+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1kvp | ||||||
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タイトル | STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY | ||||||
要素 | SPV4 CAPSID PROTEIN VP1 | ||||||
キーワード | VIRUS / BACTERIOPHAGE SPV4 COAT PROTEIN / CHIMERA / Icosahedral virus | ||||||
機能・相同性 | Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / symbiont entry into host cell / structural molecule activity / Capsid protein F 機能・相同性情報 | ||||||
生物種 | Enterobacteria phage phiX174 (ファージ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 27 Å | ||||||
データ登録者 | McKenna, R. | ||||||
引用 | ジャーナル: Structure / 年: 1998 タイトル: Structural analysis of the Spiroplasma virus, SpV4: implications for evolutionary variation to obtain host diversity among the Microviridae. 著者: P R Chipman / M Agbandje-McKenna / J Renaudin / T S Baker / R McKenna / 要旨: BACKGROUND: Spiroplasma virus, SpV4, is a small, non-enveloped virus that infects the helical mollicute Spiroplasma melliferum. SpV4 exhibits several similarities to the Chlamydia phage, Chp1, and ...BACKGROUND: Spiroplasma virus, SpV4, is a small, non-enveloped virus that infects the helical mollicute Spiroplasma melliferum. SpV4 exhibits several similarities to the Chlamydia phage, Chp1, and the Coliphages alpha 3, phi K, G4 and phi X174. All of these viruses are members of the Microviridae. These viruses have isometric capsids with T = 1 icosahedral symmetry, cause lytic infections and are the only icosahedral phages that contain single-stranded circular DNA genomes. The aim of this comparative study on these phages was to understand the role of their capsid proteins during host receptor recognition. RESULTS: The three-dimensional structure of SpV4 was determined to 27 A resolution from images of frozen-hydrated particles. Cryo-electron microscopy (cryo-EM) revealed 20, approximately 54 A long, ...RESULTS: The three-dimensional structure of SpV4 was determined to 27 A resolution from images of frozen-hydrated particles. Cryo-electron microscopy (cryo-EM) revealed 20, approximately 54 A long, 'mushroom-like' protrusions on the surface of the capsid. Each protrusion comprises a trimeric structure that extends radially along the threefold icosahedral axes of the capsid. A 71 amino acid portion of VP1 (the SpV4 capsid protein) was shown, by structural alignment with the atomic structure of the F capsid protein of phi X174, to represent an insertion sequence between the E and F strands of the eight-stranded antiparallel beta-barrel. Secondary structure prediction of this insertion sequence provided the basis for a probable structural motif, consisting of a six-stranded antiparallel beta sheet connected by small turns. Three such motifs form the rigid stable trimeric structures (mushroom-like protrusions) at the threefold axes, with hydrophobic depressions at their distal surface. CONCLUSIONS: Sequence alignment and structural analysis indicate that distinct genera of the Microviridae might have evolved from a common primordial ancestor, with capsid surface variations, such as ...CONCLUSIONS: Sequence alignment and structural analysis indicate that distinct genera of the Microviridae might have evolved from a common primordial ancestor, with capsid surface variations, such as the SpV4 protrusions, resulting from gene fusion events that have enabled diverse host ranges. The hydrophobic nature of the cavity at the distal surface of the SpV4 protrusions suggests that this region may function as the receptor-recognition site during host infection. #1: ジャーナル: Nature / 年: 1992 タイトル: Atomic Structure of Single-Stranded DNA Bacteriophage Phi X174 and its Functional Implications 著者: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L. #2: ジャーナル: Isr.J.Med.Sci. / 年: 1984 タイトル: Characterization of Spiroplasma Virus Group 4 (Sv4) 著者: Renaudin, J. / Pascarel, M.C. / Garnier, M. / Carle, P. / Bove, J.M. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1kvp.cif.gz | 31.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1kvp.ent.gz | 14.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1kvp.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 1kvp_validation.pdf.gz | 236.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1kvp_full_validation.pdf.gz | 235.8 KB | 表示 | |
