[English] 日本語
Yorodumi
- PDB-6ybu: Crystal structure of a native BcsE (349-523) RQ complex with c-di... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ybu
TitleCrystal structure of a native BcsE (349-523) RQ complex with c-di-GMP and ATP bound
Components(Bacterial cellulose secretion regulator ...) x 3
KeywordsSIGNALING PROTEIN / Bacterial biofilms / Bacterial cellulose / Bacterial secretion system / ATP binding protein / c-di-GMP binding protein
Function / homology
Function and homology information


bacterial cellulose biosynthetic process / cellulose biosynthetic process / cyclic-di-GMP binding / cell division / ATP binding / cytoplasm
Similarity search - Function
Cellulose biosynthesis protein BcsE / Cellulose biosynthesis protein BcsE / Cellulose synthase operon protein BcsQ / Protein YhjR / Cellulose biosynthesis protein BcsQ / Cellulose biosynthesis protein BcsR-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Chem-C2E / Cell division protein / Cellulose biosynthesis protein BcsR / Protein YhjR / Cellulose biosynthesis protein BcsQ / Cyclic di-GMP binding protein BcsE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsAbidi, W. / Zouhir, S. / Roche, S. / Krasteva, P.V.
Funding support5items
OrganizationGrant numberCountry
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)
CitationJournal: Sci Adv / Year: 2021
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.
History
DepositionMar 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterial cellulose secretion regulator BcsQ
B: Bacterial cellulose secretion regulator BcsQ
C: Bacterial cellulose secretion regulator BcsR
D: Bacterial cellulose secretion regulator BcsR
E: Bacterial cellulose secretion regulator BcsE, residues 349-523
F: Bacterial cellulose secretion regulator BcsE, residues 349-523
G: Bacterial cellulose secretion regulator BcsQ
H: Bacterial cellulose secretion regulator BcsQ
I: Bacterial cellulose secretion regulator BcsR
J: Bacterial cellulose secretion regulator BcsR
K: Bacterial cellulose secretion regulator BcsE, residues 349-523
L: Bacterial cellulose secretion regulator BcsE, residues 349-523
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,42428
Polymers222,77512
Non-polymers7,64916
Water4,089227
1
A: Bacterial cellulose secretion regulator BcsQ
B: Bacterial cellulose secretion regulator BcsQ
C: Bacterial cellulose secretion regulator BcsR
D: Bacterial cellulose secretion regulator BcsR
E: Bacterial cellulose secretion regulator BcsE, residues 349-523
F: Bacterial cellulose secretion regulator BcsE, residues 349-523
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,21214
Polymers111,3886
Non-polymers3,8258
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Bacterial cellulose secretion regulator BcsQ
H: Bacterial cellulose secretion regulator BcsQ
I: Bacterial cellulose secretion regulator BcsR
J: Bacterial cellulose secretion regulator BcsR
K: Bacterial cellulose secretion regulator BcsE, residues 349-523
L: Bacterial cellulose secretion regulator BcsE, residues 349-523
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,21214
Polymers111,3886
Non-polymers3,8258
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.990, 72.570, 161.250
Angle α, β, γ (deg.)90.000, 98.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Bacterial cellulose secretion regulator ... , 3 types, 12 molecules ABGHCDIJEFKL

#1: Protein
Bacterial cellulose secretion regulator BcsQ / Cellulose biosynthesis protein BcsQ / Cellulose synthase operon protein YhjQ / Cellulose synthase / ...Cellulose biosynthesis protein BcsQ / Cellulose synthase operon protein YhjQ / Cellulose synthase / putative / Bacterial cellulose synthesis subunit Q


Mass: 27960.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Bacterial cellulose synthesis subunit Q. / Source: (gene. exp.) Escherichia coli (E. coli)
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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B1KWQ0, UniProt: P0DP92*PLUS
#2: Protein
Bacterial cellulose secretion regulator BcsR / FIG004405: Putative cytoplasmic protein / Protein YhjR / Protein of uncharacterized function ...FIG004405: Putative cytoplasmic protein / Protein YhjR / Protein of uncharacterized function (DUF2629) / Bacterial cellulose synthesis subunit R


Mass: 7452.367 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The coding region corresponding to the BcsRQ tandem was cloned into the pProEx-Htb with a cleavable N-terminal hexahistidine tag to BcsR. The sample were purified and crystallised without ...Details: The coding region corresponding to the BcsRQ tandem was cloned into the pProEx-Htb with a cleavable N-terminal hexahistidine tag to BcsR. The sample were purified and crystallised without the His-tag. The GPMGS correspond to the Nter additional residues remaining after cleavage. Bacterial cellulose synthesis subunit R.
