[English] 日本語
Yorodumi
- PDB-2qe7: Crystal structure of the f1-atpase from the thermoalkaliphilic ba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qe7
TitleCrystal structure of the f1-atpase from the thermoalkaliphilic bacterium bacillus sp. ta2.a1
Components
  • ATP synthase subunit alpha
  • ATP synthase subunit beta
  • ATP synthase subunit epsilon
  • ATP synthase subunit gamma
KeywordsHYDROLASE / blockage of ATP hydrolysis / F1-ATPase / ATP synthase / single particle analysis / thermoalkaliphilic
Function / homology
Function and homology information


proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / ATP binding / plasma membrane
Similarity search - Function
ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 ...ATP synthase delta/epsilon subunit, C-terminal domain / ATP Synthase; domain 1 / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, F1 complex, gamma subunit / ATP synthase delta/epsilon subunit, C-terminal domain / ATP synthase, Delta/Epsilon chain, long alpha-helix domain / ATP synthase alpha/beta chain, C-terminal domain / Lysin / Thrombin, subunit H - #170 / Elongation Factor Tu (Ef-tu); domain 3 - #20 / Pyruvate Kinase; Chain: A, domain 1 / Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 / Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 / ATP synthase, gamma subunit, helix hairpin domain / ATP synthase, F1 complex, delta/epsilon subunit / ATP synthase, F1 complex, delta/epsilon subunit, N-terminal / F0F1 ATP synthase delta/epsilon subunit, N-terminal / ATP synthase, Delta/Epsilon chain, beta-sandwich domain / ATP synthase, F1 complex, gamma subunit conserved site / ATP synthase gamma subunit signature. / ATP synthase, F1 complex, beta subunit / ATP synthase, alpha subunit, C-terminal domain superfamily / ATP synthase, F1 complex, gamma subunit / ATP synthase, F1 complex, gamma subunit superfamily / ATP synthase / ATP synthase, alpha subunit, C-terminal / ATP synthase, F1 complex, alpha subunit / ATP synthase, F1 complex, alpha subunit nucleotide-binding domain / ATP synthase alpha/beta chain, C terminal domain / ATPase, F1/V1 complex, beta/alpha subunit, C-terminal / ATP synthase subunit alpha, N-terminal domain-like superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily / ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain / ATP synthase alpha/beta family, beta-barrel domain / ATPase, alpha/beta subunit, nucleotide-binding domain, active site / ATP synthase alpha and beta subunits signature. / ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain / ATP synthase alpha/beta family, nucleotide-binding domain / Elongation Factor Tu (Ef-tu); domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Thrombin, subunit H / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Beta Barrel / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP synthase epsilon chain / ATP synthase subunit beta / ATP synthase gamma chain / ATP synthase subunit alpha
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsStocker, A. / Keis, S. / Vonck, J. / Cook, G.M. / Dimroth, P.
CitationJournal: Structure / Year: 2007
Title: The Structural Basis for Unidirectional Rotation of Thermoalkaliphilic F(1)-ATPase.
Authors: Stocker, A. / Keis, S. / Vonck, J. / Cook, G.M. / Dimroth, P.
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 8, 2013Group: Refinement description
Revision 1.3Aug 30, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP synthase subunit alpha
B: ATP synthase subunit alpha
C: ATP synthase subunit alpha
D: ATP synthase subunit beta
E: ATP synthase subunit beta
F: ATP synthase subunit beta
G: ATP synthase subunit gamma
H: ATP synthase subunit epsilon


Theoretical massNumber of molelcules
Total (without water)362,7648
Polymers362,7648
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.210, 173.020, 218.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13D
23E
14D
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROAA27 - 50027 - 500
211GLUGLUPROPROBB27 - 50027 - 500
122GLUGLUPROPROAA27 - 50027 - 500
222GLUGLUPROPROCC27 - 50027 - 500
133ASNASNLEULEUDD2 - 4622 - 462
233ASNASNLEULEUEE2 - 4622 - 462
144ASNASNLEULEUDD2 - 4622 - 462
244ASNASNLEULEUFF2 - 4622 - 462

