[English] 日本語
Yorodumi
- PDB-6yay: Crystal structure of a Selenium-derivatized complex of the bacter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yay
TitleCrystal structure of a Selenium-derivatized complex of the bacterial cellulose secretion regulators BcsR and BcsQ, crystallized in the presence of ADP
Components
  • Bacterial cellulose secretion regulator BcsQ
  • Bacterial cellulose secretion regulator BcsR
KeywordsSIGNALING PROTEIN / Bacterial biofilms / Bacterial cellulose / Bacterial secretion system / ATP binding protein
Function / homology
Function and homology information


bacterial cellulose biosynthetic process / cell division / ATP binding / cytoplasm
Similarity search - Function
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 / Cell division protein / Cellulose biosynthesis protein BcsR / Protein YhjR / Cellulose biosynthesis protein BcsQ
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsAbidi, W. / Caleechurn, M. / 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 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1628
Polymers73,0994
Non-polymers1,0634
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS measurements confirmed the existence of a stable and monodisperse BcsR2Q2 heterotetramer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11370 Å2
ΔGint-80 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.060, 78.780, 66.600
Angle α, β, γ (deg.)90.000, 99.280, 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

#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: 29479.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bacterial cellulose synthesis subunit Q. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The ...Details: Bacterial cellulose synthesis subunit Q. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The purified selenium derivated BcsRQ complex was treated with EDTA and incubated with ADP prior to crystallisation.
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: 7069.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Bacterial cellulose synthesis subunit R. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The ...Details: Bacterial cellulose synthesis subunit R. The coding region corresponding to the BcsRQ tandem was cloned into the pET21b expression vector with a C-terminal hexahistidine Tag on BcsQ. The purified selenium derivated BcsRQ complex was treated with EDTA and incubated with ADP prior to crystallisation.
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: PEG 2000, MES pH6.5, glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 66678 / % possible obs: 98.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 43.53 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.56
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 3.52 % / Mean I/σ(I) obs: 1.15 / Num. unique obs: 10300 / CC1/2: 0.612 / % possible all: 94

