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- PDB-4ag5: Structure of VirB4 of Thermoanaerobacter pseudethanolicus -

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Basic information

Entry
Database: PDB / ID: 4ag5
TitleStructure of VirB4 of Thermoanaerobacter pseudethanolicus
ComponentsTYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
KeywordsHYDROLASE / TYPE IV SECRETION / CONJUGATION
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #730 / TraG, P-loop domain / TraG P-loop domain / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Type IV secretory pathway VirB4 components-like protein
Similarity search - Component
Biological speciesTHERMOANAEROBACTER PSEUDETHANOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWallden, K. / Williams, R. / Yan, J. / Lian, P.W. / Wang, L. / Thalassinos, K. / Orlova, E.V. / Waksman, G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system.
Authors: Karin Walldén / Robert Williams / Jun Yan / Pei W Lian / Luchun Wang / Konstantinos Thalassinos / Elena V Orlova / Gabriel Waksman /
Abstract: Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer ...Type IV secretion (T4S) systems mediate the transfer of proteins and DNA across the cell envelope of bacteria. These systems play important roles in bacterial pathogenesis and in horizontal transfer of antibiotic resistance. The VirB4 ATPase of the T4S system is essential for both the assembly of the system and substrate transfer. In this article, we present the crystal structure of the C-terminal domain of Thermoanaerobacter pseudethanolicus VirB4. This structure is strikingly similar to that of another T4S ATPase, VirD4, a protein that shares only 12% sequence identity with VirB4. The VirB4 domain purifies as a monomer, but the full-length protein is observed in a monomer-dimer equilibrium, even in the presence of nucleotides and DNAs. We also report the negative stain electron microscopy structure of the core complex of the T4S system of the Escherichia coli pKM101 plasmid, with VirB4 bound. In this structure, VirB4 is also monomeric and bound through its N-terminal domain to the core's VirB9 protein. Remarkably, VirB4 is observed bound to the side of the complex where it is ideally placed to play its known regulatory role in substrate transfer.
History
DepositionJan 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
B: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
C: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
D: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,96313
Polymers176,6644
Non-polymers1,3009
Water2,900161
1
A: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
D: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0647
Polymers88,3322
Non-polymers7325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-29.3 kcal/mol
Surface area27370 Å2
MethodPISA
2
B: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
C: TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9006
Polymers88,3322
Non-polymers5684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-29.2 kcal/mol
Surface area25400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.080, 110.800, 156.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LIKE PROTEIN / VIRB4 ATPASE


Mass: 44165.949 Da / Num. of mol.: 4 / Fragment: ATPASE DOMAIN, RESIDUES 203-594
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOANAEROBACTER PSEUDETHANOLICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: B0KAW2

