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データベース: PDB / ID: 4wrn
タイトルCrystal structure of the polymerization region of human uromodulin/Tamm-Horsfall protein
要素Maltose-binding periplasmic protein,Uromodulin
キーワードSTRUCTURAL PROTEIN / ZP DOMAIN / EGF DOMAIN / EXTRACELLULAR MATRIX / GLYCOPROTEIN
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 / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development ...citric acid secretion / metanephric thick ascending limb development / metanephric distal convoluted tubule development / connective tissue replacement / protein transport into plasma membrane raft / Asparagine N-linked glycosylation / organ or tissue specific immune response / collecting duct development / urea transmembrane transport / metanephric ascending thin limb development / regulation of protein transport / micturition / protein localization to vacuole / intracellular chloride ion homeostasis / juxtaglomerular apparatus development / antibacterial innate immune response / renal urate salt excretion / urate transport / renal sodium ion absorption / glomerular filtration / neutrophil migration / intracellular phosphate ion homeostasis / response to water deprivation / potassium ion homeostasis / intracellular sodium ion homeostasis / regulation of urine volume / endoplasmic reticulum organization / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / IgG binding / extrinsic component of membrane / ciliary membrane / leukocyte cell-cell adhesion / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / cellular response to unfolded protein / multicellular organismal response to stress / cellular defense response / renal water homeostasis / side of membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / tumor necrosis factor-mediated signaling pathway / ERAD pathway / : / ATP-binding cassette (ABC) transporter complex / RNA splicing / cell chemotaxis / apoptotic signaling pathway / regulation of blood pressure / lipid metabolic process / autophagy / Golgi lumen / intracellular calcium ion homeostasis / spindle pole / outer membrane-bounded periplasmic space / defense response to Gram-negative bacterium / basolateral plasma membrane / response to lipopolysaccharide / periplasmic space / cilium / apical plasma membrane / inflammatory response / response to xenobiotic stimulus / negative regulation of cell population proliferation / calcium ion binding / DNA damage response / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / membrane
類似検索 - 分子機能
Zona pellucida, ZP-N domain / Zona pellucida, ZP-C domain / Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site ...Zona pellucida, ZP-N domain / Zona pellucida, ZP-C domain / Uromodulin-like, D8C domain / EGF domain / EGF domain / : / : / : / ZP-N domain / Zona pellucida domain, conserved site / ZP domain signature. / Zona pellucida, ZP-C domain / ZP-C domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / : / Calcium-binding EGF domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / EGF-type aspartate/asparagine hydroxylation site / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / 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 / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / 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 / Uromodulin / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
類似検索 - 構成要素
生物種Escherichia coli O157:H7 (大腸菌)
Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.2 Å
データ登録者Bokhove, M. / De Sanctis, D. / Jovine, L.
資金援助 スウェーデン, 7件
組織認可番号国
Karolinska Institutet スウェーデン
Center for Biosciences スウェーデン
Swedish Research Council2012-5093 スウェーデン
Gustafsson Foundation for Research in Natural Sciences and Medicine スウェーデン
Sven and Ebba-Christina Hagberg foundation スウェーデン
European Molecular Biology Organization
European UnionERC 260759
引用
ジャーナル: Proc Natl Acad Sci U S A / 年: 2016
タイトル: A structured interdomain linker directs self-polymerization of human uromodulin.
著者: Marcel Bokhove / Kaoru Nishimura / Martina Brunati / Ling Han / Daniele de Sanctis / Luca Rampoldi / Luca Jovine /
要旨: Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite ...Uromodulin (UMOD)/Tamm-Horsfall protein, the most abundant human urinary protein, plays a key role in chronic kidney diseases and is a promising therapeutic target for hypertension. Via its bipartite zona pellucida module (ZP-N/ZP-C), UMOD forms extracellular filaments that regulate kidney electrolyte balance and innate immunity, as well as protect against renal stones. Moreover, salt-dependent aggregation of UMOD filaments in the urine generates a soluble molecular net that captures uropathogenic bacteria and facilitates their clearance. Despite the functional importance of its homopolymers, no structural information is available on UMOD and how it self-assembles into filaments. Here, we report the crystal structures of polymerization regions of human UMOD and mouse ZP2, an essential sperm receptor protein that is structurally related to UMOD but forms heteropolymers. The structure of UMOD reveals that an extensive hydrophobic interface mediates ZP-N domain homodimerization. This arrangement is required for filament formation and is directed by an ordered ZP-N/ZP-C linker that is not observed in ZP2 but is conserved in the sequence of deafness/Crohn's disease-associated homopolymeric glycoproteins α-tectorin (TECTA) and glycoprotein 2 (GP2). Our data provide an example of how interdomain linker plasticity can modulate the function of structurally similar multidomain proteins. Moreover, the architecture of UMOD rationalizes numerous pathogenic mutations in both UMOD and TECTA genes.
#1: ジャーナル: Proc Soc Exp Biol Med / 年: 1950
タイトル: Characterization and separation of an inhibitor of viral hemagglutination present in urine.
#2: ジャーナル: J.Biol.Chem. / 年: 1991
タイトル: Isolation of the cDNA encoding glycoprotein-2 (GP-2), the major zymogen granule membrane protein. Homology to uromodulin/Tamm-Horsfall protein.
著者: Hoops, T.C. / Rindler, M.J.
#3: ジャーナル: Nat.Genet. / 年: 1998
タイトル: Mutations in the human alpha-tectorin gene cause autosomal dominant non-syndromic hearing impairment.
著者: Verhoeven, K. / Van Laer, L. / Kirschhofer, K. / Legan, P.K. / Hughes, D.C. / Schatteman, I. / Verstreken, M. / Van Hauwe, P. / Coucke, P. / Chen, A. / Smith, R.J. / Somers, T. / Offeciers, F. ...著者: Verhoeven, K. / Van Laer, L. / Kirschhofer, K. / Legan, P.K. / Hughes, D.C. / Schatteman, I. / Verstreken, M. / Van Hauwe, P. / Coucke, P. / Chen, A. / Smith, R.J. / Somers, T. / Offeciers, F.E. / Van de Heyning, P. / Richardson, G.P. / Wachtler, F. / Kimberling, W.J. / Willems, P.J. / Govaerts, P.J. / Van Camp, G.
#4: 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.
#5: ジャーナル: Am J Kidney Dis / 年: 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 / 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.
#7: 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.
#8: 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.
#9: ジャーナル: Kidney Int / 年: 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.
履歴
登録2014年10月24日登録サイト: RCSB / 処理サイト: PDBE
改定 1.02016年1月27日Provider: repository / タイプ: Initial release
改定 1.12016年2月10日Group: Database references
改定 1.22016年2月17日Group: Database references
改定 1.32017年9月6日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 2.02020年7月29日Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
カテゴリ: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.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 / _atom_site_anisotrop.type_symbol / _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.src_method / _entity.type / _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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_conn_type.id
解説: Carbohydrate remediation / Provider: repository / タイプ: Remediation
改定 2.12024年1月10日Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
カテゴリ: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 2.22024年11月20日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Maltose-binding periplasmic protein,Uromodulin
B: Maltose-binding periplasmic protein,Uromodulin
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)154,5589
ポリマ－153,0792
非ポリマー1,4797
水00
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-60 kcal/mol
Surface area56680 Å2
手法PISA
単位格子
Length a, b, c (Å)242.320, 242.320, 258.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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要素