Source: (gene. exp.) Escherichia coli (E. coli)
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: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J7QAC9, UniProt: P0ADJ3*PLUS
#3: Protein
Bacterial cellulose secretion regulator BcsE, residues 349-523 / Cellulose biosynthesis protein BcsE / Bacterial cellulose synthesis subunit E


Mass: 20280.561 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The coding region of BcsE corresponding to residue 349 to 523 was cloned into a modified pRSF-Duet to express the truncated protein without a tag. The first additional MGSM residues come ...Details: The coding region of BcsE corresponding to residue 349 to 523 was cloned into a modified pRSF-Duet to express the truncated protein without a tag. The first additional MGSM residues come from the cloning. Bacterial cellulose synthesis subunit E.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: bcsE, yhjS, b3536, JW3504 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P37657

-
Non-polymers , 4 types, 243 molecules

#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-C2E / 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) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 277.4 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris-HCl pH 9.0, 22-25% PEG 6000, 500 mM LiCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980057954788 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980057954788 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 86110 / % possible obs: 98.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 52.41 Å2 / CC1/2: 0.995 / Net I/σ(I): 11.45
Reflection shellResolution: 2.49→2.64 Å / Redundancy: 6.77 % / Mean I/σ(I) obs: 1.26 / Num. unique obs: 12814 / CC1/2: 0.542 / % possible all: 91.4

-
Processing

Software
NameVersionClassification
PHENIX1.17rc2_3619refinement
Cootmodel building
PHASERphasing
XDSdata scaling
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YAR, 6TJ0

6yar

6tj0


Resolution: 2.49→47.71 Å / SU ML: 0.3472 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7448
RfactorNum. reflection% reflection
Rfree0.2249 4331 5.03 %
Rwork0.1808 --
obs0.1831 86096 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.92 Å2
Refinement stepCycle: LAST / Resolution: 2.49→47.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13815 0 496 227 14538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002114668
X-RAY DIFFRACTIONf_angle_d0.490120069
X-RAY DIFFRACTIONf_chiral_restr0.03812261
X-RAY DIFFRACTIONf_plane_restr0.00312827
X-RAY DIFFRACTIONf_dihedral_angle_d13.61668933
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.42981200.3591823X-RAY DIFFRACTION67.16
2.52-2.550.35091330.30052721X-RAY DIFFRACTION99.86
2.55-2.580.30321510.27972771X-RAY DIFFRACTION99.76
2.58-2.610.30421590.26212712X-RAY DIFFRACTION99.79
2.61-2.640.31071310.25182731X-RAY DIFFRACTION99.79
2.64-2.680.30291610.25692720X-RAY DIFFRACTION99.86
2.68-2.720.29181540.2532730X-RAY DIFFRACTION99.69
2.72-2.760.3131350.242744X-RAY DIFFRACTION99.93
2.76-2.80.32551350.25422732X-RAY DIFFRACTION99.83
2.8-2.850.35761490.2562740X-RAY DIFFRACTION99.9
2.85-2.90.28571410.24552771X-RAY DIFFRACTION99.86
2.9-2.950.33451410.23052721X-RAY DIFFRACTION99.79
2.95-3.010.3031450.22222756X-RAY DIFFRACTION99.72
3.01-3.070.27461420.20992712X-RAY DIFFRACTION99.83
3.07-3.130.28771450.20562759X-RAY DIFFRACTION99.93
3.13-3.210.28681440.20022718X-RAY DIFFRACTION99.83
3.21-3.290.23041480.20342814X-RAY DIFFRACTION99.9