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.001785, -0.971851, 0.235591), (0.247257, -0.227848, -0.94178), (0.968948, 0.059933, 0.23989)0.495249, -13.4137, -8.6946
3given(-0.01717, 0.262378, 0.964812), (-0.970925, -0.234808, 0.046576), (0.238766, -0.935961, 0.258781)10.6763, -2.23016, -9.43767
4given(-0.021542, -0.972552, 0.231685), (0.267291, -0.228906, -0.936033), (0.963375, 0.041763, 0.264885)0.128083, -12.7281, -6.78129
5given(0.004944, 0.261873, 0.96509), (-0.966448, -0.246603, 0.071865), (0.256814, -0.933065, 0.251867)11.2511, -0.401973, -9.31946
DetailsThe biological assembly consists of one single TA2F1 molecule with alpha3-beta3-gamma-epsilon subunit stoichiometry. The alpha3-beta3 core complex possesses pseudo three-fold symmetry and the asymmetric part of the molecule represented by subunits gamma and epsilon exists in three alternate conformations.

-
Components

#1: Protein ATP synthase subunit alpha /


Mass: 55016.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpA / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG5, EC: 3.6.1.34
#2: Protein ATP synthase subunit beta /


Mass: 50266.012 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpD / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG3, EC: 3.6.1.34
#3: Protein ATP synthase subunit gamma /


Mass: 31932.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpG / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG4, EC: 3.6.1.34
#4: Protein ATP synthase subunit epsilon /


Mass: 14983.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: TA2.A1 / Gene: atpC / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): RNE41(DE3) / References: UniProt: Q71CG2, EC: 3.6.1.34

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.63 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 8.8
Details: 1M LiCl, 0.1M Tris-HCl, 20% PEG 6000 , pH 8.8, MICRO-BATCH, temperature 296K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2005 / Details: Dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 90041 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 72.595 Å2 / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 10.2
Reflection shellResolution: 3.06→3.25 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.716 / % possible all: 74.9