#1: タンパク質 Maltose-binding periplasmic protein,Uromodulin / MBP / MMBP / Maltodextrin-binding protein / Tamm-Horsfall urinary glycoprotein / THP


分子量: 76539.414 Da / 分子数: 2
変異: I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A, R393N,R586A, R588A,I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, ...変異: I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A, R393N,R586A, R588A,I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A, R393N,R586A, R588A
由来タイプ: 組換発現
詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 25-391 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I26T, D106A, ...詳細: THIS PROTEIN IS A CHIMERA. RESIDUES 25-391 ARE FROM E. COLI MALTOSE BINDING PROTEIN (MBP), CORRESPOND TO RESIDUES 27-393 OF SWISS-PROT DATABASE ENTRY P0AEX9 AND CONTAIN MUTATIONS I26T, D106A, K107A, E196A, N197A, A239H, K243H, K263A, A336V, I341V, E383A, E386A, D387A AND R391N (CORRESPONDING TO I28T, D108A, K109A, E198A, N199A, A241H, K245H, K265A, A338V, I343V, E385A, E388A, D389A AND R393N IN P0AEX9). RESIDUES 395-710 ARE FROM HUMAN UROMODULIN PROTEIN AND CORRESPOND TO RESIDUES 295-610 OF SWISS-PROT DATABASE ENTRY P07911 AND CONTAIN MUTATIONS N613Q, R686A AND R688A (CORRESPONDING TO N513Q, R586A AND R588A).
由来: (組換発現) Escherichia coli O157:H7 (大腸菌), (組換発現) Homo sapiens (ヒト)
遺伝子: malE, Z5632, ECs5017, UMOD / プラスミド: pHLSEC / 細胞株 (発現宿主): HEK293S / 発現宿主: Homo sapiens (ヒト)
参照: UniProt: P0AEY0, UniProt: P07911, UniProt: P0AEX9*PLUS
#2: 多糖 alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