3.29-3.380.26481420.20082712X-RAY DIFFRACTION99.96
3.38-3.480.23691460.18312772X-RAY DIFFRACTION99.97
3.48-3.590.2411440.16462723X-RAY DIFFRACTION99.9
3.59-3.720.21281450.15882778X-RAY DIFFRACTION99.86
3.72-3.870.20451440.16682757X-RAY DIFFRACTION99.76
3.87-4.040.1881460.15252769X-RAY DIFFRACTION99.9
4.04-4.250.19481450.15312754X-RAY DIFFRACTION99.93
4.25-4.520.19131460.13922785X-RAY DIFFRACTION99.86
4.52-4.870.17641450.13782776X-RAY DIFFRACTION99.86
4.87-5.360.18261450.14572756X-RAY DIFFRACTION99.93
5.36-6.130.20991480.17692801X-RAY DIFFRACTION99.86
6.13-7.720.20011480.17362825X-RAY DIFFRACTION99.93
7.72-47.710.14331530.14852882X-RAY DIFFRACTION99.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3333130204860.45545326805-0.8125929157021.296164427960.4425608522151.13016502708-0.0734897676072-0.5480882648950.01106879006110.0995184258865-0.0903210624082-0.262978780968-0.04288514863760.3875839265494.63294147256E-50.3540507823630.0277299284645-0.04515956852880.6400158982560.150510729470.458523040696-24.1906718051-9.8072098709261.2539760895
20.7605583311540.0191726952566-0.3457827270410.4858340943191.269371563022.442630627480.0799619351499-0.2326658395890.01130743425280.1498833318290.183649594033-0.2161715341150.2322752542690.797705032369-0.0002218294202130.3987397698980.0660924836707-0.08337958716030.8605931391980.1733684291420.539627906967-17.5321601493-11.231530838261.8197692702
30.376413187933-0.17090241172-0.7205631129441.08295359073-0.0815160807182.02439412427-0.0949331459750.0742216139765-0.214998859908-0.0183147658023-0.1115049948620.02742353721330.0917983057080.342760245709-0.0001519020413940.3140953423170.04458570585380.0374249153970.3868026867140.1216806620890.413908293247-29.2072447291-15.654801892941.8719937964
40.9451084329651.051693835720.2390537609480.9456800955560.4836535866630.625932250044-0.178467535892-0.1996498855660.03793559278870.0332259073490.09671060985650.4394408212660.1003401348270.00084605346043-0.0001421370949790.3851454974930.06456873706360.06023478059690.4433626789560.0951703302420.396951337951-38.4257708965-14.840328412956.4768469447
50.906438355854-0.5594993398260.7491238393390.890092047426-0.3167577207960.6010931738090.07270571253750.2755011215550.0358217973505-0.080768216572-0.273010015063-0.15346281175-0.09576133859170.451489074352-0.010480700250.33120205812-0.02070540119370.01846187916540.6119646870230.1911135459420.455459840795-19.3949979892.6538071361227.8123656774
60.514054794341-0.564804076366-0.2874106407651.357720121061.193627056031.21547601382-0.152666916745-0.04120098425640.107976318161-0.01717236838460.213520985996-0.178600824664-0.2313243110730.48585474915-0.004544318698290.291151771425-0.0932672886455-0.01013812611060.8024718298210.2302978924270.593441255073-11.2029146353.9426171094334.1606791159
70.668060330572-0.365738842576-0.2452655850520.559702097747-0.8389033474951.84042697484-0.0679355944678-0.08094266380730.116562792460.170060401446-0.004847959661220.0439021729472-0.327471046750.237328108585-3.28517617737E-50.454576145949-0.0638425373055-0.08648222668230.4023756137350.07484477359940.485703117181-30.01543066439.438408459746.4549553669
80.421016667576-0.571035676196-0.3304451760161.068863523360.6533821503592.14599208202-0.02461574405990.1820345145270.0615291831734-0.133254987919-0.02379734731710.153166782945-0.147737915839-0.02432395741192.59391068128E-50.3567990612380.0133890661503-0.07315206885230.4660317963030.1313559873570.411088179213-34.27220635498.5423060315629.744148756
