[English] 日本語
Yorodumi
- PDB-6l7c: CsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l7c
TitleCsgFG complex with substrate CsgAN6 peptide in Curli biogenesis system
Components
  • CsgF
  • Curli production assembly/transport protein CsgG
  • Major curlin subunit CsgA
KeywordsPROTEIN 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
Curlin associated / Curlin associated repeat / Type VIII secretion system, CsgF / Type VIII secretion system (T8SS), CsgF protein / Curli production assembly/transport component CsgG / Curli production assembly/transport component CsgG / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Curli production assembly/transport component CsgG / Major curlin subunit CsgA / Curli production assembly/transport component CsgF / Curli production assembly/transport component CsgF / Curli production assembly/transport component CsgG / Major curlin subunit
Similarity search - Component
Biological speciesEscherichia coli O69:H11 str. 08-4661 (bacteria)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsYan, Z.F. / Yin, M. / Chen, J.N. / Li, X.M.
CitationJournal: 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
DepositionNov 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0842
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Curli production assembly/transport protein CsgG
B: Curli production assembly/transport protein CsgG
C: Curli production assembly/transport protein CsgG
D: Curli production assembly/transport protein CsgG
E: Curli production assembly/transport protein CsgG
F: Curli production assembly/transport protein CsgG
G: Curli production assembly/transport protein CsgG
H: Curli production assembly/transport protein CsgG
I: Curli production assembly/transport protein CsgG
J: CsgF
K: CsgF
L: CsgF
M: CsgF
N: CsgF
O: CsgF
P: CsgF
Q: CsgF
R: CsgF
S: Major curlin subunit CsgA
T: Major curlin subunit CsgA
U: Major curlin subunit CsgA
V: Major curlin subunit CsgA
W: Major curlin subunit CsgA
X: Major curlin subunit CsgA
Y: Major curlin subunit CsgA
Z: Major curlin subunit CsgA
a: Major curlin subunit CsgA


Theoretical massNumber of molelcules
Total (without water)428,43327
Polymers428,43327
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area98510 Å2
ΔGint-456 kcal/mol
Surface area92880 Å2

-
Components

#1: Protein
Curli production assembly/transport protein CsgG


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
CsgF / Curli assembly component / Curli assembly component CsgF / Curli assembly protein CsgF / Curli ...Curli assembly component / Curli assembly component CsgF / Curli assembly protein CsgF / Curli nucleation outer membrane protein / Curli production assembly/transport component / Curli production assembly/transport component CsgF / 2nd curli operon / Curli production assembly/transport protein CsgF


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
Major curlin subunit CsgA


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

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Curli transport CsgFG complex and substrate CsgAN6 peptide
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139702 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more