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- PDB-6z12: Salmonella AcrB solubilised in the SMA copolymer -

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データを開く


IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6z12
タイトルSalmonella AcrB solubilised in the SMA copolymer
要素Efflux pump membrane transporter
キーワードMEMBRANE PROTEIN / AcrB
機能・相同性
機能・相同性情報


xenobiotic transport / efflux transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
類似検索 - 分子機能
Hydrophobe/amphiphile efflux-1 HAE1 / Acriflavin resistance protein / Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains / AcrB/AcrD/AcrF family
類似検索 - ドメイン・相同性
Efflux pump membrane transporter / Efflux pump membrane transporter
類似検索 - 構成要素
生物種Salmonella enterica I (サルモネラ菌)
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: 4.6 Å
データ登録者Muench, s.p. / Johnson, R.M.
資金援助 英国, 3件
組織認可番号国
Wellcome Trust109158/B/15/Z 英国
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N002776/1 英国
Wellcome Trust108372/A/15/Z 英国
引用ジャーナル: Microorganisms / 年: 2020
タイトル: Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from .
著者: Rachel M Johnson / Chiara Fais / Mayuriben Parmar / Harish Cheruvara / Robert L Marshall / Sophie J Hesketh / Matthew C Feasey / Paolo Ruggerone / Attilio V Vargiu / Vincent L G Postis / ...著者: Rachel M Johnson / Chiara Fais / Mayuriben Parmar / Harish Cheruvara / Robert L Marshall / Sophie J Hesketh / Matthew C Feasey / Paolo Ruggerone / Attilio V Vargiu / Vincent L G Postis / Stephen P Muench / Vassiliy N Bavro /
要旨: is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of ... is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the AcrB transporter remained unknown to-date, with much of our structural understanding coming from the orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of AcrB. Together, these reveal several important differences with respect to the protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance.
履歴
登録2020年5月11日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年7月22日Provider: repository / タイプ: Initial release
改定 1.12024年5月15日Group: Data collection / Database references
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

ムービー
  • 登録構造単位
  • Jmolによる作画
  • ダウンロード
  • EMマップとの重ね合わせ
  • マップデータ: EMDB-4460
  • UCSF Chimeraによる作画
  • ダウンロード
ムービービューア
構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Efflux pump membrane transporter
B: Efflux pump membrane transporter
C: Efflux pump membrane transporter


分子量 (理論値)分子数
合計 (水以外)341,2783
ポリマ－341,2783
非ポリマー00
水00
1
A: Efflux pump membrane transporter


分子量 (理論値)分子数
合計 (水以外)113,7591
ポリマ－113,7591
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_5551
2
B: Efflux pump membrane transporter


分子量 (理論値)分子数
合計 (水以外)113,7591
ポリマ－113,7591
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_5551
3
C: Efflux pump membrane transporter


分子量 (理論値)分子数
合計 (水以外)113,7591
ポリマ－113,7591
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_5551

