- EMDB-14167: Amyloid fibril from the antimicrobial peptide uperin 3.5 -
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基本情報
登録情報
データベース: EMDB / ID: EMD-14167
タイトル
Amyloid fibril from the antimicrobial peptide uperin 3.5
マップデータ
試料
複合体: uperin 3.5
タンパク質・ペプチド: Uperin-3.5
機能・相同性
Uperin / Uperin family / cytolysis in another organism / other organism cell membrane / defense response to Gram-positive bacterium / protein homodimerization activity / extracellular region / membrane / Uperin-3.5
United States - Israel Binational Science Foundation (BSF)
2017280
Joachim Herz Stiftung
Add-on Fellowship
引用
ジャーナル: Nat Commun / 年: 2022 タイトル: The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. 著者: Robert Bücker / Carolin Seuring / Cornelia Cazey / Katharina Veith / Maria García-Alai / Kay Grünewald / Meytal Landau / 要旨: The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties ...The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids.
ソフトウェア - 名称: RELION (ver. 3.1.3) / ソフトウェア - 詳細: Internal CTFFIND4 / 詳細: CTF refined after 3D reconstruction
Segment selection
選択した数: 2447463 / ソフトウェア - 名称: crYOLO (ver. 1.8-beta) / 詳細: 4 unique helical units per segment
初期モデル
モデルのタイプ: NONE 詳細: Ab-initio initial model from stochastic gradient descent with fixed helical parameters estimated from two-dimensional class averages.
最終 角度割当
タイプ: NOT APPLICABLE / ソフトウェア - 名称: RELION (ver. 3.1.3)
FSC曲線 (解像度の算出)
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原子モデル構築 1
詳細
- Initial model building of a single helical layer using ChimeraX and Coot - Expansion to three layers, refinement in ISOLDE - Truncation of outer layers, re-expansion to three layers, refinement using phenix.real_space_refine
精密化
空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 59.34 / 当てはまり具合の基準: CC
得られたモデル
PDB-7qv5: Amyloid fibril from the antimicrobial peptide uperin 3.5