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Yorodumi- PDB-6l7c: CsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system -
+Open data
-Basic information
Entry | Database: PDB / ID: 6l7c | ||||||
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Title | CsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Biofilm / Curli biogenesis system / CsgFG Complex / Substrate CsgA | ||||||
Function / homology | Function and homology information curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / regulation of amyloid fibril formation / single-species biofilm formation / pilus / cell outer membrane / outer membrane-bounded periplasmic space / amyloid fibril formation ...curli secretion complex / curli assembly / protein secretion by the type VIII secretion system / protein transmembrane transport / regulation of amyloid fibril formation / single-species biofilm formation / pilus / cell outer membrane / outer membrane-bounded periplasmic space / amyloid fibril formation / cell adhesion / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli O69:H11 str. 08-4661 (bacteria) Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å | ||||||
Authors | Yan, Z.F. / Yin, M. / Chen, J.N. / Li, X.M. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Assembly and substrate recognition of curli biogenesis system. Authors: Zhaofeng Yan / Meng Yin / Jianan Chen / Xueming Li / Abstract: A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents ...A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents for biofilm-related infections. Here we report a systematic study of the curli biogenesis system, highlighted by structural, biochemical and functional analysis of the secretion channel complexes (CsgF-CsgG) with and without the curli substrate. The dual-pore architecture of the CsgF-CsgG complex was observed and used to develop an approach to inhibit the curli secretion by physically reducing the size of the CsgF pore. We further elucidated the assembly of the CsgFG complex with curli components (CsgA and CsgB) and curli-cell association through CsgF. Importantly, the recognition of the CsgA substrate by CsgG was uncovered. Nine crevices outside of the CsgG channel provide specific and highly-conserved recognition sites for CsgA N-terminus. Together with analysis of CsgE, our study provides comprehensive insights into curli biogenesis. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6l7c.cif.gz | 457.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l7c.ent.gz | 376 KB | Display | PDB format |
PDBx/mmJSON format | 6l7c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6l7c_validation.pdf.gz | 790.5 KB | Display | wwPDB validaton report |
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Full document | 6l7c_full_validation.pdf.gz | 802.2 KB | Display | |
Data in XML | 6l7c_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 6l7c_validation.cif.gz | 89.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/6l7c ftp://data.pdbj.org/pub/pdb/validation_reports/l7/6l7c | HTTPS FTP |
-Related structure data