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要素

#1: タンパク質 Efflux pump membrane transporter


分子量: 113759.227 Da / 分子数: 3 / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica I (サルモネラ菌)
遺伝子: acrB, A4O23_10955, A4O45_03810, A5895_15265, AAC70_12525, AAL03_14960, AAM89_07765, AAV76_19425, ABK55_05725, ABO08_03475, AC391_10965, ACH21_19020, ACK40_00105, ACK79_15085, ACS18_20650, ...遺伝子: acrB, A4O23_10955, A4O45_03810, A5895_15265, AAC70_12525, AAL03_14960, AAM89_07765, AAV76_19425, ABK55_05725, ABO08_03475, AC391_10965, ACH21_19020, ACK40_00105, ACK79_15085, ACS18_20650, ACV85_05805, ADQ53_03685, ADQ64_15580, ADT85_17470, AF726_08820, AG46_12710, AG53_15950, AGQ41_04335, AGQ90_03080, AGR09_08325, AGR46_16415, AH060_16145, AH079_04350, AH254_22600, AH360_16970, AH543_16315, AH557_09130, AH612_19020, AH874_13175, AHN36_15795, AHN91_21865, AHQ94_20600, AHS94_22030, AHU36_11045, AHU48_23190, AHX56_08240, AHY46_22370, AHZ72_05105, AIA22_12165, AIB97_16815, AID13_02815, AIE18_09140, AIF85_07160, AL864_02820, AL929_23130, ALX58_14045, AU885_11650, AVA95_03925, AVB28_08510, AVG51_11480, AVH38_04545, AXK79_19705, AXM38_07800, AXM50_14470, AXM56_16685, AXM65_18530, AXM93_08445, AXN14_02155, AXN15_07580, AXN21_06965, AXN39_11550, AXN51_12700, AXN72_08000, AXO05_08570, AXO78_17315, AXO93_15340, AXQ08_14655, AXR02_08970, AXR82_02315, AXR91_01290, AXS04_01695, AXS89_02055, AXT07_05965, AXT19_05915, B9C63_11810, BXE81_09065, BXG02_07180, BXG42_09370, BXH36_10215, BXH66_08040, BXL85_11765, BXO48_06645, BZ557_12735, BZ723_04100, BZ903_08940, BZV91_08875, BZW24_03920, BZW54_04755, C9E93_06140, C9E94_19180, C9F01_08965, C9F05_01290, C9P23_10335, C9Y45_03940, CB317_01000, CC394_01545, CC530_00775, CC828_04535, CE94_19610, CF93_04280, CPY04_22475, CQE41_07070, CQF73_09855, CQH69_04135, CQM91_23105, CSM01_01615, CSN39_10900, CSN48_19880, CSN51_17860, CSO96_14135, CSP66_16145, CST74_11845, CST78_12945, CV491_04375, CWG53_02155, CWG97_11285, D4346_01325, D4392_10020, D4396_04285, D4408_06485, D4427_06950, D4428_05215, D4444_11555, D4471_08450, D4490_01015, D4494_10470, D4507_05270, D4514_03660, D4515_01545, D4546_09390, D4551_09260, D4D97_05485, D4D98_08570, D4E01_09290, D4E37_05350, D4E64_10565, D4E75_00440, D4E90_05185, D4F17_01060, D4F19_04440, D4F20_07155, D4F29_07730, D4F49_16455, D4F54_04680, D4F77_10190, D4F87_02985, D4F98_10640, D4G07_10045, D4G10_11575, D4G50_05510, D4X66_01450, D4X67_01465, D4X81_08350, D4Y13_13605, D4Y27_04430, D4Y38_00790, D4Y42_06150, D4Y56_03795, D4Y61_08865, D4Y96_04575, D4Z14_05470, D4Z16_07845, D4Z17_03400, D4Z29_11545, D4Z41_08675, D4Z50_07970, D4Z57_03410, D4Z58_04655, D4Z75_04825, D5764_07825, D5769_02495, D5773_00875, D5782_03660, D5810_01285, D5836_17200, D5848_11770, D5856_03150, D5861_06225, D5881_04345, D5889_07675, D5895_01345, D5905_18015, D5915_03200, D5970_05735, D5972_06010, D5A61_03660, D5A65_05805, D5A76_04875