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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||
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| タイトル | NMT1-NAC bound human RNC with full length ARF1 - State 1 | |||||||||
マップデータ | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement - local resolution filtered | |||||||||
試料 |
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キーワード | myristoylation / NMT1 / co-translational / NAC / ribosome / RNC | |||||||||
| 機能・相同性 | 機能・相同性情報negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / positive regulation of skeletal muscle tissue growth / mitotic cleavage furrow ingression / translation termination factor activity ...negative regulation of striated muscle cell apoptotic process / regulation of skeletal muscle fiber development / myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / positive regulation of cell proliferation involved in heart morphogenesis / Late Phase of HIV Life Cycle / positive regulation of skeletal muscle tissue growth / mitotic cleavage furrow ingression / translation termination factor activity / trans-Golgi Network Vesicle Budding / ketone metabolic process / regulation of opsin-mediated signaling pathway / Glycosphingolipid transport / negative regulation of protein localization to endoplasmic reticulum / nascent polypeptide-associated complex / translation release factor complex / regulation of receptor internalization / cardiac ventricle development / Intra-Golgi traffic / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of protein localization to mitochondrion / cytoplasmic translational termination / regulation of Arp2/3 complex-mediated actin nucleation / regulation of translational termination / Synthesis of PIPs at the Golgi membrane / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / translation release factor activity / translation release factor activity, codon specific / heart trabecula morphogenesis / skeletal muscle tissue regeneration / protein methylation / translation at presynapse / Nef Mediated CD4 Down-regulation / exit from mitosis / optic nerve development / response to insecticide / sequence-specific mRNA binding / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / dendritic spine organization / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein-DNA complex disassembly / positive regulation of ubiquitin-protein transferase activity / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / long-term synaptic depression / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / protein localization to membrane / peptidyl-tRNA hydrolase activity / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / alpha-beta T cell differentiation / positive regulation of DNA-templated transcription initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / TNFR1-mediated ceramide production / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / COPI-dependent Golgi-to-ER retrograde traffic / neural crest cell differentiation / supercoiled DNA binding / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / cytoplasmic translational initiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / rRNA modification in the nucleus and cytosol / negative regulation of bicellular tight junction assembly / Lysosome Vesicle Biogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Golgi Associated Vesicle Biogenesis / protein kinase A binding / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / laminin receptor activity / Synthesis of PIPs at the plasma membrane / Translation initiation complex formation 類似検索 - 分子機能 | |||||||||
| 生物種 | Homo sapiens (ヒト) | |||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.47 Å | |||||||||
データ登録者 | Denk T / Berninghausen O / Beckmann R | |||||||||
| 資金援助 | ドイツ, 1件
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引用 | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2019 タイトル: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. 著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / ...著者: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / ![]() 要旨: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
| 履歴 |
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構造の表示
| 添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
| マップデータ | emd_53230.map.gz | 93.6 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-53230-v30.xml emd-53230.xml | 119.4 KB 119.4 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_53230_fsc.xml | 21.2 KB | 表示 | FSCデータファイル |
| 画像 | emd_53230.png | 92.6 KB | ||
| Filedesc metadata | emd-53230.cif.gz | 23.2 KB | ||
| その他 | emd_53230_additional_1.map.gz emd_53230_additional_2.map.gz emd_53230_half_map_1.map.gz emd_53230_half_map_2.map.gz | 501.5 MB 945.4 MB 926.9 MB 926.9 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-53230 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53230 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9qloMC ![]() 9i2dC ![]() 9i2eC ![]() 9qlpC ![]() 9qlqC ![]() 9s3bC ![]() 9s3cC ![]() 9s3dC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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リンク
| EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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| 「今月の分子」の関連する項目 |
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マップ
| ファイル | ダウンロード / ファイル: emd_53230.map.gz / 形式: CCP4 / 大きさ: 1000 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement - local resolution filtered | ||||||||||||||||||||||||||||||||||||
| 投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
| ボクセルのサイズ | X=Y=Z: 0.727 Å | ||||||||||||||||||||||||||||||||||||
| 密度 |