Related structure data | 0842MC 0841C 6l7aC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 30584.035 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O69:H11 str. 08-4661 (bacteria) Gene: BX06_26815 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A027ZN26, UniProt: P0AEA2*PLUS #2: Protein | Mass: 15065.705 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: csgF, A6581_12775, A6592_16410, A8C65_09935, A8G17_17590, A8M42_01085, A9819_06490, A9R57_10355, AC789_1c11470, ACN002_1089, ACN81_09400, ACU57_27055, ACU90_19250, AJ318_00960, AKG99_07850, ...Gene: csgF, A6581_12775, A6592_16410, A8C65_09935, A8G17_17590, A8M42_01085, A9819_06490, A9R57_10355, AC789_1c11470, ACN002_1089, ACN81_09400, ACU57_27055, ACU90_19250, AJ318_00960, AKG99_07850, AM270_13185, AM464_23205, AMK83_16440, AML07_18510, APU18_12970, APZ14_01615, ARC77_26185, AU473_14305, AUQ13_23570, AUS26_14005, AW106_27240, AWE53_020770, AWF59_023705, AWG78_002955, AWP75_16905, AZZ83_000749, B1K96_25200, B7C53_12210, B9T59_24180, BANRA_01291, BANRA_01576, BANRA_01635, BANRA_04608, BB545_06045, BER14_09940, BHS81_06565, BHS87_05490, BIQ87_05800, BIU72_07215, BIZ41_17475, BJJ90_16050, BK292_02235, BK334_17375, BK373_20095, BK400_19610, BMT49_08095, BMT91_12220, BN17_09001, BON63_21540, BON66_00235, BON69_23620, BON76_26665, BON92_25375, BON93_01750, BTQ04_04830, BTQ06_28615, BUE81_01495, BvCms12BK_01199, BvCms2454_01967, BvCms35BK_05180, BvCmsA75A_03631, BvCmsF63A_02901, BvCmsH15A_03205, BvCmsHHP001_05125, BvCmsHHP019_01648, BvCmsHHP056_03328, BvCmsJ76A_01745, BvCmsKKP061_02124, BvCmsKSNP019_00536, BvCmsKSNP073_05115, BvCmsKSNP081_02155, BvCmsKSNP120_02370, BvCmsKSP008_00766, BvCmsKSP011_05236, BvCmsKSP015_04950, BvCmsKSP018_00729, BvCmsKSP024_02020, BvCmsKSP026_03242, BvCmsKSP036_02551, BvCmsKSP039_03584, BvCmsKSP040_00078, BvCmsKSP045_01294, BvCmsKSP054_01494, BvCmsKSP058_01099, BvCmsKSP061_05085, BvCmsKSP067_02664, BvCmsKSP076_00221, BvCmsKSP081_01991, BvCmsKSP083_04126, BvCmsNSNP006_00926, BvCmsNSNP023_01666, BvCmsNSNP027_01041, BvCmsNSNP036_01556, BvCmsNSP006_01448, BvCmsNSP007_03010, BvCmsNSP039_04491, BvCmsNSP045_01873, BvCmsNSP047_03188, BvCmsNSP052_01638, BvCmsNSP072_01737, BvCmsNSP078_01753, BvCmsOUP014_03127, BvCmsSINP011_02870, BvCmsSINP022_01393, BvCmsSINP036_02015, BvCmsSIP006_02579, BvCmsSIP010_04114, BvCmsSIP019_05011, BvCmsSIP044_01602, BVL39_23020, BW690_20185, BWP17_14750, C1I57_23660, C2M16_23325, C2U48_03735, C3449_22250, C4J69_16245, C4K41_10685, C5N07_21975, C5P01_13585, C5P43_18785, C5P44_04330, C6669_24200, C6986_06430, C6B13_08320, C7235_15270, C7B02_01110, C7B06_10030, C7B07_08350, C9025_13220, C9083_13050, C9200_05635, C9212_12645, C9255_16880, C9299_13245, C9E25_15565, C9E67_18455, C9Y80_08970, C9Y95_14355, C9Z12_15420, CA593_23315, CDL37_22840, CG692_25470, CI641_021185, CI694_24070, COD30_07495, COD46_11805, CQP61_11360, CR538_15905, CR539_09835, CRD98_09770, CRE06_18275, CRM83_09165, CSB64_07125, CT143_19775, CT146_19235, CVH05_20310, CWM24_09415, CWS33_22375, D0X26_23320, D1900_15070, D1912_33520, D2183_15675, D2184_16790, D2185_03375, D2F89_16725, D3821_20245, D3822_19530, D3C88_18190, D3O91_17020, D3Y67_15515, D4M06_16745, D7K63_17880, D7K66_17230, D7Y10_25390, D9D20_13510, D9E35_09110, D9G11_01800, D9G42_02010, D9H53_22330, D9H70_23200, D9H94_04555, D9I11_06735, D9I18_09120, D9I20_14875, D9I87_24110, D9I97_06115, D9J03_24045, D9J11_10875, D9J44_05170, D9