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


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 3 / 由来タイプ: 合成 / 式: 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
#4: 化合物 ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Zn
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

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試料調製

結晶マシュー密度: 4.91 Å3/Da / 溶媒含有率: 75 % / 解説: Rhombus
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: 8.2 / 詳細: Sodium/potassium tartrate, Tris-HCl / PH範囲: 7.0 - 8.4

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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: ID29 / 波長: 0.97625 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2013年1月24日
放射モノクロメーター: Si Crystal / プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.97625 Å / 相対比: 1
反射解像度: 3.2→35 Å / Num. all: 47837 / Num. obs: 47837 / % possible obs: 99.41 % / 冗長度: 6.3 % / Biso Wilson estimate: 108.3 Å2 / Rmerge(I) obs: 0.08846 / Net I/σ(I): 16.21
反射 シェル解像度: 3.2→3.314 Å / 冗長度: 6.2 % / Rmerge(I) obs: 1.462 / Mean I/σ(I) obs: 1.29 / % possible all: 99.52

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解析

ソフトウェア
名称バージョン分類
PHENIX(phenix.refine: 1.9_1692)精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 3SEX

3sex


解像度: 3.2→34.976 Å / SU ML: 0.49 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 28.21 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2459 2431 5.09 %0
Rwork0.221 ---
obs0.2222 47792 99.32 %-
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 141.3 Å2
精密化ステップサイクル: LAST / 解像度: 3.2→34.976 Å
タンパク質核酸リガンド溶媒全体
原子数10483 0 90 0 10573
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00410838
X-RAY DIFFRACTIONf_angle_d0.8414695
X-RAY DIFFRACTIONf_dihedral_angle_d11.2693895
X-RAY DIFFRACTIONf_chiral_restr0.0321645
X-RAY DIFFRACTIONf_plane_restr0.0041898
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION

解像度 (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.31430.40372645.60.4012445699
3.3143-3.44690.33472465.20.3224523100
3.4469-3.60360.32532485.20.29784510100
3.6036-3.79340.27582334.90.26394534100
3.7934-4.03070.28172435.10.2397452799
4.0307-4.34140.24582204.60.2101453899
4.3414-4.77730.23852525.30.19884532100
4.7773-5.46640.18352495.20.1855453399
5.4664-6.87850.248424150.2119457499
6.8785-34.9780.2152354.80.1922463498
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)
13.21020.9083-0.77532.57440.12482.96890.0399-0.43340.51790.18780.2779-0.2867-0.08070.385901.0430.09450.28891.2037-0.29231.1293-20.080667.276639.1997
21.7174-0.9468-1.08972.40520.82682.1250.2855-0.19510.4939-0.42070.2138-0.3362-0.60460.123-0.00011.3005-0.03540.47181.2434-0.13841.4849-3.842965.110510.8527
34.789-0.9875-0.0482.7996-0.27051.77740.2623-0.22690.4569-0.00620.0866-0.2627-0.13890.0285-01.02950.08390.09341.0637-0.07820.923410.054623.607222.5309
42.9039-2.2101-1.51972.14230.80852.3078-0.2353-1.16471.48660.59680.4007-0.4579-0.4327-0.252201.65840.1665-0.05722.0973-0.78291.920826.854436.040551.0718
50.7829-0.04440.59831.67330.18773.04980.2539-0.70770.26070.37070.0234-0.5333-0.02360.53820.00011.18540.08540.29961.4665-0.23911.42312.277758.18325.0366
65.2188-0.94791.41314.4801-1.2713.11120.1434-0.053-0.0648-0.22060.00880.31960.1175-0.079700.95880.03930.24470.90150.08950.8862-29.222931.111810.9487
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain B and (resi 530:709)
2X-RAY DIFFRACTION2chain A and (resi 392:529 or resi 1000 or resi 2000)
3X-RAY DIFFRACTION3chain A and (resi 530:710)
4X-RAY DIFFRACTION4chain B and (resi 19:391 or resi 900 )
5X-RAY DIFFRACTION5chain B and (resi 392:529 or resi 1000)
6X-RAY DIFFRACTION6chain B and (resi 530:709)

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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。
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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。
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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)。
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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

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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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