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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 8bwc | ||||||
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タイトル | E. coli BAM complex (BamABCDE) wild-type | ||||||
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![]() | MEMBRANE PROTEIN / Outer Membrane Protein / Protein Folding / beta barrel | ||||||
機能・相同性 | ![]() Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane / identical protein binding / membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||
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: 3.5 Å | ||||||
![]() | Machin, J.M. / Radford, S.E. / Ranson, N.A. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Darobactin B Stabilises a Lateral-Closed Conformation of the BAM Complex in E. coli Cells. 著者: Samuel F Haysom / Jonathan Machin / James M Whitehouse / Jim E Horne / Katherine Fenn / Yue Ma / Hassane El Mkami / Nils Böhringer / Till F Schäberle / Neil A Ranson / Sheena E Radford / Christos Pliotas / ![]() ![]() 要旨: The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational ...The β-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E. coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 481.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 387.1 KB | 表示 | ![]() |
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その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 55.4 KB | 表示 | |
CIF形式データ | ![]() | 81.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 16282MC ![]() 8bvqC M: このデータのモデリングに利用したマップデータ 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 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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要素
#1: タンパク質 | 分子量: 88514.742 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() 遺伝子: bamA, yaeT, A5U30_000296, A6592_02945, A8499_001882, A9X72_20365, AAG43_001505, ACN68_08270, ACN81_28495, ACU57_18535, AF998_001683, AM464_17685, APX88_24870, AT335_002559, AT845_002198, ...遺伝子: bamA, yaeT, A5U30_000296, A6592_02945, A8499_001882, A9X72_20365, AAG43_001505, ACN68_08270, ACN81_28495, ACU57_18535, AF998_001683, AM464_17685, APX88_24870, AT335_002559, AT845_002198, AW118_17900, AWP47_05630, B6R12_000956, B6R15_000220, B6R31_002460, B6R48_000717, B6R87_000718, BANRA_00651, BANRA_01136, BEA19_03425, BER14_07740, BF481_003681, BG944_001864, BGM66_002013, BHS81_00690, BJI68_15680, BJJ90_21320, BK292_13710, BK383_20200, BKL28_001074, BLM69_001467, BMT49_02215, BMT50_03970, BMT91_01325, BN17_46001, BO068_002867, BOH76_17675, BON63_15405, BON64_03425, BON65_09470, BON66_02910, BON67_09950, BON68_19005, BON69_16435, BON70_27195, BON71_14840, BON72_09420, BON73_05360, BON74_02620, BON75_17190, BON76_15510, BON77_21970, BON78_08335, BON79_15615, BON80_16360, BON81_06815, BON82_14505, BON83_24810, BON84_04065, BON87_26650, BON88_11825, BON89_11070, BON90_22375, BON92_02795, BON93_03895, BON94_19435, BON95_12990, BON96_17170, BON98_18140, BR158_000492, BRV02_001577, BTB68_000231, BTQ06_06530, BvCmsF30A_01249, BvCmsHHP056_04085, BvCmsKKP061_01626, BVL39_02145, BXT93_00750, C0P57_001486, C1Q91_003240, C2121_002944, C2M16_10840, C2R31_000619, C2U48_09565, C3F40_12200, C5N07_08620, C5Y87_12615, C9114_06985, C9160_13545, C9E67_25165, C9Z68_04825, CA593_02825, CCS08_22545, CCV12_001992, CDC27_24730, CDL36_07950, CF22_003987, CG831_000812, CIG67_16620, CO706_23095, CQ986_003586, CR538_20600, CR628_003260, CTR35_003026, CV83915_01397, CWS33_09660, CX938_000225, CXJ73_002511, CY655_00940, D0X26_09375, D1912_21110, D1H34_004224, D3G36_16715, D3Y67_16445, D4N09_06760, D4U49_05910, D9D77_16570, D9E34_01065, D9E49_02105, D9J61_11550, DAH17_03105, DAH18_22205, DAH19_12870, DAH20_13860, DAH21_22225, DAH22_03605, DAH23_11155, DAH24_11225, DAH25_12780, DAH26_11170, DAH27_18735, DAH28_17975, DAH29_14730, DAH30_10570, DAH31_15650, DAH32_15150, DAH33_22250, DAH34_04145, DAH35_21475, DAH36_21050, DAH37_16290, DAH38_20975, DAH40_22075, DAH41_15665, DAH42_01610, DAH43_04070, DAH45_06290, DAH46_02585, DAH47_00130, DAH48_03820, DAH49_04075, DAH50_07015, DD762_01135, DEN86_04025, DEN87_21110, DEN88_17015, DEN89_20325, DEN90_18665, DEN91_15525, DEN92_14715, DEN93_18270, DEN94_16145, DEN95_12205, DEN96_06230, DEN97_04385, DEN98_04390, DEN99_03155, DEO00_05230, DEO01_06055, DEO02_09495, DEO03_16425, DEO04_22130, DEO05_22000, DEO06_22645, DEO07_22470, DEO08_20705, DEO09_21855, DEO10_22115, DEO11_22010, DEO13_08600, DEO14_11200, DEO15_08380, DEO17_19865, DEO18_03450, DEO19_04170, DEO20_19760, DIV22_06310, DM870_23205, DN627_10205, DNQ45_10075, DNX30_02230, DRW19_04885, DS732_05815, DTL43_05880, DTL90_09775, DTM45_12675, DU321_03690, DXT69_01430, DXT70_16970, DXT71_01950, DXT73_18965, E0I42_19020, E2112_01200, E2113_05810, E2114_18200, E2115_17415, E2116_17440, E2117_05485, E2118_15330, E2119_15620, E2120_18160, E2121_14045, E2122_04495, E2123_15040, E2124_16725, E2125_18030, E2127_15050, E2128_01390, E2129_02820, E2130_17625, E2131_12100, E2132_15165, E2133_09940, E2134_12015, E2135_11675, E2136_14045, E2646_16120, E3O05_11515, E4K51_05750, E4T14_02285, E4T84_08860, E5H86_15850, E5M02_17400, E5P22_04130, E5P23_04750, E5P24_16165, E5P25_12900, E5P26_03475, E5P27_14125, E5P28_14015, E5P29_07840, E5P30_07230, E5P31_13525, E5P32_01600, E5P33_01100, E5P34_12070, E5P35_01145, E5P36_00555, E5P37_21230, E5P39_14350, E5P40_06990, E5P41_07170, E5P42_02575, E5P43_09410, E5P44_10415, E5P45_09040, E5P46_08190, E5P47_11175, E5P48_06230, E5P49_11800, E5P50_17540, E5P51_06990, E5P52_06800, E5S34_18420, E5S35_00130, E5S36_11165, E5S37_18815, E5S38_07550, E5S39_17385, E5S42_18205, E5S43_01760, E5S44_09525, E5S45_04825, E5S46_19575, E5S47_12360, E5S48_12815, E5S51_08320, E5S52_09495, E5S53_16295, E5S54_18365, E5S55_16285, E5S57_07225, E5S58_05565, E5S59_11205, E5S61_20105, E5S62_13815, E6C80_03245, E6D34_00950, EA239_13380, EA435_20340, EAI46_03605, EAN77_17385, EAX79_05520, EC1094V2_3674, EC95NR1_04363, ECs0179, ED648_00125, EHD79_10695, EI021_19885, EIA08_06365, EIZ93_07885, EKI52_10395, EL79_3697, EL80_3644, ELT16_21295, ELT17_01290, ELT20_04510, ELT21_15085, ELT22_08915, ELT23_12135, ELT24_18765, ELT25_21005, ELT26_05540, ELT27_04430, ELT28_17160, ELT29_02955, ELT30_18480, ELT31_08735, ELT32_04825, ELT33_15830, ELT34_19930, ELT35_06860, ELT36_13995, ELT38_13410, ELT39_20820, ELT40_02090, ELT41_02015, ELT44_21565, ELT45_20755, ELT46_21905, ELT48_12220, ELT49_18515, ELT50_04880, ELT52_04095, ELT55_19355, ELT56_04900, ELT58_11855, ELT59_17805, ELT60_20990, ELT61_17455, ELT63_15940, ELT72_19860, ELU07_12965, ELU82_16735, ELU83_06320, ELU85_21230, ELU88_20065, ELU89_12480, ELU90_03595, ELU91_18160, ELU94_15850, ELU95_07310, ELU97_22235, ELU98_09250, ELU99_07115, ELV00_10965, ELV01_05815, ELV02_21170, ELV03_21745, ELV04_21635, ELV07_04635, ELV08_10240, ELV09_11020, ELV10_05925, ELV11_07255, ELV12_07985, ELV13_13185, ELV15_10235, ELV16_14945, ELV20_03255, ELV21_07945, ELV22_16495, ELV23_20045, ELV26_20265, ELV28_04145, ELV29_15990, ELV40_17675, ELX48_04100, ELX61_13270, ELX66_06770, ELX68_15925, ELX69_11295, ELX76_14590, ELX79_12450, ELX85_10405, ELX96_04985, ELY02_13720, ELY31_21175, ELY32_08495, ELY39_01365, ELY41_06580, ELY48_16875, EN85_001940, EPS76_09925, ERS085406_00578, ERS139208_01237, EWK56_14925, EYV17_16485, EYV18_21785, F0L67_09105, F2N20_00125, F2N31_00125, F3N40_16060, F7F11_02035, F7N46_12575, F9413_16900, F9461_04780, F9B07_03480, F9V24_09540, F9X20_09395, FDM60_08780, FE584_15725, FE587_16410, FEJ01_15100, FFF58_06145, FHO90_19930, FIJ20_13935, FJQ40_14175, FKO60_12