90.056440560516-0.0001530931993010.01325314964340.352856399606-0.04480859014870.104597046938-0.5007739601650.374523971490.2055840669150.3931214337030.387263289180.66330575761-0.426991813125-0.162722889582-0.0004351552389771.187499126320.1460065141130.008955345789490.988654495574-0.04279366465630.851220207702-35.017793589718.451845385859.3535700577
100.2372266832390.118674221301-0.01720088390720.1504370817490.0738433748183-0.008666874428550.102316883321-0.838617180179-0.1087143747390.908775349154-0.3501974046490.4410174065370.0134949951006-0.671077210991-0.002491806215090.456310497487-0.03914652403440.01582773692160.628683466347-0.07122644693570.41758479603-39.49319718758.5086957726162.3518740861
111.036545247160.547696833331-0.8115635734823.749109661791.472506105621.74733289857-0.4732154701980.540049180086-0.231097922032-1.325585402920.1887606709911.936808856530.936682111512-0.964786139739-0.2393413197431.34003404909-0.0563843453125-0.05378278474160.851098408176-0.08470138444941.14220465576-33.0927106342-25.10886311827.2051120533
120.3178140576450.1713799244260.285956575580.87221006643-0.4021641618621.268889362020.1214239746940.720344436883-0.195839433762-0.610239046242-0.515351876016-0.251413452660.1434418961040.143475336894-0.01846826847650.5019251321790.106625030951-0.02152203787990.629022924598-0.008177528836950.526091226052-34.4257032217-14.818150074923.568429477
139.768813191270.9807078185433.311305448323.96090467423-1.644866227012.2218464498-0.103082810751-0.9832039879731.252160600271.50474015754-0.3045316939660.644328837347-2.058940749660.246227206927-0.510993401631.0554166608-0.05925106315760.1944822055840.497017770879-0.01492898192610.906642281855-66.2076975727-25.946739767671.2490290623
141.066738407910.724146973519-0.1914014986020.331125738625-0.2175436885070.9685778397950.09344752574780.323860002111-0.105126436794-0.149209592881-0.133683387232-0.03385883793840.145261816247-0.0432422173823-4.18887074439E-50.4863421958720.08515414666270.04557711923610.3528038608710.07109113187370.390349500461-56.1637202053-33.618579868959.8935897548
150.9130602372520.0342396110343-0.3645209776162.09282824506-1.122598284960.5930626174820.06482455489260.20309807464-0.0352064846636-0.277681649422-0.195106647283-0.3147298811150.2967525428180.0877505619835.69634864917E-60.5464087014750.09973957354180.06591024847050.3869313784350.001269420259440.376424892914-52.061308003-38.672902099858.3793874983
160.05402183174610.0266556051327-0.03722410039240.102508561990.09652381336390.0562641630340.533144391049-0.4430013514820.559549783637-0.215218044597-1.18557604270.1136565855110.4518008918640.287866547566-0.0002227888870520.753157521598-0.04322501058160.03902974037090.4720220742010.005433880879530.586347996587-40.9761098108-18.066134388973.3216163129
170.1643924703530.0311322895095-0.369107940345-0.0113957859301-0.1864060054440.827815296038-0.5919401647620.653338515174-0.311341449510.8872441525720.07128931246510.171503435954-0.07589234320060.21787713984-0.0003479950243370.5500036153090.05860844579470.01513260701610.7449602042260.006282840961140.574556930033-34.168574526-6.8911326861373.0859114129
180.161232608271-0.0334612611597-0.1043990310210.5262767307040.2281769115980.0818028663419-0.2387774880010.505474699382-0.51857566521-0.5235049228760.1512517381260.2141993272790.0935868989148-0.329492383902-0.0005310602519750.671802514151-0.0292189666349-0.1119319756620.3781329930770.1148199900880.534529348252-55.039995061821.759857646214.9379536466
