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- PDB-7tt5: BamABCDE bound to substrate EspP in the open-sheet EspP state -

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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: 7tt5
タイトルBamABCDE bound to substrate EspP in the open-sheet EspP state
要素
  • Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP chimera
  • Outer membrane protein assembly factor BamA
  • Outer membrane protein assembly factor BamC
  • Outer membrane protein assembly factor BamD
  • Outer membrane protein assembly factor BamE
キーワードMEMBRANE PROTEIN / membrane protein folding / membrane dynamics / outer membrane protein / BAM / beta-barrel
機能・相同性
機能・相同性情報


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / detection of maltose stimulus / maltose transport complex / protein insertion into membrane / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / maltose transport ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / detection of maltose stimulus / maltose transport complex / protein insertion into membrane / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / cell outer membrane / outer membrane-bounded periplasmic space / periplasmic space / serine-type endopeptidase activity / DNA damage response / cell surface / proteolysis / extracellular region / membrane
類似検索 - 分子機能
Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily ...Peptidase S6, IgA endopeptidase / Peptidase family S6 domain / Immunoglobulin A1 protease / Peptidase family S6 domain profile. / Autotransporter beta-domain / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / NlpB/DapX lipoprotein / Outer membrane protein assembly factor BamC / Outer membrane protein assembly factor BamC, C-terminal / NlpB/DapX lipoprotein / Autotransporter, pectate lyase C-like domain superfamily / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Lipoprotein SmpA/OmlA / Outer membrane lipoprotein BamD-like / SmpA / OmlA family / Outer membrane lipoprotein / BamE-like / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Pectin lyase fold/virulence factor / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily
類似検索 - ドメイン・相同性
Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Maltose/maltodextrin-binding periplasmic protein / Serine protease EspP / Outer membrane protein assembly factor BamC
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
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: 4.3 Å
データ登録者Doyle, M.T. / Jimah, J.R. / Dowdy, T. / Ohlemacher, S.I. / Larion, M. / Hinshaw, J.E. / Bernstein, H.D.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK052037 米国
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK060100 米国
引用ジャーナル: Cell / 年: 2022
タイトル: Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding.
著者: Matthew Thomas Doyle / John R Jimah / Tyrone Dowdy / Shannon I Ohlemacher / Mioara Larion / Jenny E Hinshaw / Harris D Bernstein /
要旨: Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known ...Transmembrane β barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the β barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model β barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "β signal" motif of EspP to correctly orient β strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated β sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that β sheets progressively fold toward BamA to form a β barrel. Along with in vivo experiments that tracked β barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate β barrel folding.
履歴
登録2022年1月31日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02022年3月30日Provider: repository / タイプ: Initial release
改定 1.12022年4月13日Group: Database references / カテゴリ: citation / Item: _citation.journal_volume / _citation.page_first

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
P: Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP chimera
A: Outer membrane protein assembly factor BamA
E: Outer membrane protein assembly factor BamE
D: Outer membrane protein assembly factor BamD
C: Outer membrane protein assembly factor BamC


分子量 (理論値)分子数
合計 (水以外)243,7905
ポリマ－243,7905
非ポリマー00
水00
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: cross-linking
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 Maltose/maltodextrin-binding periplasmic protein,Serine protease EspP chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP


分子量: 83429.984 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌) / 遺伝子: malE, b4034, JW3994, espP, L7020, ECO57PM78 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: P0AEX9, UniProt: Q7BSW5, 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ
#2: タンパク質 Outer membrane protein assembly factor BamA