, D5A82_03865, D5A94_12405, D5B23_01450, D5B60_01340, D5B66_05165, D5B94_03135, D5C00_05295, D5C12_08175, D5C21_07220, D5C32_06325, D5C34_10465, D5C40_07860, D5C41_08390, D5C46_12375, D5C64_03810, D5C69_08580, D5O45_04325, D5O48_05730, D5O74_04490, D5O78_09935, D5O80_07835, D5O86_11185, D5P09_09970, D5P22_01470, D5P31_04355, D5P36_04640, D5P42_03925, D5P52_00720, D5P54_05700, D5P59_05915, D5P71_08860, D5P75_03560, D5P94_16990, D5Q05_03935, D5Q09_06085, D5Q39_11635, D5Q43_00445, D5W53_06130, D5W81_01065, D5W91_06810, D5X16_03865, D5X20_07410, D5X39_00990, D5X56_02780, D5X61_00680, D5X72_03440, D5X88_07550, D5X91_04060, D5Y01_00825, D5Y06_08270, D5Y08_23240, D5Y41_01425, D6331_01310, D6379_03305, D6389_04215, D6413_06485, D6429_04170, D6448_15635, D6453_04205, D6455_06220, D6467_08685, D6J43_21925, D6J46_01025, D6J55_02800, D6J67_02330, D6J74_05385, D6J84_08940, D6K21_03765, D6K24_01080, D6K59_04410, D6L05_07630, D6P24_03240, D6P41_01305, D6P57_11975, D6P63_03960, D6Q07_11960, D6Q21_01005, D6Q25_01020, D6Q70_23040, D6Q87_10085, D6Q96_09190, D6Q97_04185, D6R14_09640, D6R58_05020, D6R62_09555, D6R98_02810, D6S02_04705, D6S13_01360, D6S22_05290, D6S36_05340, D6S45_01045, D6S47_07470, D6S50_05845, D6S52_07325, D6S74_01450, D6S83_06345, D6S89_03890, D6T18_03025, D6T31_08100, D6T37_07430, D7M89_05935, D7M98_11725, D7N03_02455, D7N07_08155, D7N22_06745, D7N26_22710, D7N30_05075, D7N47_05845, D7N51_15930, D7N52_04690, D7N80_02885, D7N86_17235, D7O13_06330, D7O17_07925, D7O23_11190, D7O25_01030, D7O28_08970, D7O59_06225, D7O77_04615, D8Q64_01020, D8Q73_05540, D8R14_01045, D8R18_08390, D8R62_10510, D8R78_07850, D8S31_02190, D8S34_08660, D8S35_08175, D8S37_06530, D8S38_08610, D8S62_04305, D8S66_05780, D9O60_02875, D9O71_05360, D9O80_03040, D9O86_13290, D9O95_03895, D9P04_07965, D9P12_05975, D9P13_14425, D9P19_07675, D9P28_09530, D9P30_03370, D9P43_10815, D9P51_02955, D9P55_07730, D9P58_06870, D9P68_09885, D9P88_00985, D9P92_02905, D9P97_06685, D9Q07_09260, D9Q11_05725, D9Q23_03710, D9Q29_06205, D9Q37_07930, D9Q49_08285, D9Q50_10325, DAR35_01005, DAW17_06730, DAX91_07060, DFQ85_05430, DFR01_09160, DK013_01025, DK030_06300, DK052_23015, DK083_04615, DK093_01040, DK094_01025, DK101_08130, DK113_08305, DK117_07485, DK127_09260, DK678_00070, DK681_09420, DK687_04055, DK711_01855, DK719_05700, DK739_06740, DK741_10685, DK756_03460, DK767_12285, DKI70_07030, DKJ03_09570, DKJ07_05835, DKS84_08230, DKT00_02710, DKT04_15920, DKT21_12805, DKT27_10265, DKT52_07220, DKU65_14915, DKV05_06000, DKV20_06200, DKV25_04445, DL088_11075, DL104_17055, DL110_05250, DL111_06640, DL115_01355, DL130_03140, DL146_02805, DLB02_07650, DLB18_08505, DLB23_01000, DLB36_10070, DLB43_07510, DLB46_07880, DLB62_03890, DLB73_00105, DLC24_04935, DLE90_18415, DLF22_04805, DLF29_05020, DLF30_08180, DLF33_10805, DLF35_01005, DLF36_02845, DLM06_04560, DLM09_00995, DLM10_09965, DLM30_04930, DLQ73_12