6YBB

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

PDB DOI: https://doi.org/10.2210/pdb6YBB/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli, Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-03-16 Released: 2021-02-24
Deposition Author(s): Abidi, W., Zouhir, S., Roche, S., Krasteva, P.V.
Funding Organization(s): ATIP-Avenir, European Research Council (ERC), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), European Institute of Chemistry and Biology (IECB)

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

PubMed: 33563593 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 144.7 kDa
Atom Count: 9,133
Modelled Residue Count: 1,118
Deposited Residue Count: 1,254
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial cellulose secretion regulator BcsQ, R156E mutant	A, B	250	Escherichia coli	Mutation(s): 1 Gene Names: bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725... bcsQ, yhjQ, A8C65_00290, ACU57_05335, BMT91_17060, BON75_10030, BvCmsHHP019_01723, BvCmsSINP011_05061, C2U48_15650, D3O91_11725, D9H68_14440, D9I18_15755, D9I97_13990, DAH34_22885, DAH37_19450, E2127_16420, E2128_18010, E2129_18145, E2134_17810, EAI42_04085, EC1094V2_71, NCTC10429_00778, NCTC11022_03734, NCTC9058_01652
UniProt
Find proteins for P0DP92 (Escherichia coli (strain K12)) Explore P0DP92 Go to UniProtKB: P0DP92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DP92
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial cellulose secretion regulator BcsR	C, D	67	Escherichia coli	Mutation(s): 0 Gene Names: yhjR, A6V01_14365, A8C65_00295, A9R57_18690, AC789_1c39040, ACN002_3620, ACN68_06780, ACN81_08775, ACU57_05330, ACU90_15155... yhjR, A6V01_14365, A8C65_00295, A9R57_18690, AC789_1c39040, ACN002_3620, ACN68_06780, ACN81_08775, ACU57_05330, ACU90_15155, AM270_16530, AM464_10395, AMK83_17075, AML07_15400, APZ14_14840, AUQ13_21010, AUS26_05355, AW106_19925, BANRA_02188, BANRA_03431, BANRA_04333, BANRA_04566, BB545_03705, BHS81_21135, BHS87_19835, BJJ90_00965, BK292_24575, BMT91_17065, BN17_34711, BOH76_20305, BON63_23095, BON69_12460, BON71_17720, BON72_13310, BON76_21180, BON94_21140, BON95_21275, BTQ06_14355, BUE81_10045, BvCms12BK_03867, BvCms2454_00062, BvCms28BK_00015, BvCmsHHP001_04915, BvCmsHHP019_01722, BvCmsHHP056_04702, BvCmsKKP036_02918, BvCmsKKP061_02263, BvCmsKSNP073_03410, BvCmsKSNP081_04400, BvCmsKSP011_02716, BvCmsKSP024_02867, BvCmsKSP026_02341, BvCmsKSP045_00352, BvCmsKSP067_01939, BvCmsNSNP036_04602, BvCmsNSP006_05307, BvCmsNSP047_03956, BvCmsNSP072_04054, BvCmsOUP014_03413, BvCmsSINP011_05062, BvCmsSIP019_02407, BvCmsSIP044_03516, BVL39_08345, BW690_01625, BZL31_14290, C2U48_15645, C5N07_21610, C5P01_24180, C6669_10230, C7235_01450, C7B02_19840, C9098_17010, C9114_22000, C9141_22075, C9160_22970, C9162_26275, C9182_22470, C9201_19395, C9306_17625, C9E25_16190, C9Z03_00095, C9Z28_19620, C9Z37_15395, C9Z39_13945, C9Z69_16745, C9Z89_13935, CA593_08480, CI641_010930, COD30_23820, COD46_13475, CR538_01230, CRD98_22705, CRM83_21580, CWS33_18425, D0X26_22825, D2184_20785, D2185_17650, D3821_09240, D3Y67_04435, D6T60_22230, D9D20_19605, D9E35_13135, D9H68_14435, D9I18_15750, D9I97_13985, D9J11_18915, D9J44_18935, D9K48_10615, D9K54_10550, DAH18_11545, DAH30_06135, DAH32_17855, DAH34_22880, DAH37_19445, DBQ99_02170, DEN89_25155, DEN97_17470, DEO04_20390, DEO19_17140, DIV22_07035, DJ503_16110, DL545_01700, DL800_25095, DP277_20930, DQF57_09495, DQO13_19235, DS732_25515, DTL43_22125, DXT69_13975, DXT71_18500, DXT73_16115, E0I42_16815, E0J34_09730, E0K84_22700, E2119_10885, E2127_16425, E2128_18015, E2129_18150, E2134_17815