-
Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMF

1bmf


Resolution: 3.06→39.997 Å / Isotropic thermal model: isotropic group / Cross valid method: THROUGHOUT / σ(F): -3 / σ(I): -3 / Stereochemistry target values: ml
RfactorNum. reflection% reflectionSelection details
Rfree0.306 2094 2.5 %random
Rwork0.2519 ---
all-90041 --
obs-83712 94.61 %-
Solvent computationBsol: 137.521 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso mean: 77.22 Å2
Baniso -1Baniso -2Baniso -3
1-22.643 Å2-0 Å2-0 Å2
2---7.208 Å20 Å2
3----15.435 Å2
Refinement stepCycle: LAST / Resolution: 3.06→39.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24330 0 0 0 24330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_bond_d_na
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d0.662
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d11.059
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsAuth asym-IDRefine-IDTypeRms dev position (Å)
11chain A & BAX-RAY DIFFRACTIONPOSITIONAL0.037
21chain A & CAX-RAY DIFFRACTIONB-FACTOR0.044
31chain D & EDX-RAY DIFFRACTIONPOSITIONAL0.046
41chain D & FDX-RAY DIFFRACTIONB-FACTOR0.037
LS refinement shellResolution: 3.06→3.1312 Å / Rfactor Rfree error: 0.062
RfactorNum. reflection% reflection
Rfree0.3993 137 -
Rwork0.3196 --
obs--93 %
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)
10.0952-0.25410.14970.71350.02521.8918-0.21010.157-0.04060.09750.12180.0885-0.0868-0.25710.0560.23510.06470.11590.4274-0.05260.3313-43.044130.9149-21.8949
21.0123-0.19770.7250.61820.6223-0.50140.2582-0.25850.02020.3630.09080.11130.44890.0531-0.33810.90210.26040.06270.54940.01710.2743-23.91821.41275.568
32.8197-1.46420.7912.37110.0602-2.5739-1.1061-2.0398-0.07651.92710.98320.12350.7374-0.9088-0.00762.2620.5420.2631.7879-0.01320.4853-32.61225.800517.5828
40.9527-0.4038-0.10940.6388-0.09540.82810.0264-0.09020.1112-0.0941-0.0456-0.12260.04790.0530.03360.2017-0.05690.05390.2393-0.00240.3415-2.652433.024-57.3203
50.2009-1.01381.00482.2709-0.54780.7113-0.05830.1932-0.46030.35650.1889-0.5828-0.0460.083-0.04740.16070.0073-0.14220.33850.03180.552315.696617.8409-36.7699
6-3.74441.17641.31024.1019-1.82194.3669-0.24850.6228-0.42720.4948-0.5032-1.9062-0.42911.40440.74370.4796-0.2268-0.50821.4046-0.15811.367935.047724.561-38.3527
70.3079-0.43560.00830.8784-0.92811.4726-0.1620.0539-0.0715-0.07220.11460.17310.2501-0.18860.07970.3283-0.13760.07770.3499-0.08950.4919-34.1965-10.964-52.5764
83.0965-0.60081.96373.1397-0.158-0.18310.0116-0.61130.15190.53150.2788-0.05740.1063-0.569-0.25610.9964-0.03060.12711.12190.09070.6716-11.6918-25.449-21.0794
91.7855-0.56380.4705-0.95320.80961.594-0.1679-0.0044-0.31350.2055-0.15620.33190.7538-0.08570.35210.4340.01340.3670.10390.07160.6796-20.2111-39.9221-34.4549
10-0.81660.05330.59381.98560.0080.6165-0.4202-0.0150.3324-0.14090.44520.5420.044-0.857-0.030.268-0.22540.10520.76-0.16770.4791-57.247512.054-51.8438
11-0.4035-0.0244-0.08190.2877-0.181.10890.0191-0.02310.0955-0.07990.09940.3030.049-0.7137-0.0670.243-0.16860.1380.6133-0.07490.5012-54.9327-1.2415-28.0737
120.86711.6493-0.74111.1953-0.52130.8216-0.1008-0.2043-0.75930.03860.0015-0.4542-0.13790.17680.30170.253-0.08660.13110.5998-0.13020.5575-43.65969.2288-31.0282
131.13590.52350.6569-0.2928-0.16340.69950.1403-0.216-0.33810.228-0.16310.03940.0959-0.1148-0.00360.7274-0.16970.1850.4520.08910.5016-37.8393-7.5708-3.2966
141.0002-0.26840.7779-0.02230.17551.3678-0.0075-0.17580.1808-0.1162-0.0576-0.0071-0.404-0.32950.13630.18260.0597-0.06980.2026-0.02430.3373-29.0151.7314-42.4981