300, DLQ79_01000, DLQ86_15735, DLQ92_03590, DLR05_06915, DLR06_01490, DLR25_05290, DLR57_10745, DM001_07440, DM006_09100, DM016_05255, DM323_06700, DM347_08405, DM358_08140, DM367_10780, DM371_02430, DM700_18145, DM703_02460, DM705_08310, DM743_09605, DMA85_03170, DMA89_15850, DMB03_08830, DMB04_15185, DML85_00605, DML97_09050, DMM16_01960, DMM17_11150, DMM22_02845, DMM24_11405, DMM43_07890, DMO61_03735, DMO65_01050, DMO79_09060, DMU74_10415, DMU80_09050, DMU82_12600, DMU94_09600, DMV06_03650, DMV13_03350, DMV20_20060, DMV32_00825, DMV34_02950, DMZ76_01020, DN020_06485, DN087_03575, DN092_04545, DN123_07690, DN125_01440, DN130_05830, DN132_04380, DN181_04005, DN182_06745, DN220_06100, DN241_03340, DN257_05145, DN259_05090, DN271_19320, DN282_15665, DN317_01415, DN319_10795, DN322_05135, DN358_10690, DN362_06885, DNI00_08045, DNI25_05135, DNI46_06020, DNI61_09285, DNI77_05260, DNI82_12125, DNI85_03675, DNJ05_06165, DNJ30_02305, DNL79_03545, DNM18_05050, DNM22_08605, DNM39_12310, DNM44_03995, DNM47_08685, DNM48_03895, DNM80_06910, DNN00_05420, DNU17_09140, DNU22_04660, DNU30_01285, DNU40_06770, DNU46_14660, DNU67_08335, DNU68_11160, DNU78_13165, DNU82_03725, DNU84_13710, DNU93_05320, DNV11_03960, DNV18_07230, DNV24_12015, DNV55_05965, DNV93_02810, DNW15_00865, DNY10_04300, DNY38_00420, DNY86_09760, DNZ14_01330, DNZ24_04550, DNZ41_01315, DNZ69_08840, DNZ74_07090, DNZ75_08705, DNZ81_03425, DNZ91_05745, DO557_05890, DO565_08085, DO591_06685, DO596_04935, DO617_04810, DO619_02490, DO630_04000, DO638_05650, DO649_13400, DO654_06280, DO661_06270, DO663_04365, DO672_01035, DO679_08555, DO681_04055, DO690_00395, DO696_07715, DO712_22550, DO727_09960, DO731_01530, DO771_06730, DO807_07800, DO827_06795, DO973_04300, DO981_01690, DO994_01335, DOA98_08020, DOB00_09740, DOB23_01440, DOB53_16610, DOB60_05740, DOB76_01635, DOC12_00300, DOC15_05765, DOC25_09930, DOC31_08415, DOC34_09315, DOC40_14960, DOC63_04280, DOG94_02935, DOH04_12155, DOH12_22545, DOH33_03235, DOH41_03550, DOH63_02830, DOH69_10710, DOH74_13625, DOH75_06000, DOH81_09930, DOI30_01020, DOI60_10480, DOI66_05845, DOJ02_05395, DOQ45_03150, DOQ73_06415, DOQ79_01065, DOR42_03375, DOR43_04775, DOR46_16150, DOR51_23780, DOR52_02535, DOR63_07395, DOR64_10515, DOR75_06845, DOV68_03030, DOV71_04785, DOV77_15350, DOV89_01625, DOW27_10165, DOW52_22585, DOW74_04075, DOX21_02055, DOX30_03420, DP688_13895, DP693_00825, DP698_06830, DP703_05145, DP712_02970, DP713_03380, DP716_06840, DP727_22840, DP728_16275, DP736_07365, DP748_02490, DP766_03155, DP778_03250, DP792_05710, DP800_16220, DP812_13225, DP837_03195, DP859_02865, DP873_09820, DP884_06665, DPA01_04065, DPA17_01430, DPA21_08565, DPA36_04755, DPA81_08695, DPA91_07750, DPB01_05745, DPB58_05530, DPB61_01065, DPB73_06705, DPB80_01010, DPC17_04415, DPC26_12120, DPC30_09225, DPC31_21295, DPC91_07340, DPD28_03410, DPD35_09350, DPD61_05565, DPD71_12990, DPD