, E2135_13675, E2855_04489, E2863_04566, E3B71_14240, E5P22_13630, E5P28_15170, E5P37_17785, E5S35_16770, E5S47_16125, EAI42_04080, EC1094V2_70, EC3234A_62c00180, EC3426_04694, EC95NR1_02922, ED600_16775, EEP23_03690, EHH55_25990, EJC75_16880, EKI52_16535, EL75_0168, EL79_0179, EL80_0171, ELT20_13340, ELV08_08625, EPT01_13645, EQ825_24275, ERS085365_03384, ERS085374_03939, ERS085379_03461, ERS085416_01810, ERS139211_03246, EXX13_15900, EXX71_20125, EXX78_22145, EYD11_00910, EYY78_10840, F0312_08835, F1E03_18480, F1E19_10145, F7F23_20655, F7F29_18335, FORC82_0211, FQ915_11140, FQR64_01380, FRV13_18835, FTV90_03830, FTV92_19380, FV293_20875, FWK02_16270, FY127_16255, HW43_22525, NCTC10090_03288, NCTC10418_00365, NCTC10429_00777, NCTC10865_00350, NCTC11022_03735, NCTC11126_00353, NCTC11181_02507, NCTC11341_02195, NCTC13148_03788, NCTC8009_01140, NCTC8179_05669, NCTC8500_00017, NCTC8960_02842, NCTC8985_04684, NCTC9045_00297, NCTC9055_02150, NCTC9058_01653, NCTC9062_02927, NCTC9111_00632, NCTC9703_04725, NCTC9706_02488, PGD_04560, PU06_03455, RG28_22775, RK56_020175, RX35_03299, SAMEA3472043_03895, SAMEA3472055_04880, SAMEA3472070_03765, SAMEA3472114_02155, SAMEA3484427_00198, SAMEA3484429_02974, SAMEA3752553_00829, SAMEA3752557_03916, SAMEA3752559_00583, SAMEA3753064_01978, SAMEA3753290_02280, SAMEA3753300_03978, SK85_03853, UN86_19365, WQ89_12680, WR15_14750
UniProt
Find proteins for P0ADJ3 (Escherichia coli (strain K12)) Explore P0ADJ3 Go to UniProtKB: P0ADJ3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ADJ3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial cellulose secretion regulator BcsE, residues 217-523	E, F	310	Escherichia coli K-12	Mutation(s): 0 Gene Names: bcsE, yhjS, b3536, JW3504
UniProt
Find proteins for P37657 (Escherichia coli (strain K12)) Explore P37657 Go to UniProtKB: P37657
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P37657
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C2E (Subject of Investigation/LOI) Query on C2E Download Ideal Coordinates CCD File SDF format, chain K [auth E] SDF format, chain L [auth E] SDF format, chain N [auth F] SDF format, chain O [auth F] MOL2 format, chain K [auth E] MOL2 format, chain L [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth F] mmCIF format, chain K [auth E] mmCIF format, chain L [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth F]	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		Interactions Focus chain K [auth E] Focus chain L [auth E] Focus chain N [auth F] Focus chain O [auth F] Interactions & Density Focus chain K [auth E] Focus chain L [auth E] Focus chain N [auth F] Focus chain O [auth F]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	H [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain H [auth A] Focus chain J [auth B]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain P [auth F] MOL2 format, chain M [auth E] MOL2 format, chain P [auth F] mmCIF format, chain M [auth E] mmCIF format, chain P [auth F]	M [auth E], P [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain P [auth F] Interactions & Density Focus chain M [auth E] Focus chain P [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B]	G [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth B]

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 = 61.43	α = 90
b = 169.59	β = 90
c = 177.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
XDS	data scaling
XDS	data processing
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-02-24

Deposition Author(s):

Funding Organization	Location	Grant 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)		--