分子量: 89750.094 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: bamA, yaeT, A5U30_000296, A6583_16645, A6592_02945, A8499_001882, A8C65_17810, A8W81_000025, A8X68_000025, A9819_00835, A9X72_20365, AAG43_001505, ABE90_006985, ABT96_000025, ACN002_0182, ...遺伝子: bamA, yaeT, A5U30_000296, A6583_16645, A6592_02945, A8499_001882, A8C65_17810, A8W81_000025, A8X68_000025, A9819_00835, A9X72_20365, AAG43_001505, ABE90_006985, ABT96_000025, ACN002_0182, ACN68_08270, ACN81_28495, ACU57_18535, ACW72_001733, ADS93_001956, AM270_18200, AM340_01130, AM464_17685, AMK64_000516, AML23_20635, AO169_000701, APX88_24870, AT335_002559, AT845_002198, AUQ29_01520, AW059_09880, AW086_02640, AW118_17900, AWP47_05630, AZZ83_003988, B2D52_000440, B5N24_001028, B6L15_001192, B6R12_000956, B6R15_000220, B6R17_000025, B6R27_000717, B6R48_000717, B6R87_000718, B7C15_000579, BANRA_00651, BANRA_01136, BANRA_02264, BANRA_03348, BB545_20940, BE930_13645, BE963_14875, BER14_07740, BF271_001557, BF481_003681, BFL24_00980, BG944_001864, BH692_11645, BHF52_16775, BHS81_00690, BHS87_00845, BIQ87_00835, BIZ41_19035, BJI68_15680, BJJ90_21320, BK292_13710, BK373_09635, BK375_04605, BKD45_001078, BM922_001344, BMR21_15875, BMT49_02215, BMT50_03970, BMT91_01325, BN17_46001, BO068_002867, BOH76_17675, BON63_15405, BON65_09470, BON66_02910, BON70_27195, BON72_09420, BON73_05360, BON76_15510, BON83_24810, BON87_26650, BON92_02795, BON93_03895, BON94_19435, BON95_12990, BON96_17170, BON98_18140, BOY03_001155, BR158_000492, BTQ06_06530, BUE81_01665, BUE82_19935, BvCms2454_04098, BvCmsC61A_04373, BvCmsHHP056_04085, BvCmsKKP005_03200, BvCmsKKP057_02480, BvCmsKKP061_01626, BvCmsKSP067_02017, BvCmsNSNP036_02496, BvCmsSIP024_03985, BvCmsSIP082_04451, BVL39_02145, BWI89_14010, BXT93_00750, C2121_002944, C2M16_10840, C2U48_09565, C3F40_12200, C4952_002853, C5715_17305, C5F72_21580, C5N07_08620, C5Y87_12615, C6B13_04285, C6B22_09400, C6L19_002522, C6N50_002416, C7B02_09115, C9114_06985, C9160_13545, C9E67_25165, C9Z43_09565, C9Z68_04825, CA593_02825, CBT22_000299, CCS08_22545, CCV12_001992, CCZ91_001641, CD42_002689, CDC27_24730, CDL36_07950, CDL57_02195, CF32_003760, CG831_000812, CIG67_16620, CLG78_001120, CN875_001371, CO706_23095, COD50_18665, CS116_000025, CT143_22180, CV83915_01397, CWS33_09660, CXJ73_002511, CY655_00940, D0X26_09375, D1912_21110, D2183_03850, D3G36_16715, D3O91_03230, D3Y67_16445, D4U49_05910, D4V09_06970, D5H22_05945, D6T60_04010, D9D31_08925, D9D77_16570, D9E34_01065, D9E49_02105, D9F92_13935, D9H13_16285, D9J11_16865, D9J61_11550, D9K17_15735, DAH18_22205, DAH23_11155, DAH34_04145, DAH37_16290, DAH50_07015, DB282_21960, DD762_01135, DEN86_04025, DEN89_20325, DEN95_12205, DEO15_08380, DIV22_06310, DL654_15755, DLW88_03710, DLX40_11020, DM968_04600, DN627_10205, DNQ45_10075, DNX30_02230, DP258_09315, DRW19_04885, DS732_05815, DS966_12865, DTL43_05880, DTL90_09775, DTM10_02825, DTM45_12675, DU321_03690, DXT69_01430, DXT71_01950, DXT73_18965, E0I42_19020, E0N24_06830, E0P28_15490, E2112_01200, E2119_15620, E2123_15040, E2127_15050, E2128_01390, E2129_02820, E2135_11675, E4K51_05750, E4K54_08000, E5P52_06800, E5S34_18420, E5S35_00130, E5S38_07550, E5S43_01760, E5S47_12360, E5S52_09495, E5S61_20105, E5S62_13815, EA239_13380, EA435_20340, EAI46_03605, EAN77_17385, EAX79_05520, EC1094V2_3674, EC3234A_2c01590, EC95NR1_04363, ECs0179, ED648_00125, EGC08_05740, EH88_001876, EHD79_10695, EHH55_16945, EI021_19885, EI041_03120, EIA08_06365, EIA13_13590, EIZ93_07885, EKI52_10395, EL79_3697, EL80_3644, ELT17_01290, ELT21_15085, ELT29_02955, ELT31_08735, ELT33_15830, ELT48_12220, ELT49_18515, ELT58_11855, ELT72_19860, ELU83_06320, ELU85_21230, ELU95_07310, ELV08_10240, ELV10_05925, ELV13_13185, ELV