-
Processing

Software
NameVersionClassification
PHENIX1.17rc2_3619refinement
Cootmodel building
PHASERphasing
SHELXDEphasing
XDSdata scaling
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.09→46.64 Å / SU ML: 0.271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.8254
RfactorNum. reflection% reflection
Rfree0.2231 1711 5.02 %
Rwork0.192 --
obs0.1936 34116 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.37 Å2
Refinement stepCycle: LAST / Resolution: 2.09→46.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4349 0 64 47 4460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224520
X-RAY DIFFRACTIONf_angle_d0.49796163
X-RAY DIFFRACTIONf_chiral_restr0.038695
X-RAY DIFFRACTIONf_plane_restr0.0026821
X-RAY DIFFRACTIONf_dihedral_angle_d12.47242702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.150.46391280.44852490X-RAY DIFFRACTION91.38
2.15-2.220.41161420.37782689X-RAY DIFFRACTION99.37
2.22-2.30.36271450.31432715X-RAY DIFFRACTION99.2
2.3-2.390.28511420.26552700X-RAY DIFFRACTION99.16
2.39-2.50.31671440.23282705X-RAY DIFFRACTION99.13
2.5-2.630.26361430.20932676X-RAY DIFFRACTION99.47
2.63-2.80.26231420.19882723X-RAY DIFFRACTION99.34
2.8-3.010.22561450.18592729X-RAY DIFFRACTION99.52
3.01-3.320.2241400.18222711X-RAY DIFFRACTION99.27
3.32-3.80.19571450.17192726X-RAY DIFFRACTION99.45
3.8-4.780.17481470.1552746X-RAY DIFFRACTION99.66
4.78-46.640.18391480.16532795X-RAY DIFFRACTION99.86
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1310488724580.1585945766350.04404680007660.203091595282-0.09869682134360.1803178722480.0152488632518-0.152207756594-0.102008882707-0.9193778481140.1779396005020.5459957877290.00427710367172-0.03753080279084.42141213437E-50.659191464613-0.0125233234085-0.1187196558130.538010914794-0.01124191448930.5775493758917.34587574958-17.66048878097.7979324466
20.599332691824-0.0899800363543-0.2092569272940.01104404551280.0294335448490.1185476601050.4349314617570.0973346898647-0.495622261438-0.304591895613-0.06193692172050.0744770008953-0.0506429816090.150429271091-5.75917331539E-51.09415990871-0.0101008417136-0.2651010927010.595707077678-0.06273307314520.6816594964779.17540487875-19.2522063718-0.291529663703
30.650327151440.0907395513269-0.2230389387180.1382575743080.2164998236340.4453736178070.07541412794230.621197266629-0.0942303116408-1.36316269681-0.00211219531736-0.00460300947135-0.004855479567080.477947320134-0.01068286759291.25327083091-0.0460755012651-0.06234012539940.673951577178-0.0008255035745220.46735628087416.9833188976-12.8883896712-6.89548838284
41.12488268142-0.324344056084-0.3588546370040.163230140797-0.1220095010570.653809521786-0.03541777248320.1867814578330.170362788705-0.2064204832830.119512908749-0.174376920303-0.1251059144090.175648412066-0.0001073963168691.26376143028-0.0774323336276-0.109804215980.5839954923250.01905380923710.62758096160615.676394136-4.29949593193-1.97379295901
50.90324604906-0.526489104676-0.7016547843270.2906947293780.3856505264490.5558952647280.1350912955470.207057757421-0.174827546338-1.760531329620.2090725362030.229174911658-0.160194575070.0889569205730.07728757471931.12113803113-0.0467634918531-0.3078147063190.564225296047-0.03454352079770.6547690370661.88106151278-13.3042227443-6.2038664474
60.16768671261-0.00794344250323-0.0421732616140.1241984146320.06948306718910.04297528125940.706206748750.5404353726370.236193890363-0.144756928318-0.2598529954260.216034151927-0.435643033230.4388651125697.57500735159E-51.15458212451-0.000735443556107-0.1755726847580.651391059247-0.02482668809520.7820406805234.11313414656-3.172234585933.5795714322
70.2188926192750.3661636379550.5360007664690.8431679478750.8226234538630.8268221931860.171429888955-0.1555482728930.0357259639467-0.304764923722-0.099372136870.6233602944580.450101352212-0.55438593645.89337072582E-50.44967773248-0.061297263101-0.02104743966550.581297080083-0.01540684815810.6415357614492.50927832418-14.199088370121.5035270542
80.2324031002260.308863657008-0.1067750438350.39632488734-0.181680477870.1472168555750.4819810560790.4340296768780.441943665799-0.572861314846-0.215899145071-0.161311707120.126851276963-0.1096158703220.0001245366120350.556573908559-0.0854435526337-0.0536611496350.638002452170.02304815596340.7395958390721.12026893012-20.93134906918.6043226489
90.166024048204-0.392595419784-0.1848197054080.751476222690.3846550927941.066538301660.4224631224810.0198527288864-0.609443332343-0.472643616423-0.04810559771230.145479021980.8630193768980.03486622776720.0001412460764940.743194537322-0.0754709190142-0.1496559685050.5554977433570.01240046038370.6588722864978.41496791422-26.76930033428.95092073895
