6YBB

Crystal structure of a native BcsE (217-523) - BcsR-BcsQ (R156E mutant) complex with c-di-GMP and ATP bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Architecture and regulation of an enterobacterial cellulose secretion system.

Abidi, W.Zouhir, S.Caleechurn, M.Roche, S.Krasteva, P.V.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd8049
  • Primary Citation of Related Structures:  
    6YAR, 6YAY, 6YB3, 6YB5, 6YBB, 6YBU, 6YG8

  • PubMed Abstract: 

    Many free-living and pathogenic enterobacteria secrete biofilm-promoting cellulose using a multicomponent, envelope-embedded Bcs secretion system under the control of intracellular second messenger c-di-GMP. The molecular understanding of system assembly and cellulose secretion has been largely limited to the crystallographic studies of a distantly homologous BcsAB synthase tandem and a low-resolution reconstruction of an assembled macrocomplex that encompasses most of the inner membrane and cytosolic subunits and features an atypical layered architecture. Here, we present cryo-EM structures of the assembled Bcs macrocomplex, as well as multiple crystallographic snapshots of regulatory Bcs subcomplexes. The structural and functional data uncover the mechanism of asymmetric secretion system assembly and periplasmic crown polymerization and reveal unexpected subunit stoichiometry, multisite c-di-GMP recognition, and ATP-dependent regulation.


  • Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91198 Gif- sur-Yvette, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial cellulose secretion regulator BcsQ, R156E mutant
A, B
250Escherichia coliMutation(s): 1 
Gene Names: 
UniProt
Find proteins for P0DP92 (Escherichia coli (strain K12))
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UniProt GroupP0DP92
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial cellulose secretion regulator BcsR
C, D
67Escherichia coliMutation(s): 0 
Gene Names: 
yhjRA6V01_14365A8C65_00295A9R57_18690AC789_1c39040ACN002_3620ACN68_06780ACN81_08775ACU57_05330ACU90_15155AM270_16530AM464_10395AMK83_17075AML07_15400APZ14_14840AUQ13_21010AUS26_05355AW106_19925BANRA_02188BANRA_03431BANRA_04333BANRA_04566BB545_03705BHS81_21135BHS87_19835BJJ90_00965BK292_24575BMT91_17065BN17_34711BOH76_20305BON63_23095BON69_12460BON71_17720BON72_13310BON76_21180BON94_21140BON95_21275BTQ06_14355BUE81_10045BvCms12BK_03867BvCms2454_00062BvCms28BK_00015BvCmsHHP001_04915BvCmsHHP019_01722BvCmsHHP056_04702BvCmsKKP036_02918BvCmsKKP061_02263BvCmsKSNP073_03410BvCmsKSNP081_04400BvCmsKSP011_02716BvCmsKSP024_02867BvCmsKSP026_02341BvCmsKSP045_00352BvCmsKSP067_01939BvCmsNSNP036_04602BvCmsNSP006_05307BvCmsNSP047_03956BvCmsNSP072_04054BvCmsOUP014_03413BvCmsSINP011_05062BvCmsSIP019_02407BvCmsSIP044_03516BVL39_08345BW690_01625BZL31_14290C2U48_15645C5N07_21610C5P01_24180C6669_10230C7235_01450C7B02_19840C9098_17010C9114_22000C9141_22075C9160_22970C9162_26275C9182_22470C9201_19395C9306_17625C9E25_16190C9Z03_00095C9Z28_19620C9Z37_15395C9Z39_13945C9Z69_16745C9Z89_13935CA593_08480CI641_010930COD30_23820COD46_13475CR538_01230CRD98_22705CRM83_21580CWS33_18425D0X26_22825D2184_20785D2185_17650D3821_09240D3Y67_04435D6T60_22230D9D20_19605D9E35_13135D9H68_14435D9I18_15750D9I97_13985D9J11_18915D9J44_18935D9K48_10615D9K54_10550DAH18_11545DAH30_06135DAH32_17855DAH34_22880DAH37_19445DBQ99_02170DEN89_25155DEN97_17470DEO04_20390DEO19_17140DIV22_07035DJ503_16110DL545_01700DL800_25095DP277_20930DQF57_09495DQO13_19235DS732_25515DTL43_22125DXT69_13975DXT71_18500DXT73_16115E0I42_16815E0J34_09730E0K84_22700E2119_10885E2127_16425E2128_18015E2129_18150E2134_17815E2135_13675E2855_04489E2863_04566E3B71_14240E5P22_13630E5P28_15170E5P37_17785E5S35_16770E5S47_16125EAI42_04080EC1094V2_70EC3234A_62c00180EC3426_04694EC95NR1_02922ED600_16775EEP23_03690EHH55_25990EJC75_16880EKI52_16535EL75_0168EL79_0179EL80_0171ELT20_13340ELV08_08625EPT01_13645EQ825_24275ERS085365_03384ERS085374_03939ERS085379_03461ERS085416_01810ERS139211_03246EXX13_15900EXX71_20125EXX78_22145EYD11_00910EYY78_10840F0312_08835F1E03_18480F1E19_10145F7F23_20655F7F29_18335FORC82_0211FQ915_11140FQR64_01380FRV13_18835FTV90_03830FTV92_19380FV293_20875FWK02_16270FY127_16255HW43_22525NCTC10090_03288NCTC10418_00365NCTC10429_00777NCTC10865_00350NCTC11022_03735NCTC11126_00353NCTC11181_02507NCTC11341_02195NCTC13148_03788NCTC8009_01140NCTC8179_05669NCTC8500_00017NCTC8960_02842NCTC8985_04684NCTC9045_00297NCTC9055_02150NCTC9058_01653NCTC9062_02927NCTC9111_00632NCTC9703_04725NCTC9706_02488PGD_04560PU06_03455RG28_22775RK56_020175RX35_03299SAMEA3472043_03895SAMEA3472055_04880SAMEA3472070_03765SAMEA3472114_02155SAMEA3484427_00198SAMEA3484429_02974SAMEA3752553_00829SAMEA3752557_03916SAMEA3752559_00583SAMEA3753064_01978SAMEA3753290_02280SAMEA3753300_03978SK85_03853UN86_19365WQ89_12680WR15_14750

UniProt
Find proteins for P0ADJ3 (Escherichia coli (strain K12))
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UniProt GroupP0ADJ3
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Bacterial cellulose secretion regulator BcsE, residues 217-523
E, F
310Escherichia coli K-12Mutation(s): 0 
Gene Names: bcsEyhjSb3536JW3504
UniProt
Find proteins for P37657 (Escherichia coli (strain K12))
Explore P37657 
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UniProt GroupP37657
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C2E (Subject of Investigation/LOI)
Query on C2E

Download Ideal Coordinates CCD File 
K [auth E],
L [auth E],
N [auth F],
O [auth F]
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
M [auth E],
P [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.43α = 90
b = 169.59β = 90
c = 177.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata processing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ATIP-Avenir--
European Research Council (ERC)BioMatrix, ERC StG #757507
Centre National de la Recherche Scientifique (CNRS)--
Institute for Integrative Biology of the Cell (I2BC)--
European Institute of Chemistry and Biology (IECB)--

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-24
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description