15_10235, ELV22_16495, ELV28_04145, ELX56_19515, ELX68_15925, ELX69_11295, ELX70_19445, ELX76_14590, ELX79_12450, ELX83_20565, ELX96_04985, ELY05_11510, ELY23_06725, ELY24_11330, ELY32_08495, ELY41_06580, ELY48_16875, ELY50_16100, EO241_11840, EPS76_09925, EQO00_21045, ERS085358_03248, ERS085366_02728, ERS085386_01534, ERS085406_00578, ERS139208_01237, Esc0902E_01770, ETECE1373_03878, ETECE36_04781, ETECE925_03841, EVY14_15655, EWK56_14925, EXX79_00130, EYX55_12715, EYY34_22845, F2N31_00125, F3N40_16060, F7F11_02035, F9386_00130, F9400_16030, F9407_10195, F9B07_03480, F9S76_22105, F9V07_07545, F9V24_09540, F9X20_009325, F9X20_09395, FC554_18175, FDM60_08780, FE587_16410, FEJ01_15100, FFF58_06145, FKO60_12300, FMP09_04885, FNJ67_21425, FOI11_012800, FOI11_22880, FPI65_00965, FPS82_06080, FQE77_12285, FQF29_01490, FV293_02855, FVB16_04485, FWK02_04400, FY127_02905, FZC17_23605, FZN26_20765, FZN31_19945, G3565_18205, G3813_000507, G4A38_19380, G5603_21720, G5632_13895, G6P89_20320, G6Z99_21860, G7635_002428, G9448_10075, GAJ26_21420, GBE29_06495, GF147_13240, GF646_01340, GF699_14310, GFY34_15765, GFY48_19125, GFZ60_03455, GIB53_10160, GJ11_00925, GKE84_08560, GKF52_14765, GKF86_01230, GKF89_14740, GKG12_02080, GKZ24_00130, GLW94_14850, GNO40_01290, GNZ05_09785, GOP20_16705, GP650_06555, GP662_15415, GP711_09570, GP946_16470, GQE42_12760, GQE87_01075, GQF58_20385, GQF59_21055, GQM04_14355, GQM10_19940, GQR15_00125, GQW76_10525, GQW80_13555, GRC73_19630, GRQ19_00125, GRW05_07735, GRW80_16610, GRW81_09850, GTP88_05365, GUB08_19200, GUB92_12195, GUC01_17920, GUI33_00125, GW978_09700, GXU05_001394, GXV26_001250, H0O72_10145, H4P47_19600, H4P50_20595, H4P51_20445, H5C78_04235, HCF72_000025, HH411_000472, HHH44_003655, HI055_000768, HIE29_003111, HIE44_000363, HIF90_000025, HIR12_003073, HIT56_004097, HJM92_002768, HJN04_003141, HJO75_000268, HJQ60_000684, HJS37_001619, HJS41_003075, HJU54_003394, HKA49_001644, HL425_05545, HL563_02695, HL601_07740, HLU10_20000, HLU56_21470, HLV18_20665, HLZ20_18085, HLZ50_06920, HmCms169_00369, HmCms184_03902, HmCmsJML074_02992, HMJ82_00130, HMS79_10015, HMT08_17625, HMU06_10015, HMU48_04715, HMV41_18210, HMV95_04545, HMW38_10535, HNC30_00130, HNC36_16200, HNC52_16470, HNC59_20385, HNC66_11645, HNC75_04035, HNC99_17465, HND12_10395, HNO08_14350, HNV65_08935, HNV94_05360, HPE39_04400, HV109_19340, HVV39_17670, HVV53_21540, HVW04_10185, HVW11_05940, HVW22_02345, HVW43_11715, HVY77_20925, HVZ33_19710, HVZ71_20360, HX136_20560, HZ71_000489, HZ72_000275, I6H01_17735, I6H02_18690, JE86ST02C_01710, JE86ST05C_01740, MJ49_06155, MS7163_00195, NCTC10082_01374, NCTC10089_04067, NCTC10090_02151, NCTC10429_04185, NCTC10865_05056, NCTC11022_04904, NCTC11112_03444, NCTC11181_01353, NCTC12950_04415, NCTC13127_05445, NCTC13148_05206, NCTC13216_02723, NCTC4450_07390, NCTC8008_03664, NCTC8009_07311, NCTC8621_04193, NCTC8959_04852, NCTC8960_01553, NCTC9048_04425, NCTC9050_02018, NCTC9073_03384, NCTC9111_04256, NCTC9434_02619, NCTC9703_03426, NCTC9706_01328, NCTC9775_02319, NCTC9777_00463, NCTC9969_04257, ND22_002541, PGD_03818, PU06_23000, RG28_03870, SAMEA3472043_02535, SAMEA3472044_04148, SAMEA3472056_00964, SAMEA3472064_04397, SAMEA3472080_03761, SAMEA3472120_03174, SAMEA3472147_00389, SAMEA3484427_01384, SAMEA3484429_01097, SAMEA3485101_01115, SAMEA3485110_03703, SAMEA3751407_04805, SAMEA3752312_01935, SAMEA3752386_04693, SAMEA3752557_00883, SAMEA3753064_03379, SAMEA3753290_00402, SAMEA3753300_01854, SM09_00918, THOESC010_36610, TUM18780_35950, UN91_10540, WP2S18E08_37660, WP4S18E07_36860, WP4S18E08_36510, WQ89_09595, WR15_02370
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: C3TPJ2
#3: タンパク質 Outer membrane protein assembly factor BamE