101.435230576460.317362092897-0.2884303858831.225171874060.6124733665660.711439453182-0.137128872823-0.09707954657130.180809495788-0.0372331161017-0.0391827381336-0.0392833347678-0.611081275535-0.0998914510019-0.006209234884210.5069032705930.0409316453559-0.003224207840090.478436159712-0.03115843989340.49453746422814.55804424836.0009719843428.1345200271
110.289425095873-0.3998054671560.2716521186561.33779771860.4024213736650.419971827349-0.02590391158420.07331257035460.0855630005382-0.409221497027-0.1486886739730.459490053916-0.395444578230.06634220707760.0004035935327620.619498060240.0522814861516-0.1456181295460.542457247541-0.01485218619010.5970777318757.806007636148.7736454777318.7360668636
121.190355580310.4147449645190.4477285698741.133246037951.348214378712.17404317374-0.03362636704340.1036225898510.000544221657299-0.4221555049680.151606526496-0.16598453391-0.2275928546850.2306931546785.12126078554E-50.427286859311-0.01455796109940.1032239025310.4820125951130.0005383176184570.4325394266125.7679244985-3.1434957592119.3207217852
130.565226988448-0.5747689706130.2383199830221.451985061170.3916729591420.7286485345090.115989023907-0.0272345167535-0.2532191954170.6278317079110.0523587330112-0.3942976364450.21695642183-0.05244282874013.95427789396E-50.4535002954940.0169393496925-0.007345034086810.481785308585-0.03452120725430.5279502574923.0200617259-5.8160116117934.4454081123
140.01113424450150.007114000336960.01103104269180.002940530546190.01008465104220.00924202399564-0.0346279689030.235358817437-0.1687078709250.1089169315511.186709712190.0737145617738-0.01489708228360.3205979673060.0001253337911191.14937976203-0.04436446282-0.01791610383040.972743778480.1479179474381.2696214975626.842114045912.99343804618.018470424
150.1162735902440.06441313593790.1460481706690.06342718808170.04034753230490.1268464204460.2296209397350.03911817243310.4742100140440.218486886086-0.0471905421374-0.48773759285-0.6587868247460.876836797736-0.0002271008934090.971029417189-0.07779384246630.20582626990.917010242408-0.07801769370270.98946298323533.274766165-3.573375495869.09337253731
160.0142047457115-0.006066168333440.0008400438385020.0159788650592-0.02018107064120.015736670878-0.178772417388-0.230859355924-0.2106996455120.032590083929-0.1018202247880.0125536403704-0.1029219625780.6752652828120.0001975635709330.847303420216-0.0228074206196-0.02125396992311.18494170439-0.1888789003291.6227879813943.6734057649-20.307262424311.7952638891
171.34176380317-0.511792858817-0.1208810845111.50040075714-0.6166614958810.366150842556-0.205222213050.554292802137-0.90475496881-0.3874165895180.575838212629-0.2068320486850.2732556914570.5487611741860.6383469472690.6067071846870.1893154357550.2540503677590.788921265034-0.2086581360490.8214181256432.8333037472-23.93354940538.53628560482
180.472652128415-0.0323659313694-0.03744455894570.07376688797270.0585405112450.0492834825369-0.06526880824270.114473160379-0.0383614954624-0.428288437173-0.7655649670570.6210682142820.460225074540.0458139880055-0.0002939993419860.9949068094840.06732567232170.1112160040411.18531058738-0.03655822914331.20085916923-7.3958025868-10.172092280425.1816488884
190.0300681480616-0.0368833327195-0.07302553134060.4010312342590.6968082906451.19311482840.027784268814-0.7581211735480.3989260766910.329476958894-0.1130068777530.4769914456890.699856987437-0.5498050943210.05985015675110.495416041151-0.06934086425090.1999744073820.777785986015-0.01391082958060.695933429449-0.258906214507-8.8284802618636.0058710542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 26 )
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 43 )
3X-RAY DIFFRACTION3chain 'A' and (resid 44 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 102 )
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 139 )
7X-RAY DIFFRACTION7chain 'A' and (resid 140 through 190 )
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 202 )
9X-RAY DIFFRACTION9chain 'A' and (resid 203 through 242 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 76 )
11X-RAY DIFFRACTION11chain 'B' and (resid 77 through 102 )
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 202 )
13X-RAY DIFFRACTION13chain 'B' and (resid 203 through 240 )
14X-RAY DIFFRACTION14chain 'C' and (resid 17 through 26 )
15X-RAY DIFFRACTION15chain 'C' and (resid 27 through 36 )
16X-RAY DIFFRACTION16chain 'C' and (resid 37 through 42 )
17X-RAY DIFFRACTION17chain 'C' and (resid 43 through 60 )
18X-RAY DIFFRACTION18chain 'D' and (resid 28 through 44 )
19X-RAY DIFFRACTION19chain 'D' and (resid 45 through 61 )

+
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