96_04945, DPE17_03960, DPE32_06850, DPE40_05345, DPE61_01100, DPE66_10470, DPE72_00995, DPE76_10585, DPE91_07335, DPE98_01700, DPF18_01415, DPF55_03280, DPF57_13210, DPF65_05290, DPF69_04225, DPJ06_06690, DPJ07_04770, DPJ18_21730, DPJ21_23060, DPJ65_05985, DPJ69_12010, DPJ81_01030, DPK19_02945, DPK49_18945, DPL03_00940, DPP06_22450, DPP34_02995, DPP49_05140, DPP57_09185, DPP70_04625, DPR96_17095, DPS51_01190, DPS62_02400, DPS71_04035, DPS75_05935, DPS77_06815, DPS96_17080, DPT22_03505, DPT41_07335, DPT74_05620, DPT84_17600, DPT95_03965, DPU11_05080, DPU13_04230, DPY66_15080, DPY81_09375, DPZ06_03150, DPZ23_03295, DPZ65_01920, DPZ67_03455, DPZ88_09965, DPZ95_04280, DQ003_10345, DQ017_21125, DQ037_03770, DQ055_06250, DQ072_13750, DQ076_16795, DQ078_07335, DQ082_06505, DQ790_02530, DQ802_06935, DQ816_09465, DQ836_21070, DQ837_05050, DQ839_09850, DQ845_10875, DQ858_00055, DQ871_15205, DQ880_07325, DQ895_06115, DQ901_09380, DQ919_02340, DQ933_07675, DQ978_14715, DQ985_10135, DQC12_07750, DQC17_05135, DQC26_03870, DQC75_03590, DQC77_06245, DQC81_16925, DQC82_09655, DQC88_01435, DQD09_24240, DQD11_01060, DQD13_03865, DQD28_13095, DQD46_02455, DQD59_03945, DQE08_00395, DQE20_03160, DQE31_05590, DQE33_13015, DQE40_13690, DQE42_08765, DQJ22_01340, DQJ50_08905, DQJ58_03830, DQJ63_05540, DQJ66_02440, DQJ71_08430, DQJ77_01030, DQJ83_05310, DQJ90_08450, DQK19_10845, DQK43_01440, DQK45_13610, DQK53_05425, DQK57_20355, DQK72_09740, DQQ27_15440, DQR39_03355, DQR40_15910, DQR74_07115, DQR85_07280, DQR90_05875, DQS34_02500, DQS55_04230, DQS56_07240, DQS62_04550, DQS71_07420, DQS74_06295, DQS89_04330, DQS98_04035, DQT21_23885, DQT31_01485, DQT40_01975, DQT47_08080, DQT59_08365, DQT67_04950, DQT85_05480, DQY62_10275, DQY86_01365, DQY91_07170, DQZ13_08220, DQZ68_04575, DQZ89_03655, DRA21_00825, DRA23_02570, DRA25_06475, DRA26_15005, DRA30_07960, DRA37_10395, DRD38_06525, DRD40_04685, DRD55_03550, DRD57_02825, DRD79_08175, DRE09_03295, DRE12_04035, DRE16_07695, DRE32_01375, DRE41_16345, DRE46_06240, DRE58_03660, DRE69_05135, DRE85_05775, DRE92_01430, DRF10_01070, DRF26_07295, DRF38_06650, DRK15_08305, DRK36_10935, DRK49_10210, DRK71_14235, DRK91_06225, DRL06_03150, DRL40_04985, DRL53_01550, DRL62_15150, DRL63_08155, DRL65_05050, DRL68_04235, DRL89_01035, DRL96_01185, DRM19_02850, DRM39_10070, DRM41_05515, DRM43_02825, DRM75_09425, DRT10_03415, DRT15_04045, DRT45_11245, DRT49_10675, DRT56_11825, DRT73_05670, DRT76_09345, DRT77_01030, DRU07_04960, DRU14_01025, DRU25_12475, DRU99_06930, DRV08_07615, DRV17_01045, DRV44_09955, DRV53_06735, DRV60_09675, DRV62_04555, DRW94_06120, DRX19_09970, DRX40_11405, DRX43_00440, DRY30_09095, DRY35_08945, DRY53_03870, DRY54_04540, DRY73_06120, DRZ18_11450, DS161_03605, DS168_01430, DS172_06735, DS181_05705, DS188_01805, DS209_03915, DS212_06790, DS228_01025, DS242_04605, DS251_06835, DS266_01340, DS269_03610, DS300_04175, DS306_05655, DS313_01340, DS324_09265, DS336_04600, DS340_09465, DS346_12760, DS368_20110, DS372_11155, DS390_10475, DS438_03885, DS468_03185, DS470_17635, DS485_05030, DS497_03915, DS570_05955, DS572_04860, DS605_10670, DS615_10365, DS651_15910, DS657_02820, DS688_11950, DS689_13215, DS708_08160, DSA82_08035, DSA90_01010, DSA91_03875, DSA99_10695, DSB20_06505, DSB26_11025, DSB29_01055, DSB36_03930, DSB44_04370, DSE94_03270, DSF03_05385, DSF06_15125, DSF13_00100, DSF32_06125, DSF57_04690, DSF62_14785, DSF92_08520, DSF93_06370, DSG01_03865, DSG07_07830, DSG23_03190, DSG69_22660, DSG96_09425, DSH12_03820, DSM73_23085, DSM81_02825, DSM84_01405, DSM85_11930, DSM96_17705, DSN05_00365, DSN18_08025, DSN41_12095, DSQ65_01425, DSQ94_01375, DSR19_03505, DSR78_10785, DSR82_03690, DSR83_08440, DSR88_10410, DSS12_01435, DSS23_05770, DSS37_03960, DSS38_06180, DSS62_22355, DSS75_06400, DSS77_03870, DST00_18010, DST18_17355, DT136_10790, DT138_00540, DT142_21420, DT150_04765, DT159_10485, DT168_04075, DT188_03155, DT193_04870, DT208_00940, DT222_17390, DTE69_04010, DTE86_06360, DTF17_05870, DTF33_02970, DTF39_03290, DTF59_06550, DTF80_05780, DTF85_01005, DTF97_01065, DTG02_02595, DTG11_04415, DTG12_07185, DTG17_13435, DTG24_05555, DTG32_01040, DTG45_10785, DTG47_08540, DTG49_04600, DTG64_04755, DTG68_11905, DTG84_10305, DTH05_03950, DTH08_07170, DTH13_09220, DTT89_02880, DTT93_01025, DTT96_06630, DTT99_02425, DTU24_08720, DTU25_07215, DTU37_09945, DTU48_07545, DTU57_10990, DTU59_09415, DTU60_01035, DTU87_17590, DTV05_07485, DTV16_05625, DTV63_11510, DTV88_17040, DTV89_05155, DTW09_15585, DTW19_02845, DU084_01010, DU092_06545, DU116_00420, DU129_23205, DU131_04030, DU148_01355, DU157_05050, DU159_12015, DU161_00750, DU165_03845, DU168_05890, DU203_03365, DU210_17755, DU215_13830, DU245_04670, DU257_01045, DU748_01890, DU754_02765, DU756_10340, DU758_06015, DU761_12840, DU762_05800, DU777_01410, DU806_14595, DU811_19780, DU834_07665, DU842_16540, DU844_07525, DU852_09995, DU854_02500, DU861_06795, DU873_02415, DU877_10080, DU916_06380, DU946_01030, DU947_01060, DU949_04885, DU954_06100, DUA40_08690, DUA46_06400, DUA52_07680, DUA53_05475, DUA65_00100, DUA91_01005, DUA93_13100, DUB05_08355, DUB53_09680, DUB79_09560, DUB80_04325, DUB82_06390, DUC24_06685, DUC35_07030, DUE02_23055, DUP59_09460, DUP60_01040, DUP67_00775, DUP70_02675, DUP71_10245, DUP74_21535, DUP91_09330, DUQ24_04285, DUQ35_01340, DUQ37_21005, DUQ39_06135, DUQ41_06535, DUQ55_11365, DUQ58_03480, DUQ62_06195, DUQ64_00590, DUQ71_20825, DUQ75_09255, DUQ82_05805, DUQ83_02605, DUQ85_06520, DUR69_18605, DUR85_01530, DUR88_02530, DUR90_07210, DUR96_16820, DUU13_17140, DUU22_03635, DUU35_10475, DUU38_03210, DUU43_07880, DUU44_03135, DUU47_14840, DUU54_17805, DUU71_16085, DUU78_10680, DUU80_06735, DUU92_05345, DUV18_06490, DUV49_17005, DUV51_09990, DUV63_07195, DUV70_07150, DUV72_12440, DUV91_06335, DUW11_05640, DUW53_01