分子量: 10391.554 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Escherichia coli (大腸菌)
遺伝子: bamE, AAS29_002226, BOB65_003886, BR331_19465, BRV34_003496, BRV41_003951, FA849_11240, FA868_10515, FEL34_03710, FGY90_15150, FHD44_22100, HJ940_004168, HJ942_003983
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A3L5AP29
#4: タンパク質 Outer membrane protein assembly factor BamD


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) Escherichia coli (大腸菌) / 遺伝子: bamD, EAMG_00990 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A1X3I1M6
#5: タンパク質 Outer membrane protein assembly factor BamC


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) Escherichia coli (大腸菌)
遺伝子: bamC, nlpB, A6592_19755, A8C65_04235, A8W81_002200, A8X68_004535, A9X72_07035, AAG43_000963, ABT96_004580, ACN002_2512, ACN68_11560, ACN81_26800, ACU57_04515, ACW72_004516, AM270_06735, ...遺伝子: bamC, nlpB, A6592_19755, A8C65_04235, A8W81_002200, A8X68_004535, A9X72_07035, AAG43_000963, ABT96_004580, ACN002_2512, ACN68_11560, ACN81_26800, ACU57_04515, ACW72_004516, AM270_06735, AM464_03885, AMK64_004175, AML23_07690, AO169_004464, APX88_06575, AT335_000411, AT845_001008, AUQ29_15820, AW086_17130, AW118_06195, AWP47_27020, B2D52_004705, B5N24_004745, B6L15_004627, B6R12_002797, B6R15_001739, B6R17_003253, B6R27_002526, B6R48_002788, B6R87_002569, B9T59_21405, BANRA_01021, BANRA_03560, BANRA_04601, BB545_17690, BE963_28130, BER14_02350, BF271_000600, BF481_001132, BG821_002569, BHF52_09620, BHS81_15170, BIQ87_14450, BIZ41_13405, BJI68_01535, BK272_07480, BK292_09100, BK373_06140, BK375_00595, BKD45_004383, BMC34_001196, BMC79_004175, BMR21_01425, BMT91_12040, BO068_001811, BOH76_02570, BON65_15590, BON66_22990, BON70_19385, BON72_10980, BON73_16825, BON76_02345, BON83_11105, BON86_12870, BON87_06150, BON92_23095, BON93_11745, BON94_05640, BON95_12010, BON96_16290, BTQ06_24710, BUE81_00175, BUE82_06175, BvCms2454_00576, BvCmsC61A_03920, BvCmsHHP019_02257, BvCmsHHP056_03727, BvCmsKKP005_05022, BvCmsKKP057_02213, BvCmsKKP061_00365, BvCmsKSNP073_01370, BvCmsKSP011_03652, BvCmsKSP067_01143, BvCmsNSNP036_03233, BvCmsSIP082_02181, BVL39_14450, BWI89_00815, BXT93_09065, BZL69_23975, C2121_003940, C4952_000194, C5542_000116, C5F72_07725, C5N07_10515, C5Y87_17305, C6B22_04570, C6N50_000623, C9160_05285, C9Z62_03680, C9Z68_02140, CA593_14465, CBT22_004760, CCS08_18120, CCZ91_004547, CD42_000570, CDC27_13110, CDL36_08690, CDL37_24220, CF32_001012, CG692_24660, CG831_000231, CIG67_19480, CLG78_004479, CO706_10250, COD50_09400, CQP61_08535, CS116_004421, CWS33_10415, CXJ73_000266, CY655_15855, D0X26_11920, D3822_05395, D3O91_03970, D3Y67_12985, D4V09_11230, D5H22_07755, D6T60_00595, D9D31_00585, D9D43_09275, D9D77_11380, D9E34_00585, D9H13_02835, D9H94_18900, D9J11_04670, DAH34_02675, DAH37_19960, DAH50_04635, DB282_12805, DD762_13530, DEN86_22815, DEN89_10395, DEO15_01760, DIV22_31745, DL654_08500, DLX40_07815, DM968_15395, DN627_17995, DNQ45_02690, DP258_07610, DRW19_07685, DS732_18480, DTL43_01510, DTL90_08635, DTM10_01015, DTM45_09650, DU321_10720, DXT71_21935, E0I42_02740, E0N24_06335, E2112_