150.9559-0.27090.86420.1084-0.34671.471-0.1654-0.10130.0255-0.0167-0.0751-0.2345-0.2499-0.16060.22070.18360.04160.00680.1796-0.04830.3172-13.569346.5921-25.8628
160.8676-1.03-0.4239-1.0760.28582.36060.1862-0.07160.32040.0535-0.1098-0.03790.45610.3364-0.25210.15760.079-0.04910.1109-0.09660.3351-14.829636.7448-37.1526
172.469-0.02661.61830.5767-0.5031.44010.2296-0.0929-0.40530.0321-0.0991-0.3070.0744-0.1019-0.13160.2627-0.0551-0.07880.205-0.04770.36945.633535.9092-12.6105
180.7928-0.7080.29111.5322-0.55131.0940.05070.0594-0.0393-0.6762-0.1032-0.08250.4775-0.09320.00760.4763-0.06490.09940.239-0.0990.3089-13.43687.0831-72.2745
191.3877-0.19130.111-0.1222-0.59350.82-0.13690.04820.2517-0.16880.0237-0.09980.1791-0.06650.09530.2413-0.04640.14670.1673-0.06990.2781-0.68210.3486-67.5873
201.1929-0.0847-0.65370.7538-0.53440.6228-0.1199-0.1403-0.0578-0.08570.06760.18120.09890.0891-0.02990.5103-0.0010.16730.3252-0.02430.3845-14.70332.9258-57.0975
210.975-1.0223-0.58661.24350.65530.7589-0.4043-0.2492-0.06360.29330.1020.25170.4040.17190.0470.41520.30130.28570.26370.07950.29799.4821-17.5207-46.0221
220.00740.0166-0.00980.00260.0159-0.0248-0.0204-0.0955-0.03380.116-0.04040.1037-0.0276-0.043-0.5591-0.2435-0.12290.2064-0.14650.1517-0.18190.4408-2.0647-10.7983
232.0144-0.5771-0.9130.2550.11280.71820.1777-0.3266-0.0454-0.1911-0.0914-0.06420.25050.18480.7899-0.56320.27070.4384-0.11160.1448-0.022517.6849-11.844910.2186
240.2773-0.19910.28270.4058-0.47870.70720.0967-0.03240.022-0.1509-0.1383-0.090.0101-0.13590.0626-0.27130.0990.16320.02610.10750.12336.7712-5.8947-2.8735
25-0.91510.2233-0.5131-0.469-0.2345-0.7072-0.0417-0.4387-0.12680.2705-0.4557-0.299-0.54760.84330.48430.9173-0.5184-0.44361.26920.48061.00724.3046-14.368514.4629
260.43310.4725-0.99230.50290.8595-0.01690.1642-0.3122-0.0310.58060.1925-0.06110.05610.3211-0.05360.54990.32320.04491.02360.63860.411128.3254-15.96218.9821
270.0964-0.15880.04430.18490.84811.29660.048-0.232-0.01720.2265-0.0098-0.25780.31070.3876-0.09730.5660.0133-0.25430.24230.24910.294622.404-13.306313.3544
280.21850.0626-0.12320.50960.25730.13450.0056-0.5421-0.18890.3391-0.22870.0961-0.30270.0662-0.05111.1482-0.5673-0.17691.01030.08190.430323.237-11.985514.8571
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 3641 - 338
2X-RAY DIFFRACTION2AA365 - 443339 - 417
3X-RAY DIFFRACTION3AA444 - 500418 - 474
4X-RAY DIFFRACTION4BB27 - 3211 - 295
5X-RAY DIFFRACTION5BB322 - 441296 - 415
6X-RAY DIFFRACTION6BB442 - 500416 - 474
7X-RAY DIFFRACTION7CC27 - 3801 - 354
8X-RAY DIFFRACTION8CC381 - 415355 - 389
9X-RAY DIFFRACTION9CC416 - 500399 - 474
10X-RAY DIFFRACTION10DD2 - 581 - 57
11X-RAY DIFFRACTION11DD59 - 24858 - 247
12X-RAY DIFFRACTION12DD249 - 309248 - 308
13X-RAY DIFFRACTION13DD310 - 462309 - 461
14X-RAY DIFFRACTION14EE2 - 1241 - 123
15X-RAY DIFFRACTION15EE125 - 259124 - 258
16X-RAY DIFFRACTION16EE260 - 310259 - 309
17X-RAY DIFFRACTION17EE311 - 462310 - 461
18X-RAY DIFFRACTION18FF2 - 1581 - 157
19X-RAY DIFFRACTION19FF159 - 245158 - 244
20X-RAY DIFFRACTION20FF246 - 318245 - 317
21X-RAY DIFFRACTION21FF319 - 462318 - 461
22X-RAY DIFFRACTION22GG3 - 393 - 39
23X-RAY DIFFRACTION23GG40 - 19340 - 193
24X-RAY DIFFRACTION24GG217 - 266217 - 266
25X-RAY DIFFRACTION25HH1 - 201 - 20
26X-RAY DIFFRACTION26HH21 - 6621 - 66
27X-RAY DIFFRACTION27HH67 - 9467 - 94
28X-RAY DIFFRACTION28HH95 - 13595 - 135

+
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