400, DV01_10115, DVE93_04900, DVF01_04210, DVF33_03245, DVF55_03535, DVF58_17950, DVG00_04280, DVG02_02975, DVG21_09825, DVG27_01320, DVG41_07205, DVG59_06390, E0U76_06940, E1723_08390, E5N87_02445, EBB74_08700, EBB77_10485, EBB78_09315, EBB82_05950, EBB89_03075, EBC18_06325, EBC34_05750, EBC39_09715, EBC44_20925, EBC68_09380, EBD00_08225, EBD05_16450, EBD20_17095, EBD25_08895, EBD36_08845, EBD43_05210, EBD77_10535, EBJ70_10680, EBJ71_01010, EBJ89_06925, EBJ93_03490, EBJ94_10965, EBK05_09080, EBK23_03750, EBK37_10015, EBK43_02755, EBK60_12435, EBK61_03755, EBO78_16280, EBO89_05830, EBO94_06365, EBP03_08425, EBP04_03395, EBP12_01030, EBP28_05175, EC417_00970, EC420_04945, EC422_04495, EC429_01340, EC434_00995, EC448_08925, EC453_08560, EC471_06365, EC474_02880, EC491_11165, EC492_01205, EC499_09710, ECA60_08605, ECA66_03335, ECA89_08860, ECA94_02770, ECA96_08230, ECB03_04845, ECB08_02380, ECC57_03340, ECC66_14845, ECD11_05680, ECD14_09420, ECD30_08195, ED432_06430, ED436_04010, ED469_03260, ED477_03225, ED486_04135, EDK87_02770, EDL23_06330, EDL36_02800, EDL46_04335, EEA55_06135, EEA59_06700, EEA63_06475, EEA67_03960, EEA91_03575, EEA93_12055, EER52_06640, EER72_05775, EER74_06695, EER75_01000, EER80_15065, EES07_03330, EES08_04495, EES26_06675, EF649_00790, EF653_07695, EF657_16060, EF664_03080, EF665_06445, EF675_05800, EF704_09510, EFQ12_01835, EFQ27_03795, EFQ33_05115, EFQ52_05980, EFQ76_04175, EGL07_15310, EGL44_08725, EGL51_05850, EGL56_03560, EGM22_05950, EGM25_01025, EGM30_19890, EH095_03075, EH102_06310, EH104_01460, EH113_07645, EH130_06335, EHB16_03305, EHB26_04220, EHB38_03060, EHB40_08960, EHB51_06420, EHB53_05245, EHB61_03800, EHB67_09945, EHB73_13145, EHC02_01270, EHC04_15005, EHD17_01205, EHD20_04800, EHD23_03730, EHE53_08440, EHE71_11715, EHE79_04055, EHE81_05630, EHF16_05060, EIE05_03115, EIE15_00620, EIE18_03485, EIE24_02515, EIE42_04075, EIE60_01415, EIK95_05630, EIK98_05950, EIL32_01395, EIW55_09875, EIW58_12505, EIW69_03350, EIW86_10825, EIW93_08525, EK92_17045, ELE06_11115, EUC09_08855, EWC36_09200, EWD86_04885, EXB88_06730, EZX96_06900, F0D09_08975, F0D12_09400, F0D14_05560, F0D29_07175, F0D58_06620, F0H97_08960, F0I33_07995, F0M26_03705, F0M28_05115, F1011_12850, F1J30_00530, F1J33_06075, F1J42_08565, F1J81_05590, F1J82_05610, F1J83_01475, F1J85_04315, F1J88_01420, F1J90_05745, F1K42_02430, F1K59_05050, F2J39_01835, F2J40_00980, F2J48_00940, F2J50_07090, F2J62_03650, F2J66_01280, F2J78_05500, F2K19_06960, F2K22_06105, F2K26_14940, F2V07_07055, F2V23_03890, F2V25_06240, F3550_01355, F3552_00850, F3554_06545, F3591_11485, F3595_10525, F3603_03295, F3626_14980, F3E16_02765, F3E20_04290, F3E26_03740, F3E44_09410, F3E63_09210, F3E73_03605, F3E77_03585, F3E81_09345, F3P41_00915, F3P70_08045, F3P71_01925, F3P74_06490, F3P75_12190, F3P83_04915, F3Q00_03840, F3Q03_05030, F3Q14_02890, F3Q15_02920, F3Q17_04825, F3Q19_00915, F3Q28_06