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| 対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
| 詳細 | EMDB XML:
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-添付データ
-追加マップ: NMT1-NAC bound human RNC with full length ARF1...
| ファイル | emd_53230_additional_1.map | ||||||||||||
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| 注釈 | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-追加マップ: NMT1-NAC bound human RNC with full length ARF1...
| ファイル | emd_53230_additional_2.map | ||||||||||||
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| 注釈 | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement - sharpened | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: NMT1-NAC bound human RNC with full length ARF1...
| ファイル | emd_53230_half_map_1.map | ||||||||||||
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| 注釈 | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement - half map A | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: NMT1-NAC bound human RNC with full length ARF1...
| ファイル | emd_53230_half_map_2.map | ||||||||||||
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| 注釈 | NMT1-NAC bound human RNC with full length ARF1 - State 1 - Homogeneous Refinement - half map B | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
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試料の構成要素
+全体 : NMT1-NAC bound human RNC with full length ARF1
+超分子 #1: NMT1-NAC bound human RNC with full length ARF1
+分子 #1: full length ARF1-V5-hCMV staller mRNA
+分子 #2: prolyl-tRNA
+分子 #5: 28S rRNA
+分子 #6: 5S rRNA
+分子 #7: 5.8S rRNA
+分子 #55: 18S rRNA
+分子 #3: Eukaryotic peptide chain release factor subunit 1
+分子 #4: ADP-ribosylation factor 1
+分子 #8: 60S ribosomal protein L8
+分子 #9: 60S ribosomal protein L3
+分子 #10: 60S ribosomal protein L4
+分子 #11: 60S ribosomal protein L5
+分子 #12: Large ribosomal subunit protein eL6
+分子 #13: Large ribosomal subunit protein uL30
+分子 #14: 60S ribosomal protein L7a
+分子 #15: 60S ribosomal protein L9
+分子 #16: Ribosomal protein uL16-like
+分子 #17: 60S ribosomal protein L11
+分子 #18: 60S ribosomal protein L13
+分子 #19: 60S ribosomal protein L14
+分子 #20: 60S ribosomal protein L15
+分子 #21: 60S ribosomal protein L13a
+分子 #22: 60S ribosomal protein L17
+分子 #23: 60S ribosomal protein L18
+分子 #24: 60S ribosomal protein L19
+分子 #25: 60S ribosomal protein L18a
+分子 #26: 60S ribosomal protein L21
+分子 #27: 60S ribosomal protein L22
+分子 #28: 60S ribosomal protein L23
+分子 #29: 60S ribosomal protein L24
+分子 #30: 60S ribosomal protein L23a
+分子 #31: 60S ribosomal protein L26
+分子 #32: 60S ribosomal protein L27
+分子 #33: 60S ribosomal protein L27a
+分子 #34: 60S ribosomal protein L29
+分子 #35: 60S ribosomal protein L30
+分子 #36: 60S ribosomal protein L31
+分子 #37: 60S ribosomal protein L32
+分子 #38: 60S ribosomal protein L35a
+分子 #39: 60S ribosomal protein L34
+分子 #40: 60S ribosomal protein L35
+分子 #41: 60S ribosomal protein L36
+分子 #42: Large ribosomal subunit protein eL37
+分子 #43: 60S ribosomal protein L38
+分子 #44: 60S ribosomal protein L39
+分子 #45: Ubiquitin-60S ribosomal protein L40
+分子 #46: 60S ribosomal protein L41
+分子 #47: 60S ribosomal protein L36a
+分子 #48: 60S ribosomal protein L37a
+分子 #49: 60S ribosomal protein L28
+分子 #50: 60S acidic ribosomal protein P0
+分子 #51: Large ribosomal subunit protein uL11
+分子 #52: Nascent polypeptide-associated complex subunit alpha
+分子 #53: Isoform 2 of Transcription factor BTF3
+分子 #54: Glycylpeptide N-tetradecanoyltransferase 1
+分子 #56: 40S ribosomal protein SA
+分子 #57: 40S ribosomal protein S3a
+分子 #58: 40S ribosomal protein S2
+分子 #59: 40S ribosomal protein S3
+分子 #60: Small ribosomal subunit protein eS4, X isoform
+分子 #61: 40S ribosomal protein S5
+分子 #62: 40S ribosomal protein S6
+分子 #63: 40S ribosomal protein S7
+分子 #64: 40S ribosomal protein S8
+分子 #65: 40S ribosomal protein S9
+分子 #66: 40S ribosomal protein S10
+分子 #67: 40S ribosomal protein S11
+分子 #68: 40S ribosomal protein S12
+分子 #69: 40S ribosomal protein S13
+分子 #70: 40S ribosomal protein S14
+分子 #71: 40S ribosomal protein S15
+分子 #72: 40S ribosomal protein S16
+分子 #73: 40S ribosomal protein S17
+分子 #74: 40S ribosomal protein S18
+分子 #75: 40S ribosomal protein S19
+分子 #76: 40S ribosomal protein S20
+分子 #77: 40S ribosomal protein S21
+分子 #78: 40S ribosomal protein S15a
+分子 #79: 40S ribosomal protein S23
+分子 #80: 40S ribosomal protein S24
+分子 #81: 40S ribosomal protein S25
+分子 #82: 40S ribosomal protein S26
+分子 #83: 40S ribosomal protein S27
+分子 #84: 40S ribosomal protein S28
+分子 #85: 40S ribosomal protein S29
+分子 #86: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+分子 #87: Ubiquitin
+分子 #88: Receptor of activated protein C kinase 1
+分子 #89: MAGNESIUM ION
+分子 #90: GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
+分子 #91: ZINC ION
+分子 #92: water
-実験情報
-構造解析
| 手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
| 試料の集合状態 | particle |
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試料調製
| 緩衝液 | pH: 7.5 |
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| 凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
| 顕微鏡 | TFS KRIOS |
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| 撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 平均電子線量: 40.0 e/Å2 |
| 電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
| 電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.5 µm |
| 実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
ムービー
コントローラー
万見について




キーワード
Homo sapiens (ヒト)
データ登録者
ドイツ, 1件
引用







































































Z (Sec.)
Y (Row.)
X (Col.)






















































解析
FIELD EMISSION GUN