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.45→54.04 Å / Num. obs: 69350 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 46.15 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 2.45→2.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AG6
Resolution: 2.45→54.04 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 30.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 3374 5.1 %
Rwork0.2334 --
obs0.2362 66795 95.85 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.709 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.8478 Å20 Å20 Å2
2--16.8289 Å20 Å2
3----9.9811 Å2
Refinement stepCycle: LAST / Resolution: 2.45→54.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 80 161 10083
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910115
X-RAY DIFFRACTIONf_angle_d1.15213774
X-RAY DIFFRACTIONf_dihedral_angle_d16.0493584
X-RAY DIFFRACTIONf_chiral_restr0.0691574
X-RAY DIFFRACTIONf_plane_restr0.0051762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.53760.32662780.28375796X-RAY DIFFRACTION88
2.5376-2.63920.36573200.28785764X-RAY DIFFRACTION89
2.6392-2.75930.31643480.25376054X-RAY DIFFRACTION93
2.7593-2.90470.3193590.2556268X-RAY DIFFRACTION96
2.9047-3.08670.33543420.25416434X-RAY DIFFRACTION98
3.0867-3.3250.29563520.22986472X-RAY DIFFRACTION99
3.325-3.65960.2633380.22086567X-RAY DIFFRACTION99
3.6596-4.18890.26553720.216502X-RAY DIFFRACTION98
4.1889-5.27690.24883290.19716697X-RAY DIFFRACTION100
5.2769-54.05310.30083360.25886867X-RAY DIFFRACTION99
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)
10.14270.05880.14980.29380.40410.34230.4892-0.29680.508-0.0462-0.13570.0242-0.4942-0.208-0.00030.34460.10440.03850.2421-0.08710.34074.676336.295270.8798
20.22610.4566-0.05261.0884-0.25370.08190.07070.0373-0.0266-0.30990.0101-0.10810.1676-0.25600.3360.07890.01310.12560.04240.25030.917824.984467.7692
30.30410.13230.42930.5340.63270.6575-0.1955-0.82110.30390.21520.8452-0.35220.41640.54670.01710.37690.09640.04430.27430.01930.2246-1.831215.986673.1886
4-0.00850.43890.230.3975-0.48510.5210.1596-0.1852-0.08940.2995-0.0385-0.28630.45940.10730.00020.3090.0361-0.03520.2884-0.00060.22991.74296.142175.6988
50.0051-0.0535-0.01990.03530.01330.1017-0.2225-0.3736-0.0906-0.13670.17870.00510.2301-0.379700.3317-0.0841-0.0660.17650.17420.3366-16.44852.923865.1252
60.62980.7810.04470.64870.21930.0575-0.36950.69370.89110.0260.46820.28380.4454-0.00370.01360.3797-0.0151-0.20690.43890.12090.3403-14.892153.3138
71.07671.024-0.48370.93180.63780.5817-0.2037-0.19370.30550.10530.28810.55840.37960.1802-0.00240.2765-0.094-0.10470.2530.03230.3569-20.5905-6.859760.61
81.1071.39690.13271.62250.94610.9742-0.0430.188-0.0882-0.00910.1342-0.08040.00420.0921-00.29320.0008-0.05720.21380.01320.2319-5.9778-1.245262.1684
90.79180.59420.17470.43960.15260.2202-0.0443-1.61030.30920.3363-0.4460.7371-0.2546-0.7811-0.02070.21520.04750.05470.20780.12310.2938-13.56417.684872.8581
102.40411.011-0.77093.4141.20711.8843-0.14490.37640.0644-0.62360.2481-0.1744-0.2020.0010.08270.22910.0330.02060.10310.10430.08242.348922.346258.2888
111.99810.04950.16495.46892.56061.8199-0.30130.78250.1449-1.46641.275-0.8448-1.1055-0.33710.4620.460.0699-0.2580.24340.32680.0966-0.049631.833713.9511
121.6091-1.39150.59790.6952-0.42780.30080.25420.20120.00820.0348-0.11780.0895-0.1762-0.265900.3634-0.0461-0.07650.29510.04830.20580.975616.785314.9171
130.242-0.04910.01430.23070.08430-0.56080.9456-0.3696-1.42230.79810.62770.7888-0.70030.00020.57990.0077-0.30510.6170.08690.59390.32133.69396.9013
140.3058-0.329-0.50.2960.28890.50210.39070.4950.6706-0.1672-0.48480.2213-0.0125-0.0480.00020.2830.0326-0.08870.47620.0920.451222.00670.757618.8267
150.1647-0.24960.00210.5365-0.14120.40220.3806-0.541-0.1464-0.0538-0.0217-0.0030.12110.04430.00010.3744-0.0371-0.12530.09180.01960.325418.9584-6.112731.6591
161.71760.13180.43950.68820.50840.91790.43250.9229-0.3330.0894-0.5039-0.32790.37450.4947-0.02790.30540.0528-0.0570.3117-0.02010.337523.9981-12.173121.9556
170.0946-0.24380.39911.3363-0.18790.24560.4156-0.1721-0.0345-0.9739-1.13120.36090.2593-0.2693-0.17610.3956-0.1216-0.12520.347-0.0660.268510.0479-9.788117.2313
181.2433-1.28371.15861.0404-0.470.5394-0.02910.3749-0.4158-0.0950.032-0.16790.0056-0.06010.00020.2971-0.013-0.11040.34670.03740.31078.00992.990117.3326
191.1625-0.55290.53031.98230.62310.3996-0.09890.0268-0.04520.214-0.1378-0.1812-0.2782-0.30280.00010.2733-0.0897-0.10670.22130.03630.277310.074113.121925.1928
201.0465-0.37150.00470.9972-0.08441.0010.0997-0.02720.00660.41680.1530.1512-0.6649-1.03220.01190.33930.0495-0.05340.5907-0.01190.2322-4.674224.594425.709
210.5161-0.27880.99480.1274-0.46512.0854-0.2635-0.6634-1.2382-0.08090.5378-0.23882.1163-1.01010.05380.5410.9535-0.63110.9567-1.12430.993437.38169.661466.4677
220.9890.71321.4811.24950.78512.3284-3.3172-0.86431.8514-1.5960.5034-0.9979-0.42952.6101-0.1890.32390.8952-0.33870.7487-0.71641.031843.28692.265364.4306