190.0215585273016-0.030770136364-0.03996039285290.1724849119650.1209524601550.0332507022666-0.04426967003920.452409087868-0.5482661780560.337089838398-0.09667498178430.0392528146399-0.0163508963916-0.1296319697710.0001203647141140.535840226938-0.000450681460880.006500752892250.3000421506880.04266119005720.401611624381-53.209693267730.336523857414.7463494878
200.0749698372393-0.3759449598840.1540947458980.9181850537950.006303900635040.95994123692-0.0300523583832-0.629710133869-0.03645251394620.3255951183540.0442403753099-0.227354760028-0.2379181928390.006332949832232.31322871308E-50.531150658508-0.1265777338040.01358660607350.3688624421910.04580337842340.417420243215-46.847309423130.115421829623.9258513237
210.211867999972-0.2184054802060.2522878157930.233617392880.0195121013490.42551215045-0.172479068471-0.138305451151-0.1917842847020.09249281130130.09023716401910.126131012768-0.012753621911-0.1079589958730.0003767497173180.553620627077-0.102065279246-0.04610847884940.3934373707270.08886378638520.412170239921-47.334987405623.70056140524.0118091935
220.06061586173120.0991989674970.1193151261920.4621309219060.1819807637120.2472202651210.240798538168-0.387598905164-0.5243156878240.051682190273-0.2391568112360.163019035187-0.54367721218-0.0380940546972-0.0001982557833210.568282907244-0.0443675156509-0.06816640017520.4771650192750.00637386607010.485482320432-51.369550155330.186644112826.1890401908
231.54903695319-0.349151071930.182144868221.54747764945-1.687409775321.209059340680.0132176964079-0.143399893824-0.01250403363840.399878424265-0.0943859297109-0.198946438452-0.6754488879540.3248465460270.0001220099425880.658230903913-0.0828623446325-0.06352677869060.339605879232-0.02818388492260.425181523308-45.930251085932.742199204324.5136996523
240.0123511359173-0.081444927242-0.01846880433780.04130075727640.0403590431082-0.009853815878870.578592137990.1544076423720.377266983278-0.0425122021234-0.428564289267-0.724290425985-0.1470891553560.09545015053940.0004640224028140.644590977124-0.0247289903740.08215469752660.3881428639430.1811019221870.740520943362-31.930494166311.881075558912.8535196125
250.126709284316-0.02482973185690.1930397286680.0621213887022-0.07930066015710.254468530314-0.0961528634597-0.437931895208-0.203246705137-0.5146932496420.3044024786520.2404630301-0.0672228149333-0.0308942361215-7.69115254299E-50.5889250641970.0124010346237-0.0242312933810.653554973286-0.001500601784990.634333103166-34.1891135805-2.6152608310513.5182227934
260.143012181993-0.225318487012-0.1970082648760.8555043157290.7869244587680.833240979476-0.1685487919640.5383087037170.806111860139-0.286102849744-0.407141175841-0.0197588433605-0.4179912764210.151011296232-0.2612826378220.418815324576-0.0515955775854-0.01136421961360.94913026050.3616529980850.689470642233-12.8027424496.3392340058517.4419160852
27-0.0914560258619-0.09657412340450.3838412725370.586114667727-0.3045003260551.39266339853-0.00737062692162-0.085511904602-0.2038234067310.02971417409830.1949053922080.0192592520073-0.0285099739518-0.2883812262353.04743688802E-50.330361013202-0.03407493829630.03871440929970.4728044128560.04751101631870.42236150012618.9148459406-13.555201653148.4933255722
281.8487137614-0.0401175762931.157651738982.53375993124-0.160278906540.774817955887-0.0468678145163-0.0268467709663-0.003275219187440.1115318722890.1299390983410.394607716911-0.00107407675935-0.4478117923913.67658551097E-50.358863183076-0.02071432435440.09425328912260.6930674533150.08797835416290.53910032703410.7966981369-11.070456528148.659091296
