- EMDB-5573: Focused asymmetric reconstruction VI (map 8/8): Visualization of ... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-5573
タイトル
Focused asymmetric reconstruction VI (map 8/8): Visualization of Uncorrelated Tandem Symmetry Mismatches in the Internal Genome Packaging Apparatus of a dsDNA virus
マップデータ
Focused asymmetric reconstruction (FAR-6) of bacteriophage T710A capsid I state. Display section view z=160 for core protein gp15 and z=190 for core protein gp16.
symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / peptidoglycan metabolic process ...symbiont genome ejection through host cell envelope / host cell periplasmic space / : / symbiont entry into host cell via disruption of host cell wall peptidoglycan / lytic transglycosylase activity / viral portal complex / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / viral DNA genome packaging / peptidoglycan metabolic process / symbiont entry into host / viral capsid assembly / virion component / viral capsid / killing of cells of another organism / hydrolase activity / defense response to bacterium / host cell plasma membrane / identical protein binding / membrane 類似検索 - 分子機能
Capsid assembly scaffolding protein-like / Phage T7 capsid assembly protein / Internal virion protein Gp16 / Internal virion protein Gp14 / Internal virion protein Gp15 / Capsid Gp10A/Gp10B / : / Major capsid protein / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type ...Capsid assembly scaffolding protein-like / Phage T7 capsid assembly protein / Internal virion protein Gp16 / Internal virion protein Gp14 / Internal virion protein Gp15 / Capsid Gp10A/Gp10B / : / Major capsid protein / Portal protein, Caudovirales / Head-to-tail connector protein, podovirus-type / Bacteriophage head to tail connecting protein / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme-like domain superfamily 類似検索 - ドメイン・相同性
Capsid assembly scaffolding protein / Internal virion protein gp14 / Internal virion protein gp15 / Peptidoglycan transglycosylase gp16 / Portal protein / Major capsid protein 類似検索 - 構成要素
ジャーナル: Proc Natl Acad Sci U S A / 年: 2013 タイトル: Visualization of uncorrelated, tandem symmetry mismatches in the internal genome packaging apparatus of bacteriophage T7. 著者: Fei Guo / Zheng Liu / Frank Vago / Yue Ren / Weimin Wu / Elena T Wright / Philip Serwer / Wen Jiang / 要旨: Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle ...Motor-driven packaging of a dsDNA genome into a preformed protein capsid through a unique portal vertex is essential in the life cycle of a large number of dsDNA viruses. We have used single-particle electron cryomicroscopy to study the multilayer structure of the portal vertex of the bacteriophage T7 procapsid, the recipient of T7 DNA in packaging. A focused asymmetric reconstruction method was developed and applied to selectively resolve neighboring pairs of symmetry-mismatched layers of the portal vertex. However, structural features in all layers of the multilayer portal vertex could not be resolved simultaneously. Our results imply that layers with mismatched symmetries can join together in several different relative orientations, and that orientations at different interfaces assort independently to produce structural isomers, a process that we call combinatorial assembly isomerism. This isomerism explains rotational smearing in previously reported asymmetric reconstructions of the portal vertex of T7 and other bacteriophages. Combinatorial assembly isomerism may represent a new regime of structural biology in which globally varying structures assemble from a common set of components. Our reconstructions collectively validate previously proposed symmetries, compositions, and sequential order of T7 portal vertex layers, resolving in tandem the 5-fold gene product 10 (gp10) shell, 12-fold gp8 portal ring, and an internal core stack consisting of 12-fold gp14 adaptor ring, 8-fold bowl-shaped gp15, and 4-fold gp16 tip. We also found a small tilt of the core stack relative to the icosahedral fivefold axis and propose that this tilt assists DNA spooling without tangling during packaging.
ダウンロード / ファイル: emd_5573.map.gz / 形式: CCP4 / 大きさ: 173.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Focused asymmetric reconstruction (FAR-6) of bacteriophage T710A capsid I state. Display section view z=160 for core protein gp15 and z=190 for core protein gp16.
ボクセルのサイズ
X=Y=Z: 2.2 Å
密度
表面レベル
登録者による: 4.5 / ムービー #1: 4.5
最小 - 最大
-14.195051189999999 - 29.143356319999999
平均 (標準偏差)
0.59400719 (±1.91884899)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
-180
-180
-180
サイズ
360
360
360
Spacing
360
360
360
セル
A=B=C: 792.0 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
2.2
2.2
2.2
M x/y/z
360
360
360
origin x/y/z
0.000
0.000
0.000
length x/y/z
792.000
792.000
792.000
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
-50
29
166
NX/NY/NZ
106
122
134
MAP C/R/S
1
2
3
start NC/NR/NS
-180
-180
-180
NC/NR/NS
360
360
360
D min/max/mean
-14.195
29.143
0.594
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添付データ
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試料の構成要素
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全体 : Bacteriophage T710A capsid I
全体
名称: Bacteriophage T710A capsid I
要素
試料: Bacteriophage T710A capsid I
タンパク質・ペプチド: gp14
タンパク質・ペプチド: gp15
タンパク質・ペプチド: gp16
タンパク質・ペプチド: gp8
タンパク質・ペプチド: gp10A
タンパク質・ペプチド: gp9
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超分子 #1000: Bacteriophage T710A capsid I
超分子
名称: Bacteriophage T710A capsid I / タイプ: sample / ID: 1000 / Number unique components: 6
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分子 #1: gp14
分子
名称: gp14 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: Internal virion protein B / 詳細: core stack protein / コピー数: 12 / 集合状態: dodecamer / 組換発現: No / データベース: NCBI
名称: gp10A / タイプ: protein_or_peptide / ID: 5 / Name.synonym: Major capsid protein 10A 詳細: major capsid protein. The correct copy number is 415. 集合状態: icosahedral (T=7) / 組換発現: No / データベース: NCBI
The particles were selected automatically by the ethan method and then by manual screening with the EMAN boxer program. CTF parameters were determined automatically using fitctf2.py and then visually validated using EMAN ctfit program. For 3-D reconstructions, the images were first binned 4x to make initial reconstructions. After alignment parameters and reconstructions converged, the 2x binned images were used for final reconstructions with a sampling of 2.2 A/pixel.
CTF補正
詳細: phase flipping and amplitude weighted; per particle
最終 再構成
アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 17.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: jspr, EMAN2, EMAN 詳細: This is the FAR-VI map of a serials of 8 maps (Icos, SAR, FAR-I to FAR-VI). Only the core stack protein gp15, gp16 are resolved. All other proteins (gp8, gp9, gp10, gp14) are smeared. 使用した粒子像数: 12360