分子:
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集合体

登録構造単位
A: Uromodulin
B: Uromodulin
C: Uromodulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)188,7469
ポリマ-184,4963
非ポリマー4,2506
0
1


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タイプ名称対称操作
identity operation1_5551
Buried area14540 Å2
ΔGint12 kcal/mol
Surface area36420 Å2
手法PISA
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 292 through 444 or resid 761 through 778))
d_2ens_1(chain "C" and (resid 292 through 443 or (resid 444...
d_1ens_2(chain "A" and (resid 445 through 587 or resid 781))
d_2ens_2(chain "B" and (resid 445 through 587 or resid 781))

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1SERSERA1 - 153
d_21ens_1SERSERC1 - 153
d_11ens_2ALAPHEA154 - 296
d_21ens_2ALAPHEB2 - 144

NCSアンサンブル:
ID
ens_1
ens_2

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要素

#1: タンパク質 Uromodulin / / Tamm-Horsfall urinary glycoprotein / THP


分子量: 61498.816 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / Plasmid details: Urine / 参照: UniProt: P07911
#2: 多糖 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


タイプ: oligosaccharideオリゴ糖 / 分子量: 424.401 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: 多糖 beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]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オリゴ糖 / 分子量: 1479.349 Da / 分子数: 2 / 由来タイプ: 組換発現
記述子タイププログラム
DGalpb1-4DGlcpNAcb1-2[DGlcpNAcb1-4]DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-4-1-3/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_d4-g1_e4-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}[(4+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#4: 糖 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-アセチル-β-D-グルコサミン / N-アセチルグルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 2 / 由来タイプ: 組換発現 / : C8H15NO6
識別子タイププログラム
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
研究の焦点であるリガンドがあるかN

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実験情報

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実験

実験手法: 電子顕微鏡法
EM実験試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法

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試料調製

構成要素名称: Uromodulin (UMOD)/Tamm-Horsfall protein (THP) / タイプ: COMPLEX / Entity ID: #1 / 由来: NATURAL
由来(天然)生物種: Homo sapiens (ヒト)
緩衝液pH: 7
試料濃度: 0.85 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
試料支持グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R2/2
急速凍結装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 凍結前の試料温度: 294 K

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電子顕微鏡撮影

実験機器
モデル: Titan Krios / 画像提供: FEI Company
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 130000 X / Calibrated defocus min: 1400 nm / 最大 デフォーカス(補正後): 3500 nm / Cs: 2.7 mm / C2レンズ絞り径: 70 µm / アライメント法: COMA FREE
試料ホルダ凍結剤: NITROGEN
試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER
撮影平均露光時間: 6 sec. / 電子線照射量: 40 e/Å2 / 検出モード: COUNTING
フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k)
撮影したグリッド数: 1 / 実像数: 2300
電子光学装置エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV
画像スキャン動画フレーム数/画像: 40

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解析

ソフトウェア
名称分類
phenix.real_space_refine精密化
PHENIX精密化
EMソフトウェア
ID名称バージョンカテゴリ詳細
2EPU1.24画像取得
4Gctf1.06CTF補正
7UCSF Chimera1.13モデルフィッティング
8Coot0.9モデルフィッティング
9ISOLDE1.0b5モデルフィッティング
11PHENIXモデル精密化phenix.real_space_refine
12RELION3.0.5初期オイラー角割当
13RELION3.0.5最終オイラー角割当
14RELION3.0.5分類
15RELION3.0.53次元再構成
16PHENIX3次元再構成phenix.resolve_cryo_em
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
らせん対称回転角度/サブユニット: 180 ° / 軸方向距離/サブユニット: 62.5 Å / らせん対称軸の対称性: C1
粒子像の選択選択した粒子像数: 412322
3次元再構成解像度: 3.35 Å / 解像度の算出法: OTHER / 粒子像の数: 288403 / 詳細: PHENIX ResolveCryoEM FSCref=0.5 / 対称性のタイプ: HELICAL
原子モデル構築B value: 115.88 / プロトコル: FLEXIBLE FIT / 空間: REAL
原子モデル構築
IDPDB-IDPDB chain-ID 3D fitting-IDPdb chain residue range
14WRNA1296-429
24WRNA1466-587
精密化交差検証法: NONE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
原子変位パラメータBiso mean: 136.57 Å2
拘束条件
Refine-IDタイプDev ideal
ELECTRON MICROSCOPYf_bond_d0.00275006
ELECTRON MICROSCOPYf_angle_d0.54656775
ELECTRON MICROSCOPYf_chiral_restr0.038825
ELECTRON MICROSCOPYf_plane_restr0.0037847
ELECTRON MICROSCOPYf_dihedral_angle_d11.82671902
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AELECTRON MICROSCOPYNCS constraints0.00157931308534
ens_2d_2AELECTRON MICROSCOPYNCS constraints0.000707658764494

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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