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- PDB-7ttc: BamABCDE bound to substrate EspP -

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Basic information

Entry
Database: PDB / ID: 7ttc
TitleBamABCDE bound to substrate EspP
Components
  • (Outer membrane protein assembly factor ...) x 5
  • Serine protease EspP
KeywordsMEMBRANE PROTEIN / membrane protein folding / membrane dynamics / outer membrane protein / BAM / beta-barrel
Function / homology
Function and homology information


Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region ...Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / cell outer membrane / periplasmic space / serine-type endopeptidase activity / cell surface / proteolysis / extracellular region / membrane / identical protein binding
Similarity search - Function
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 / Outer membrane protein assembly factor BamB / 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 / Pyrrolo-quinoline quinone repeat / PQQ-like domain / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Quinoprotein alcohol dehydrogenase-like superfamily / Pectin lyase fold/virulence factor / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Chem-K33 / Outer membrane protein assembly factor BamD / Outer membrane protein assembly factor BamE / Outer membrane protein assembly factor BamA / Outer membrane protein assembly factor BamB / Serine protease EspP / Outer membrane protein assembly factor BamC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDoyle, M.T. / Jimah, J.R. / Dowdy, T. / Ohlemacher, S.I. / Larion, M. / Hinshaw, J.E. / Bernstein, H.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK052037 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)1ZIADK060100 United States
CitationJournal: Cell / Year: 2022
Title: Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding.
Authors: Matthew Thomas Doyle / John R Jimah / Tyrone Dowdy / Shannon I Ohlemacher / Mioara Larion / Jenny E Hinshaw / Harris D Bernstein /
Abstract: 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.
History
DepositionFeb 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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Assembly

Deposited unit
B: Outer membrane protein assembly factor BamB
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
P: Serine protease EspP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,3017
Polymers230,6226
Non-polymers6801
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Outer membrane protein assembly factor ... , 5 types, 5 molecules BAEDC

#1: Protein Outer membrane protein assembly factor BamB


Mass: 39882.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: bamB, yfgL, b2512, JW2496 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P77774
#2: Protein Outer membrane protein assembly factor BamA


Mass: 89750.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TPJ2
#3: Protein Outer membrane protein assembly factor BamE


Mass: 10391.554 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3L5AP29
#4: Protein Outer membrane protein assembly factor BamD


Mass: 25816.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bamD, EAMG_00990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X3I1M6
#5: Protein Outer membrane protein assembly factor BamC


Mass: 34401.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: W8SZY2

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Protein / Non-polymers , 2 types, 2 molecules P

#6: Protein Serine protease EspP


Mass: 30379.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: espP, L7020, ECO57PM78 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7BSW5
#7: Chemical ChemComp-K33 / 2,3-dideoxy-6-O-[2-deoxy-4-O-phosphono-2-(tetradecanoylamino)-alpha-L-gulopyranosyl]-1-O-phosphono-beta-D-threo-hexopyranose


Mass: 679.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H51NO15P2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BamABCDE bound to substrate EspP / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 8
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Specimen holderCryogen: NITROGEN
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1160GATAN K2 SUMMIT (4k x 4k)
2160GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150955 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00910419
ELECTRON MICROSCOPYf_angle_d0.89614149
ELECTRON MICROSCOPYf_dihedral_angle_d13.5723748
ELECTRON MICROSCOPYf_chiral_restr0.0531543
ELECTRON MICROSCOPYf_plane_restr0.0061848

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