00485, E2119_05135, E2123_03705, E2127_04515, E2128_16640, E2129_06730, E2135_00555, E4K51_07145, E4K54_09390, E5P52_09820, E5S34_12860, E5S38_13070, E5S47_00585, E5S52_12530, E5S61_11100, E5S62_08550, EAN77_04825, EBP16_10430, EC1094V2_1211, EC3234A_44c00830, EC95NR1_01696, ED648_19505, EGC08_02915, EH88_000114, EHD79_10200, EHH55_03705, EI021_07715, EIZ93_19650, EKI52_22355, EL79_1185, EL80_1190, ELT17_16720, ELT21_03525, ELT29_06610, ELT58_05595, ELU85_09985, ELV08_03665, ELV15_17835, ELV28_11920, ELX69_02635, ELX76_09875, ELX96_00040, ELY05_02505, ELY32_00570, ELY41_04440, ELY48_09690, EO241_29005, ERS085358_03192, ERS085366_00345, ERS085386_00039, ERS139208_00589, ETECE1373_01350, ETECE36_02095, ETECE925_01347, ExPECSC038_04470, EXX13_08605, EXX79_12495, EYX55_00585, EYY34_10895, F2N31_04780, F3N40_17940, F6U69_05120, F9386_06110, F9407_01990, F9B07_19285, F9S83_10130, F9V07_13505, F9V24_02690, FC554_01940, FDM60_09380, FE587_10155, FGG80_09005, FJQ51_23260, FKO60_11800, FOI11_000570, FOI11_19480, FPS82_08960, FV293_04230, FVB16_11325, FY127_07270, FZN30_01400, G3813_001234, G4A38_06330, G5632_01995, G9448_21585, GF646_05030, GF699_07070, GFY34_13710, GFZ60_03165, GIB53_06795, GKF86_10520, GKG12_07390, GNO40_02645, GNZ05_14470, GP650_11215, GP946_09630, GP979_00725, GQE42_04985, GQE64_06570, GQE87_07245, GQF58_03875, GQF59_03850, GQM04_18635, GQM09_02405, GQM10_11480, GQR15_07015, GQW68_23860, GRQ19_13570, GRW05_01010, GRW57_15710, GRW81_02785, GW978_16940, H0O72_12075, H4P47_06810, H4P50_06340, H4P51_06385, H5C78_16415, HCF72_001812, HH795_002546, HHG09_001243, HHH44_002689, HIE44_000224, HIF90_002766, HIN64_004060, HIT56_001086, HJO75_001595, HJQ60_001062, HJS37_000213, HJS41_002178, HJU54_002647, HL563_06480, HLU56_17545, HmCms184_03495, HmCmsJML074_00064, HMS79_11270, HMT08_04955, HMT08_28750, HMU48_07410, HMV95_10630, HNC30_03420, HNC30_26600, HNC36_05035, HNC38_17555, HNC52_03340, HNC52_27645, HNC59_20140, HNC66_18255, HNC75_00525, HNC75_28500, HNC99_16815, HND24_11145, HNV65_05630, HNY50_09775, HNY54_11535, HV109_06365, HVV53_09290, HVZ33_06850, HX136_06685, HZ72_000133, I6H00_25635, I6H01_06370, I6H02_07670, JE86ST02C_29570, JE86ST05C_29610, MJ49_18500, NCTC10090_04434, NCTC10764_00647, NCTC10865_01743, NCTC11022_02534, NCTC11126_06126, NCTC11181_03634, NCTC11341_00816, NCTC12950_01648, NCTC13148_02274, NCTC13216_00543, NCTC4450_03337, NCTC7927_01568, NCTC8008_00803, NCTC8621_01448, NCTC8960_04114, NCTC9036_01478, NCTC9044_00198, NCTC9045_01669, NCTC9048_01461, NCTC9050_04702, NCTC9077_01815, NCTC9111_01883, NCTC9117_01960, NCTC9702_01656, NCTC9703_01031, NCTC9706_04674, NCTC9969_01610, PGD_00767, RG28_09510, SAMEA3472043_00977, SAMEA3472044_02057, SAMEA3472056_00816, SAMEA3472064_02059, SAMEA3472080_01551, SAMEA3472147_00102, SAMEA3484427_00337, SAMEA3484429_00446, SAMEA3485101_04932, SAMEA3485110_01223, SAMEA3752312_00108, SAMEA3752557_01026, SAMEA3753300_00970, SM09_02636, THOESC010_12830, TUM18780_12260, UN91_14105, WP4S18E07_13160, WP4S18E08_12820, WQ89_05460, WR15_19465
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: W8SZY2