290.14623188462-0.9336054227860.4002284056741.52294973321-1.149829201111.60316046268-0.054221615951-0.2735063498510.05151804806510.2788258941280.1116806592390.0115254658531-0.2234315711010.05766382786319.85643342216E-50.4419854372030.0306275804546-0.00863842890630.425579441048-0.05191013442380.40214537996130.3729590546.8362862640946.7960110906
300.1591480365240.159991351566-0.197563270960.489451549875-0.4949775497050.743780356532-0.144099555809-0.129669263217-0.1186551388650.07109525963150.08325003060120.07257161413260.06219840231870.234079661167-4.80709481712E-50.3603484824430.05848554835950.003619697501850.427985398952-0.000864039702250.37981632806932.1273985832-9.3308054772854.2362129511
310.8275873944240.45534231558-0.149223939241.49339929558-0.4985937858710.858741923068-0.04240618165280.2275101486310.125786684938-0.05438977867830.2296384188930.104728691730.0184136051021-0.39511098373-3.97248820661E-50.3709975991050.0930113899648-0.03341494703590.4497012323260.09083564698220.41034138612221.887704911110.438776719722.7516281854
320.13348116693-0.3468090075050.08512152151071.216259719560.3221767216740.673463825438-0.1041489816920.164630618131-0.0925338611694-0.241397868232-0.07488594168160.604270548138-0.526299679657-0.253123801291.87787671739E-50.365560085470.0385768192312-0.1116673627940.5787226944090.0777651466110.52982690034812.57256228456.3489889628321.8578827376
330.2315338636-0.213987328451-0.3153493597561.1504082728-1.111226728181.735102516-0.06675467902490.154776915829-0.170825644583-0.1966620033950.1219880105530.0574089992470.2499573459510.006087191920466.31338678528E-50.399582744628-0.0260521548807-0.0136248316610.388692606676-0.03241137716260.4040352515628.4205825079-9.9792261091427.0438421796
340.785552823256-0.450265421346-0.1229861854750.676605205819-0.6218433181550.762214595936-0.09311500285650.03016593622850.05049318965290.03557167876440.117089347955-0.053668260392-0.07616796437650.112635276032.98752102843E-50.40107499893-0.033313652897-0.002530598877230.380204461609-0.003726666692360.38099894794736.96403109464.298584656521.7564729498
350.2400391036450.194072863349-0.09333317420970.154768805066-0.02793599499740.207506719856-0.2472207790170.9004705739590.02436132163920.0001300277246460.04726947321510.07547468184240.596436999110.0396044437454-0.000369601038161.06552779860.0900124820322-0.0465656307080.753660946761-0.1982348160450.7251943372632.3922036294-26.181271401825.7572202459
363.127336405440.5074934713881.792838404970.4766462885660.6932506515421.39594554566-0.235440353872-0.906460676446-0.2468207286980.3524425715070.0565998582622-0.05323431287490.859765935887-0.234173497779-0.001175342766980.4973175844360.0330894442393-0.03433172097020.1383813676380.01505687391590.37557599876334.6039331184-24.997012667636.8878156783
370.185241783318-0.1067640901450.2219291285710.223274379868-0.3420717714670.24520766315-0.36411212596-0.447206389980.02075930095220.1853120550680.08693936514910.641504403793-0.304904464701-0.0348398525967-0.0003562904468960.937402849230.1909041947120.007956910489010.612199954153-0.182888751750.6689512836126.649361172618.9135470348.7498521868
