[English] 日本語
Yorodumi
- PDB-5lfq: Crystal Structure of the Bacterial Proteasome Activator Bpa of My... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lfq
TitleCrystal Structure of the Bacterial Proteasome Activator Bpa of Mycobacterium tuberculosis (space group P3)
ComponentsBacterial proteasome activator
KeywordsSIGNALING PROTEIN / Dodecamer / four-helix bundle
Function / homologyBacterial proteasome activator / Bacterial proteasome activator / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome binding / peptidoglycan-based cell wall / protein homooligomerization / plasma membrane / Bacterial proteasome activator
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.503 Å
AuthorsBolten, M. / Delley, C.L. / Leibundgut, M. / Boehringer, D. / Ban, N. / Weber-Ban, E.
CitationJournal: Structure / Year: 2016
Title: Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.
Authors: Marcel Bolten / Cyrille L Delley / Marc Leibundgut / Daniel Boehringer / Nenad Ban / Eilika Weber-Ban /
Abstract: Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial ...Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex.
History
DepositionJul 4, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 10, 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 / 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bacterial proteasome activator
B: Bacterial proteasome activator
C: Bacterial proteasome activator
D: Bacterial proteasome activator
E: Bacterial proteasome activator
F: Bacterial proteasome activator
G: Bacterial proteasome activator
H: Bacterial proteasome activator
I: Bacterial proteasome activator
J: Bacterial proteasome activator
K: Bacterial proteasome activator
L: Bacterial proteasome activator
M: Bacterial proteasome activator
N: Bacterial proteasome activator
O: Bacterial proteasome activator
P: Bacterial proteasome activator