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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: BamABCDE bound to substrate EspP in the open-sheet EspP state
タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT
由来(天然)生物種: Escherichia coli (大腸菌)
由来(組換発現)生物種: Escherichia coli (大腸菌) / 株: BL21(DE3)
緩衝液pH: 8
試料濃度: 2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES
急速凍結装置: LEICA EM GP / 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 / 最大 デフォーカス（公称値）: 1800 nm / 最小 デフォーカス（公称値）: 600 nm
試料ホルダ凍結剤: NITROGEN
撮影
IDImaging-ID電子線照射量 (e/Å2)フィルム・検出器のモデル
1160GATAN K2 SUMMIT (4k x 4k)
2160GATAN K3 (6k x 4k)

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解析

ソフトウェア名称: PHENIX / バージョン: 1.18.2_3874: / 分類: 精密化
CTF補正タイプ: NONE
3次元再構成解像度: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 76511 / 対称性のタイプ: POINT
拘束条件
Refine-IDタイプDev ideal数
ELECTRON MICROSCOPYf_bond_d0.0047483
ELECTRON MICROSCOPYf_angle_d0.68710133
ELECTRON MICROSCOPYf_dihedral_angle_d10.22668
ELECTRON MICROSCOPYf_chiral_restr0.0431065
ELECTRON MICROSCOPYf_plane_restr0.0051326

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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