300, FOI11_012800, FOI11_22880, FPI65_00965, FPJ29_11720, FPS11_04890, FQF29_01490, FV293_02855, FVB16_04485, FWK02_04400, FY127_02905, FZC17_23605, FZN31_19945, FZU14_18300, G3565_18205, G3813_000507, G3V95_02420, G3W53_17975, G4A38_19380, G4A47_18815, G5603_21720, G7630_000814, G9448_10075, GAI66_14365, GAI89_16125, GAJ12_05920, GAJ26_21420, GF147_13240, GF699_14310, GFY34_15765, GIB53_10160, GJ11_00925, GJO56_09475, GKF66_15225, GKF89_14740, GNW61_11420, GNZ05_09785, GOP25_07210, GP711_09570, GP944_03110, GQM04_14355, GQM21_02740, GQN34_16145, GQW80_13555, GRC73_19630, GRW05_07735, GSM54_14470, GTP88_05365, GUC01_17920, GUI33_00125, H0O37_03390, H0O39_04955, H0O72_10145, H6Y26_004466, HEP30_016645, HEP34_000941, HHH44_003655, HI055_000768, HIE29_003111, HJQ60_000684, HJS37_001619, HJU54_003394, HKA49_001644, HL563_02695, HL601_07740, HLV18_20665, HLX92_18930, HLZ50_06920, HmCms169_00369, HMJ82_00130, HMU06_10015, HMV95_04545, HMW38_10535, HNC36_16200, HNC59_20385, HNC66_11645, HNC99_17465, HND12_10395, HV109_19340, HV209_01580, HVV39_17670, HVW04_10185, HVW19_15015, HVW43_11715, HVY77_20925, HVZ71_20360, HX136_20560, I6H01_17735, I6H02_18690, IFB95_000535, IH768_15425, IT029_001934, J0541_003907, J4S20_003219, JE86ST02C_01710, JE86ST05C_01740, JFD_01263, JNP96_05075, NCTC10082_01374, NCTC10089_04067, NCTC10090_02151, NCTC10429_04185, NCTC10865_05056, NCTC11112_03444, NCTC11181_01353, NCTC12950_04415, NCTC13127_05445, NCTC13148_05206, NCTC13216_02723, NCTC4450_07390, NCTC8008_03664, NCTC8009_07311, NCTC8621_04193, NCTC8959_04852, NCTC8960_01553, NCTC9037_04180, NCTC9073_03384, NCTC9111_04256, NCTC9706_01328, NCTC9775_02319, NCTC9777_00463, ND22_002541, RG28_03870, SAMEA3472044_04148, SAMEA3472056_00964, SAMEA3472147_00389, SAMEA3751407_04805, SAMEA3752557_00883, SAMEA3753106_03559, TUM18780_35950, WP4S18E07_36860, WR15_02370, XU56_000257 発現宿主: ![]() ![]() |
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#2: タンパク質 | 分子量: 39882.375 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) ![]() ![]() 遺伝子: bamB, yfgL, b2512, JW2496 発現宿主: ![]() ![]() 参照: UniProt: P77774 |
#3: タンパク質 | 分子量: 34401.250 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
#4: タンパク質 | 分子量: 25816.818 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
#5: タンパク質 | 分子量: 11610.833 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() |
-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 |
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試料調製
構成要素 |
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分子量 | 値: 0.20098298 MDa / 実験値: NO | ||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 8 | ||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 3.3 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 90 % / 凍結前の試料温度: 277 K |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 165000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 3.58 sec. / 電子線照射量: 44.8 e/Å2 フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 1 / 実像数: 6063 |
電子光学装置 | エネルギーフィルター名称: TFS Selectris / エネルギーフィルタースリット幅: 10 eV |
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解析
ソフトウェア |
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EMソフトウェア |
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CTF補正 | タイプ: NONE | |||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 656080 | |||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 169599 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||
原子モデル構築 | B value: 82 / プロトコル: FLEXIBLE FIT / 空間: REAL | |||||||||||||||||||||||||||||||||||
精密化 | 交差検証法: NONE 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2 | |||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 27.29 Å2 | |||||||||||||||||||||||||||||||||||
拘束条件 |
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