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- PDB-6yb5: Orthorhombic crystal structure of a native BcsRQ complex crystall... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yb5 | ||||||||||||||||||
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Title | Orthorhombic crystal structure of a native BcsRQ complex crystallized in the presence of ADP | ||||||||||||||||||
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![]() | SIGNALING PROTEIN / Bacterial biofilms / Bacterial cellulose / Bacterial secretion system / ATP binding protein | ||||||||||||||||||
Function / homology | ![]() bacterial cellulose biosynthetic process / negative regulation of cell division / cytoplasmic side of plasma membrane / cell division / ATP hydrolysis activity / ATP binding / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Caleechurn, M. / Abidi, W. / Zouhir, S. / Roche, S. / Krasteva, P.V. | ||||||||||||||||||
Funding support | 5items
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![]() | ![]() Title: Architecture and regulation of an enterobacterial cellulose secretion system. Authors: Wiem Abidi / Samira Zouhir / Meryem Caleechurn / Stéphane Roche / Petya Violinova Krasteva / ![]() 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- ...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. | ||||||||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 305.6 KB | Display | ![]() |
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PDB format | ![]() | 202.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 26.1 KB | Display | |
Data in CIF | ![]() | 38 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yarSC ![]() 6yayC ![]() 6yb3C ![]() 6ybbC ![]() 6ybuC ![]() 6yg8C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29245.209 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: Bacterial cellulose synthesis subunit Q. The purified native BcsRQ complex was treated with EDTA and incubated with ADP prior to crystallisation. Source: (gene. exp.) ![]() ![]() Gene: 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, ...Gene: 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 Production host: ![]() ![]() #2: Protein | Mass: 7022.876 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Bacterial cellulose synthesis subunit R. / Source: (gene. exp.) ![]() ![]() Gene: 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, ...Gene: 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 Production host: ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 277.4 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES pH 6.5 and 12% PEG 20 000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980027019978 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 81659 / % possible obs: 99 % / Redundancy: 13.2 % / Biso Wilson estimate: 24.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.59→1.69 Å / Redundancy: 11.8 % / Num. unique obs: 12421 / CC1/2: 0.562 / % possible all: 94.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YAR Resolution: 1.59→45.23 Å / SU ML: 0.1662 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2678
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→45.23 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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