23-0.01460.01020.02240.00380.04580.0153-0.4083-0.6999-0.213-0.07010.4603-0.2448-0.45650.329701.10280.8431-0.60080.9715-0.64260.708651.1534-0.088866.3872
240.08470.0045-0.07290.1771-0.10450.093-1.0129-1.51781.1270.3933-1.1230.3457-0.00410.9123-00.40870.2102-0.32250.7028-0.07240.696751.9058-2.472251.5176
251.1332-0.6941.34731.42340.15731.5496-0.39020.12490.74990.2872-0.05930.1831-0.04580.228-0.29170.22860.0102-0.21550.2604-0.02590.53334.8349-1.847738.8641
261.7094-0.81641.01310.537-0.04362.04010.03840.95880.1870.12490.0732-0.1670.75660.7171-0.31160.32740.083-0.12990.50770.13240.387841.0705-8.431331.6394
270.9959-0.3063-2.07130.71311.42015.4988-1.53670.08530.14080.0174-0.244-0.87050.77660.9401-0.22190.1784-0.3553-0.54521.04590.38641.242752.12160.779837.3516
281.4714-0.5-0.33730.73310.68282.1345-1.195-0.77171.25460.80130.6649-0.53460.23320.3935-0.23880.64230.3076-0.50650.5004-0.23690.941244.1540.002251.5811
291.3893-0.00630.40250.30090.50810.7322-1.0118-0.92961.46390.22180.25990.34390.3217-0.4898-0.02760.61640.2235-0.47380.4494-0.35781.086232.85423.199154.2463
300.0575-0.15880.07820.14670.02020.0116-0.51240.35340.81240.2687-0.5112-0.64260.2881-0.7927-00.87030.4583-0.76170.6961-0.37431.694826.576211.508256.2402
310.17750.10650.16730.0435-0.03620.3112-0.6771-0.0892-0.0448-0.24480.8502-0.57680.5881-1.171401.0566-0.35880.2591.3634-0.0030.678-23.269612.949213.9961
320.46380.05750.33210.01370.05960.5099-0.9893-0.6180.9824-0.9228-1.17930.17710.3873-0.4127-0.01120.1984-0.00570.11971.42140.54650.9822-38.244113.378211.482
330.08770.3806-0.09860.377-0.19790.0462-0.54650.07590.7201-0.31930.37810.33670.6325-0.754400.71140.0803-0.14321.62270.00650.543-41.43664.487614.5562
340.8089-0.79430.4510.3889-0.15580.2059-0.4885-0.0161-0.6606-0.02310.79380.6938-0.0829-0.1081-0.11080.1205-0.3334-0.21791.46490.43880.44-29.2474-4.34736.7806
352.7855-1.5996-1.74961.35361.18231.28440.7103-0.88341.1219-0.41450.2648-0.3699-0.556-0.40730.32140.2268-0.3537-0.51181.37370.64210.6951-33.33237.384542.0914
362.3811.03340.84730.43320.22981.5876-0.56711.14341.0494-0.07110.2650.63880.2642-0.1302-0.47170.3136-0.2309-0.21840.82890.30280.7473-35.1159-3.561848.6526
370.05190.0608-0.06870.004-0.05790.0086-0.03210.4519-0.42480.0385-0.28950.0530.2578-0.040300.3966-0.3815-0.51212.02581.2971.5267-45.7959-0.122238.3821
380.2756-1.07030.13451.1206-1.0371.25990.31010.33170.73520.0473-0.2616-0.08940.1348-0.4466-0.00010.4994-0.1628-0.13291.16540.15950.5679-35.10947.151328.8887
390.13870.4458-0.49620.1455-0.37020.51720.4654-0.31680.5886-0.06980.33040.2443-0.40560.4063-00.4077-0.18140.00411.3001-0.1990.8183-25.861313.154826.0773
400.01490.08240.13080.00690.06530.0745-0.3234-0.58910.17960.7809-0.4246-0.4207-1.28710.875800.9407-0.1982-0.00931.02460.19160.6503-26.705822.357322.0521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 205:228)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 229:262)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 263:274)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 275:297)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 298:317)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 318:344)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 345:390)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 391:458)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 459:468)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 469:588)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 205:231)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 232:278)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 279:293)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 294:329)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 330:352)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 353:404)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 405:423)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 424:461)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 462:525)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 526:587)
21X-RAY DIFFRACTION21(CHAIN C AND RESID 238:257)
22X-RAY DIFFRACTION22(CHAIN C AND RESID 258:277)
23X-RAY DIFFRACTION23(CHAIN C AND RESID 278:287)
24X-RAY DIFFRACTION24(CHAIN C AND RESID 288:298)
25X-RAY DIFFRACTION25(CHAIN C AND RESID 299:347)
26X-RAY DIFFRACTION26(CHAIN C AND RESID 348:403)
27X-RAY DIFFRACTION27(CHAIN C AND RESID 404:416)
28X-RAY DIFFRACTION28(CHAIN C AND RESID 417:459)
29X-RAY DIFFRACTION29(CHAIN C AND RESID 460:503)
30X-RAY DIFFRACTION30(CHAIN C AND RESID 504:532)
31X-RAY DIFFRACTION31(CHAIN D AND RESID 228:248)
32X-RAY DIFFRACTION32(CHAIN D AND RESID 249:258)
33X-RAY DIFFRACTION33(CHAIN D AND RESID 259:288)
34X-RAY DIFFRACTION34(CHAIN D AND RESID 289:328)
35X-RAY DIFFRACTION35(CHAIN D AND RESID 329:338)
36X-RAY DIFFRACTION36(CHAIN D AND RESID 339:408)
37X-RAY DIFFRACTION37(CHAIN D AND RESID 409:418)
38X-RAY DIFFRACTION38(CHAIN D AND RESID 419:488)
39X-RAY DIFFRACTION39(CHAIN D AND RESID 489:519)
40X-RAY DIFFRACTION40(CHAIN D AND RESID 520:545)

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