380.278033051465-0.0386142397275-0.1425254637650.06011606453890.0615797902343-0.00119612351892-0.08008614139430.5141443221230.5399228254730.199829495253-0.246599100249-0.323969327467-0.4248982434230.226011130597-0.0001438483929870.5528202692980.0179556517379-0.05707333800710.34932185776-0.02521194824260.59162373767935.757742950620.120470037939.5149609756
390.6186025599670.4338275831080.2909882446230.3625219237990.3133422983690.1395104372790.8203121049320.316812927312-0.441933444973-0.0722164183735-0.351883945976-0.08953978747920.3155300725080.485687575510.03016966637420.6306061355010.166124378805-0.0005560731044160.565415458667-0.06792394892560.40964493444652.7559337252-14.441518356373.9403275887
400.009096359657070.0601268633983-0.01223659743240.2181417854710.1395106399140.04783517350450.1795181641-0.4979630078910.1596893338480.622995041651-0.0761249173665-0.1406568397910.0942951664998-0.1457969676290.0003485279647590.5741868930590.0924688961033-0.02656799511680.35376736568-0.02395489362580.51185229514549.8844975192-11.162551752681.4860323707
410.7531989766050.1841203046130.4343493794440.667781675391-0.3637692353460.5911064410840.08204313219210.1113679871510.2253794401250.102814443556-0.09593462033380.07007185825950.0520820639388-0.01814428561951.90237144368E-50.3325095792170.04000253102480.03480634108660.28659377035-0.006272979191750.35089384398144.3367434934-3.9329881734175.2135449043
420.989562987497-0.0207497117218-0.04207791131850.1947629056740.5154941814581.755311516740.1104961779030.182787633690.1972478244520.107215200161-0.0691509174733-0.0100767471711-0.259021996870.05352584976994.76199725359E-50.4532266301310.0603128452470.02147655842290.323430676581-0.009368049264580.4141062224241.8656388542-2.1208974554878.8162794241
430.06524201331370.0337016545580.164784696798-0.01436347182480.04215940685590.1497887596740.06531051175250.1785612502990.08548162856640.1174411026020.4176730557560.08445947905270.343161003916-0.7046160091490.000420070042220.7747437197440.0215077277868-0.001793235889490.5896526723780.01304846177280.51159258560530.62874566-22.846642157964.5597155392
440.232728988197-0.03412816433260.4113035713650.704196094672-0.6594044254170.783212698712-0.5327774908250.186687266935-0.3203220478030.3095447062160.3245326352850.1788083679680.758379410764-0.1358984895510.00033861885840.522061968726-0.02799555103430.04742093647820.5106909818430.1058767786590.63179129131823.3076438557-26.208126460654.2076658162
450.162255515294-0.005163405141560.03717516743690.1410903263220.07456302865060.007027875072930.140330188875-0.8094489701720.5469766127590.421395504897-0.0624250391816-0.628360070367-0.2781145094860.241983879254-0.0004427920339640.612339301643-0.124947438697-0.02055094524820.49679555127-0.09009459281990.62457455357662.03388860678.065032798748.38804957165
460.326818053080.361543590393-0.07983454884760.371590668639-0.06257001598480.3345677401930.197738523017-0.4758191354880.331456328632-0.137611847439-0.245617561433-0.45382574724-0.01708314918610.228130258626-7.80412821072E-50.53545556025-0.01265829021650.0371372476090.4061739657080.04730580993030.53664651744965.51099039391.602814547970.813259751492
471.25471297674-0.148617616364-0.9700094931361.74888883276-0.2757788707781.73927958523-0.0162074052652-0.0573433555183-0.160339801236-0.104608360329-0.0380745635219-0.1497236794780.0556678568278-0.07849374790582.41579225892E-50.442046462798-0.044644884512-0.05125594878940.296230623181-0.008003511568390.41786145569951.7866339865-3.907649497093.51638343312