760, F3Q63_04915, F3R19_08235, F3X32_06195, F3X39_18195, F3X53_04150, F3X54_06825, F3X74_09220, F6430_00280, F7247_03195, F7801_03470, F9P04_11415, F9P26_00380, F9Q85_11085, F9W02_05115, F9X76_16290, F9X98_08000, FE718_01360, FE738_01015, FE759_06665, FKN96_12870, FL809_10360, FMV10_12745, FP220_08405, FPF85_03010, FQS21_06835, FQS30_06725, FQS47_00615, FQS59_09325, FR245_13140, FR247_08285, FRM70_05500, FRM79_14805, FRN01_11890, FRN02_05030, FRN09_04175, FRN22_13530, FY061_02260, FZ484_04550, FZ491_03810, FZ502_10420, FZ514_03745, FZ515_13330, FZ516_05975, FZ523_01470, FZ527_01765, FZ528_04325, FZT79_05320, GAW88_10720, GCH48_00965, GCX84_03060, GCY28_22200, GCY29_11985, GDH50_05360, GDH65_00960, GN92_19330, GX90_25025, JF03_19690, JR37_17475, KO25_20305, LB54_08610, LC09_03640, LC85_05730, LH24_08730, LH82_14165, LP13_20040, MB64_17020, NB08_11105, NCTC8272_02769, NU30_22415, PK04_18245, PK95_13970, PV65_06390, QC88_19815, QD42_08685, QD82_16765, QE89_08685, QE93_10380, QF21_24215, R118_18445, R126_08305, R133_19845, RU16_07410, RU46_12145, RY46_16045, RY52_16035, S021_09745, S313_01135, S315_02435, S598_12875, S639_21410, S709_07710, S764_16455, S943_05250, TE27_11430, TL61_17385, VT29_18010, WB97_02550, XJ41_07365, XK54_01525, XK85_16820, XS28_05335, XT48_02390, XZ16_15885, Y847_07225, YA74_10200, YH39_16290, YI72_11450, YJ27_07680, YL04_09955, YL55_19460, YR14_06075, YU10_04620, Z155_07555, Z599_02180, ZA28_00110, ZA51_00590, ZA74_09315, ZD91_01440, ZF07_21535, ZG82_06210, ZO67_01860
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: A0A3U3J7F4, UniProt: Q8ZRA7*PLUS

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実験情報

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実験

実験手法: 電子顕微鏡法
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

構成要素名称: AcrB / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
分子量実験値: NO
由来(天然)生物種: Salmonella enterica subsp. enterica serovar Typhi (サルモネラ菌)
由来(組換発現)生物種: Escherichia coli (大腸菌)
緩衝液pH: 7.5
試料濃度: 1 mg/ml / 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

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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
顕微鏡モデル: FEI TITAN KRIOS
電子銃電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM
電子レンズモード: BRIGHT FIELD
撮影電子線照射量: 60 e/Å2
フィルム・検出器のモデル: FEI FALCON III (4k x 4k)

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解析

ソフトウェア名称: PHENIX / バージョン: 1.12_2829: / 分類: 精密化
CTF補正タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION
対称性点対称性: C3 (3回回転対称)
3次元再構成解像度: 4.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 316000 / 対称性のタイプ: POINT
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.00645213
ELECTRON MICROSCOPYf_angle_d0.72981251
ELECTRON MICROSCOPYf_dihedral_angle_d7.06218192
ELECTRON MICROSCOPYf_chiral_restr0.0493788
ELECTRON MICROSCOPYf_plane_restr0.0056989

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る