XML形式データ | 1kvp_validation.xml.gz | 703 B | 表示 | |
CIF形式データ | 1kvp_validation.cif.gz | 4.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/kv/1kvp ftp://data.pdbj.org/pub/pdb/validation_reports/kv/1kvp | HTTPS FTP |
-関連構造データ
-リンク
-集合体
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対称性 | 点対称性: (ヘルマン・モーガン記号: 532 / シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 55834.703 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Enterobacteria phage phiX174 (ファージ) 発現宿主: Spiroplasma melliferum (バクテリア) / 参照: UniProt: P03641 |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: SPIROPLASMA VIRUS / タイプ: VIRUS |
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緩衝液 | pH: 9.2 / 詳細: 50 mM Sodium tetraborate |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
結晶化 | *PLUS 手法: other / 詳細: electron microscopy |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS EM420 |
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電子銃 | 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 49000 X / 最大 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 18 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
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3次元再構成 | 手法: COMMON-LINES AND POLAR-FOURIER-TRANSFORM FULLER ET AL. 1996, J.STRUC.BIOL.c 116, 48-55; BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130 解像度: 27 Å / 解像度の算出法: OTHER 詳細: CA TRACING OF A MODEL OF THE CAPSID PROTEIN VP1 OF SPV4 BASED ON THE CRYSTAL STRUCTURAL COORDINATES OF THE MAJOR CAPSID PROTEIN F OF PHIX174 (RESIDUES 1001 - 1427). A 71 AMINO ACID PORTION OF ...詳細: CA TRACING OF A MODEL OF THE CAPSID PROTEIN VP1 OF SPV4 BASED ON THE CRYSTAL STRUCTURAL COORDINATES OF THE MAJOR CAPSID PROTEIN F OF PHIX174 (RESIDUES 1001 - 1427). A 71 AMINO ACID PORTION OF VP1 WAS MODELLED (GLY 226 - THR 297) AS AN INSERTION LOOP BETWEEN RESIDUES THR 1187 AND THR 1188 OF THE F CAPSID PROTEIN OF PHIX174. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. RESIDUES 1001 - 1187 AND 1187 - 1426 ARE THE CA COORDINATES OF THE F CAPSID PROTEIN OF PHIX174. INSERTED BETWEEN RESIDUES 1187 AND 1188 IS A MODELLED CA TRACING OF A 71 AMINO ACID INSERTION LOOP OF SPV4 (RESIDUES 226 - 297) OF THE VP1 CAPSID PROTEIN, BASED ON THE CRYO-EM RECONSTRUCTION ENVELOPE AND STRUCTURAL ALIGNMENT AND SECONDARY STRUCTURE PREDICTION. THE RESOLUTION OF THE FINAL RECONSTRUCTED DENSITY MAP WAS DETERMINED TO BE AT LEAST 27 ANGSTROMS AS MEASURED BY STRUCTURE FACTOR COMPARISONS (BAKER ET AL. 1991, BIOPHYS. J. 60,1445-1456) AND FOURIER RING CORRELATION MEASUREMENTS (CONWAY ET AL. 1996, J. STRUC. BIOL. 116, 200-208) 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | 空間: RECIPROCAL 詳細: DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY GLYCOSYLATED MODELS OF D1D2-ICAM-1 WITH ...詳細: DETAILS--THE CRYSTAL STRUCTURE OF HRV16 WAS PLACED INTO THE CALIBRATED CRYO-EM DENSITY MAP BY ALIGNING THE ICOSAHEDRAL SYMMETRY AXES. APPROPRIATELY GLYCOSYLATED MODELS OF D1D2-ICAM-1 WITH VARIOUS INTERDOMAIN ANGLES (AS SEEN IN DIFFERENT CRYSTAL STRUCTURES OF D1D2-ICAM-1), WERE FIRST MANUALLY FITTED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE ICAM-1 FRAGMENT, AND SUBSEQUENTLY REFINED AS RIGID BODIES IN RECIPROCAL SPACE. OBSERVED STRUCTURE FACTORS WERE OBTAINED BY INVERSE FOURIER TRANSFORM OF CRYO-EM DIFFERENCE MAPS CALCULATED BY- 1) SUBSTRACTION OF THE HRV16 AND RNA CONTRIBUTION FROM THE CRYO-EM RECONSTRUCTED DENSITY OF THE COMPLEXES; 2) REDUCTION OF THE DIFFERENCE MAPS TO AN ICOSAHEDRAL ASYMMETRIC UNIT. THE COORDINATES ARE IN THE P, Q, R FRAME IN ANGSTROM UNITS AND CORRESPOND TO ICOSAHEDRAL SYMMETRY AXES. THE ORIGIN IS CHOSEN AT THE CENTER OF THE VIRUS WITH P, Q AND R ALONG MUTUALLY PERPENDICULAR TWO-FOLD AXES OF THE ICOSAHEDRON. THEY SHOULD REMAIN IN THAT FRAME FOR THE EASE OF THE USER IN CREATING THE BIOLOGICALLY SIGNIFICANT VIRAL COMPLEX PARTICLE USING THE 60 ICOSAHEDRAL SYMMETRY OPERATORS. RESIDUES NOT VISIBLE IN THE ORIGINAL CRYSTAL STRUCTURES ARE NOT INCLUDED IN THE CRYO-EM STRUCTURE MODEL. FOR EXAMPLE, HRV16 RESIDUES 2001-2009, 4008-4022 AND 4045-4068 ARE NOT VISIBLE IN THE CRYSTAL STRUCTURE (PDB ENTRY 1AYM) AND THEREFORE ARE NOT INCLUDED IN THE COORDINATES BELOW. | ||||||||||||
精密化 | 最高解像度: 27 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 27 Å
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