480.9904000146780.08252652611150.8734830635881.853875503890.380724449530.8577744660090.033397757373-0.1368370091380.1251361907220.623041420754-0.514624449602-0.356818405554-0.467728518513-0.449398070308-1.571006389020.701939920279-0.0281389514461-0.0159021556570.258710501123-0.1161568544170.46696545687346.248068324111.85164834981.2120775096
492.947457545220.9641886504033.104872520591.76662855981.353854695385.097710752510.187556070365-0.276902229930.4883754390180.07108155799210.1382491523870.0174733224454-0.49424335665-0.2133839048461.289321498780.6978941780690.0668655427835-0.02572042707790.4852671015630.146193472350.63956278364131.838081184222.023794765319.0389212218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 202 )
4X-RAY DIFFRACTION4chain 'A' and (resid 203 through 241 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 88 )
6X-RAY DIFFRACTION6chain 'B' and (resid 89 through 130 )
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 202 )
8X-RAY DIFFRACTION8chain 'B' and (resid 203 through 241 )
9X-RAY DIFFRACTION9chain 'C' and (resid 32 through 42 )
10X-RAY DIFFRACTION10chain 'C' and (resid 43 through 60 )
11X-RAY DIFFRACTION11chain 'D' and (resid 33 through 42 )
12X-RAY DIFFRACTION12chain 'D' and (resid 43 through 61 )
13X-RAY DIFFRACTION13chain 'E' and (resid 348 through 358 )
14X-RAY DIFFRACTION14chain 'E' and (resid 359 through 435 )
15X-RAY DIFFRACTION15chain 'E' and (resid 436 through 485 )
16X-RAY DIFFRACTION16chain 'E' and (resid 486 through 497 )
17X-RAY DIFFRACTION17chain 'E' and (resid 498 through 515 )
18X-RAY DIFFRACTION18chain 'F' and (resid 352 through 368 )
19X-RAY DIFFRACTION19chain 'F' and (resid 369 through 380 )
20X-RAY DIFFRACTION20chain 'F' and (resid 381 through 410 )
21X-RAY DIFFRACTION21chain 'F' and (resid 411 through 425 )
22X-RAY DIFFRACTION22chain 'F' and (resid 426 through 435 )
23X-RAY DIFFRACTION23chain 'F' and (resid 436 through 485 )
24X-RAY DIFFRACTION24chain 'F' and (resid 486 through 497 )
25X-RAY DIFFRACTION25chain 'F' and (resid 498 through 507 )
26X-RAY DIFFRACTION26chain 'F' and (resid 508 through 517 )
27X-RAY DIFFRACTION27chain 'G' and (resid 2 through 67 )
28X-RAY DIFFRACTION28chain 'G' and (resid 68 through 141 )
29X-RAY DIFFRACTION29chain 'G' and (resid 142 through 202 )
30X-RAY DIFFRACTION30chain 'G' and (resid 203 through 241 )
31X-RAY DIFFRACTION31chain 'H' and (resid 2 through 88 )
32X-RAY DIFFRACTION32chain 'H' and (resid 89 through 125 )
33X-RAY DIFFRACTION33chain 'H' and (resid 126 through 202 )
34X-RAY DIFFRACTION34chain 'H' and (resid 203 through 240 )
35X-RAY DIFFRACTION35chain 'I' and (resid 31 through 43 )
36X-RAY DIFFRACTION36chain 'I' and (resid 44 through 60 )
37X-RAY DIFFRACTION37chain 'J' and (resid 28 through 42 )
38X-RAY DIFFRACTION38chain 'J' and (resid 43 through 60 )
39X-RAY DIFFRACTION39chain 'K' and (resid 352 through 368 )
40X-RAY DIFFRACTION40chain 'K' and (resid 369 through 380 )
41X-RAY DIFFRACTION41chain 'K' and (resid 381 through 435 )
42X-RAY DIFFRACTION42chain 'K' and (resid 436 through 485 )
43X-RAY DIFFRACTION43chain 'K' and (resid 486 through 497 )
44X-RAY DIFFRACTION44chain 'K' and (resid 498 through 517 )
45X-RAY DIFFRACTION45chain 'L' and (resid 354 through 368 )
46X-RAY DIFFRACTION46chain 'L' and (resid 369 through 390 )
47X-RAY DIFFRACTION47chain 'L' and (resid 391 through 475 )
48X-RAY DIFFRACTION48chain 'L' and (resid 476 through 491 )
49X-RAY DIFFRACTION49chain 'L' and (resid 492 through 515 )

+
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://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