K48_17895, D9K54_26755, D9L89_17300, D9L99_25015, D9X97_17120, DAH26_20385, DAH27_16630, DAH36_09625, DAH37_07515, DEN86_26015, DEN89_04050, DEO11_03635, DEO19_16190, DIV22_28760, DL455_07100, DL545_15180, DL800_08370, DMI04_15810, DNB37_24555, DNQ41_09265, DNR41_04640, DOY56_16760, DP258_00480, DQE83_00815, DQF57_17655, DQO13_15190, DS732_10230, DS966_20145, DTL43_16545, DTL90_00105, DTM10_22410, DTM25_02505, DU333_10225, DW236_07305, DXT71_23350, E0E06_19720, E2119_27400, E2132_08845, E2855_01310, E2863_01207, E5M00_13230, EAI42_03980, EAI46_03030, EAI52_09335, EB509_13100, EB510_15335, EB515_17370, EC3234A_26c00110, EC3426_01949, EC95NR1_05434, ECONIH1_06410, ECs1415, ECTO6_02921, ED225_16610, ED600_22300, ED607_11755, ED611_18205, ED648_24045, ED903_22580, ED944_18280, EEA45_10640, EEP23_24640, EF173_18855, EFV06_07775, EFV08_14150, EGY17_18935, EIA08_02665, EIA21_07755, EJC75_04035, EJH97_14750, EKI52_04095, EL75_2704, EL79_2739, EL80_2716, ELT33_12235, EO241_06505, EPS94_06625, EPS97_23230, EQ825_00060, ERL57_04175, ERS085365_03587, ERS085379_02716, ERS085383_03172, ERS085404_02838, ERS085406_01151, ERS085416_00210, ERS139211_03440, ERS150873_02816, ERS150876_03011, EVY21_12440, EWK56_19810, EXM29_11820, ExPECSC022_03109, ExPECSC038_03439, EXX06_01125, EXX13_00845, EXX23_16015, EXX24_14295, EXX53_14790, EXX55_01320, EXX71_17360, EXX78_02225, EXX87_08890, EYY78_26035, GJ11_06285, HmCms184_02447, HmCmsJML079_02982, HmCmsJML146_03699, HmCmsJML204_00878, HW43_08900, JD73_25430, MJ49_00980, MS6198_11710, MS8345_01023, NCTC10418_04583, NCTC10429_05442, NCTC10766_04503, NCTC10767_04990, NCTC11022_00191, NCTC11126_00990, NCTC11341_04818, NCTC13127_04125, NCTC13462_01067, NCTC7922_00566, NCTC7927_03442, NCTC8009_05720, NCTC8179_02810, NCTC8622_05879, NCTC8960_00713, NCTC8985_01811, NCTC9007_01932, NCTC9036_03192, NCTC9045_03609, NCTC9055_04891, NCTC9058_03886, NCTC9062_05238, NCTC9075_04088, NCTC9111_03151, NCTC9119_03148, NCTC9434_03595, NCTC9701_03328, NCTC9703_02363, NCTC9706_00463, NCTC9777_03104, NCTC9962_01914, NCTC9969_03241, PU06_15680, RG28_16620, RK56_002580, RX35_02724, SAMEA3472043_03793, SAMEA3472044_05359, SAMEA3472047_01444, SAMEA3472055_02534, SAMEA3472056_01744, SAMEA3472070_03172, SAMEA3472080_02978, SAMEA3472090_04886, SAMEA3472108_02247, SAMEA3472114_01584, SAMEA3472147_02312, SAMEA3484427_03684, SAMEA3484429_03764, SAMEA3485101_00247, SAMEA3485113_04376, SAMEA3752553_01957, SAMEA3752557_01505, SAMEA3752559_02004, SAMEA3752620_04473, SAMEA3753064_00899, SAMEA3753097_05333, SAMEA3753164_01770, SAMEA3753290_02723, SK85_01106, UN86_07965, UN91_14220, WQ89_17310, WR15_23585 Production host: Escherichia coli (E. coli) / References: UniProt: B2CY45, UniProt: P0AE98*PLUS #3: Protein/peptide | Mass: 1953.963 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 Gene: csgA, FAZ80_15140, FAZ81_14840, FAZ83_14765, FAZ84_08025, FAZ86_15285 Production host: Escherichia coli (E. coli) / References: UniProt: A0A4S4PI16, UniProt: P28307*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Curli transport CsgFG complex and substrate CsgAN6 peptide Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/HE |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139702 / Symmetry type: POINT |