Theoretical massNumber of molelcules
Total (without water)240,26116
Polymers240,26116
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31870 Å2
ΔGint-189 kcal/mol
Surface area85110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.854, 100.854, 207.433
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 39:94 or resseq 96:105 or resseq 107:149))
21(chain B and (resseq 39:94 or resseq 96:105 or resseq 107:149))
31(chain C and (resseq 39:94 or resseq 96:105 or resseq 107:149))
41(chain D and (resseq 39:94 or resseq 96:105 or resseq 107:149))
51(chain E and (resseq 39:94 or resseq 96:105 or resseq 107:149))
61(chain F and (resseq 39:94 or resseq 96:105 or resseq 107:149))
71(chain G and (resseq 39:94 or resseq 96:105 or resseq 107:149))
81(chain H and (resseq 39:94 or resseq 96:105 or resseq 107:149))
91(chain I and (resseq 39:94 or resseq 96:105 or resseq 107:149))
101(chain J and (resseq 39:94 or resseq 96:105 or resseq 107:149))
111(chain K and (resseq 39:94 or resseq 96:105 or resseq 107:149))
121(chain L and (resseq 39:94 or resseq 96:105 or resseq 107:149))
131(chain M and (resseq 39:94 or resseq 96:105 or resseq 107:149))
141(chain N and (resseq 39:94 or resseq 96:105 or resseq 107:149))
151(chain O and (resseq 39:94 or resseq 96:105 or resseq 107:149))
161(chain P and (resseq 39:94 or resseq 96:105 or resseq 107:149))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPARGARG(chain A and (resseq 39:94 or resseq 96:105 or resseq 107:149))AA39 - 9411 - 66
12GLUGLUASNASN(chain A and (resseq 39:94 or resseq 96:105 or resseq 107:149))AA96 - 10568 - 77
13ASPASPGLNGLN(chain A and (resseq 39:94 or resseq 96:105 or resseq 107:149))AA107 - 14979 - 121
21ASPASPARGARG(chain B and (resseq 39:94 or resseq 96:105 or resseq 107:149))BB39 - 9411 - 66
22GLUGLUASNASN(chain B and (resseq 39:94 or resseq 96:105 or resseq 107:149))BB96 - 10568 - 77
23ASPASPGLNGLN(chain B and (resseq 39:94 or resseq 96:105 or resseq 107:149))BB107 - 14979 - 121
31ASPASPARGARG(chain C and (resseq 39:94 or resseq 96:105 or resseq 107:149))CC39 - 9411 - 66
32GLUGLUASNASN(chain C and (resseq 39:94 or resseq 96:105 or resseq 107:149))CC96 - 10568 - 77
33ASPASPGLNGLN(chain C and (resseq 39:94 or resseq 96:105 or resseq 107:149))CC107 - 14979 - 121
41ASPASPARGARG(chain D and (resseq 39:94 or resseq 96:105 or resseq 107:149))DD39 - 9411 - 66
42GLUGLUASNASN(chain D and (resseq 39:94 or resseq 96:105 or resseq 107:149))DD96 - 10568 - 77
43ASPASPGLNGLN(chain D and (resseq 39:94 or resseq 96:105 or resseq 107:149))DD107 - 14979 - 121
51ASPASPARGARG(chain E and (resseq 39:94 or resseq 96:105 or resseq 107:149))EE39 - 9411 - 66
52GLUGLUASNASN(chain E and (resseq 39:94 or resseq 96:105 or resseq 107:149))EE96 - 10568 - 77
53ASPASPGLNGLN(chain E and (resseq 39:94 or resseq 96:105 or resseq 107:149))EE107 - 14979 - 121
61ASPASPARGARG(chain F and (resseq 39:94 or resseq 96:105 or resseq 107:149))FF39 - 9411 - 66
62GLUGLUASNASN(chain F and (resseq 39:94 or resseq 96:105 or resseq 107:149))FF96 - 10568 - 77
63ASPASPGLNGLN(chain F and (resseq 39:94 or resseq 96:105 or resseq 107:149))FF107 - 14979 - 121
71ASPASPARGARG(chain G and (resseq 39:94 or resseq 96:105 or resseq 107:149))GG39 - 9411 - 66
72GLUGLUASNASN(chain G and (resseq 39:94 or resseq 96:105 or resseq 107:149))GG96 - 10568 - 77
73ASPASPGLNGLN(chain G and (resseq 39:94 or resseq 96:105 or resseq 107:149))GG107 - 14979 - 121
81ASPASPARGARG(chain H and (resseq 39:94 or resseq 96:105 or resseq 107:149))HH39 - 9411 - 66
82GLUGLUASNASN(chain H and (resseq 39:94 or resseq 96:105 or resseq 107:149))HH96 - 10568 - 77
83ASPASPGLNGLN(chain H and (resseq 39:94 or resseq 96:105 or resseq 107:149))HH107 - 14979 - 121
91ASPASPARGARG(chain I and (resseq 39:94 or resseq 96:105 or resseq 107:149))II39 - 9411 - 66
92GLUGLUASNASN(chain I and (resseq 39:94 or resseq 96:105 or resseq 107:149))II96 - 10568 - 77
93ASPASPGLNGLN(chain I and (resseq 39:94 or resseq 96:105 or resseq 107:149))II107 - 14979 - 121
101ASPASPARGARG(chain J and (resseq 39:94 or resseq 96:105 or resseq 107:149))JJ39 - 9411 - 66
102GLUGLUASNASN(chain J and (resseq 39:94 or resseq 96:105 or resseq 107:149))JJ96 - 10568 - 77
103ASPASPGLNGLN(chain J and (resseq 39:94 or resseq 96:105 or resseq 107:149))JJ107 - 14979 - 121
111ASPASPARGARG(chain K and (resseq 39:94 or resseq 96:105 or resseq 107:149))KK39 - 9411 - 66
112GLUGLUASNASN(chain K and (resseq 39:94 or resseq 96:105 or resseq 107:149))KK96 - 10568 - 77
113ASPASPGLNGLN(chain K and (resseq 39:94 or resseq 96:105 or resseq 107:149))KK107 - 14979 - 121
121ASPASPARGARG(chain L and (resseq 39:94 or resseq 96:105 or resseq 107:149))LL39 - 9411 - 66
122GLUGLUASNASN(chain L and (resseq 39:94 or resseq 96:105 or resseq 107:149))LL96 - 10568 - 77
123ASPASPGLNGLN(chain L and (resseq 39:94 or resseq 96:105 or resseq 107:149))LL107 - 14979 - 121
131ASPASPARGARG(chain M and (resseq 39:94 or resseq 96:105 or resseq 107:149))MM39 - 9411 - 66
132GLUGLUASNASN(chain M and (resseq 39:94 or resseq 96:105 or resseq 107:149))MM96 - 10568 - 77
133ASPASPGLNGLN(chain M and (resseq 39:94 or resseq 96:105 or resseq 107:149))MM107 - 14979 - 121
141ASPASPARGARG(chain N and (resseq 39:94 or resseq 96:105 or resseq 107:149))NN39 - 9411 - 66
142GLUGLUASNASN(chain N and (resseq 39:94 or resseq 96:105 or resseq 107:149))NN96 - 10568 - 77
143ASPASPGLNGLN(chain N and (resseq 39:94 or resseq 96:105 or resseq 107:149))NN107 - 14979 - 121
151ASPASPARGARG(chain O and (resseq 39:94 or resseq 96:105 or resseq 107:149))OO39 - 9411 - 66
152GLUGLUASNASN(chain O and (resseq 39:94 or resseq 96:105 or resseq 107:149))OO96 - 10568 - 77
153ASPASPGLNGLN(chain O and (resseq 39:94 or resseq 96:105 or resseq 107:149))OO107 - 14979 - 121
161ASPASPARGARG(chain P and (resseq 39:94 or resseq 96:105 or resseq 107:149))PP39 - 9411 - 66
162GLUGLUASNASN(chain P and (resseq 39:94 or resseq 96:105 or resseq 107:149))PP96 - 10568 - 77
163ASPASPGLNGLN(chain P and (resseq 39:94 or resseq 96:105 or resseq 107:149))PP107 - 14979 - 121

-
Components

#1: Protein
Bacterial proteasome activator


Mass: 15016.304 Da / Num. of mol.: 16 / Fragment: UNP residues 36-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: bpa, Rv3780, MTCY13D12.14 / Plasmid: pET24 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P9WKX3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 5-7 % (v/v) propane-1,2-diol, 100 mM HEPES-NaOH pH 8.0 - 8.2, 200 mM MgCl2
PH range: 8.0 - 8.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.5→45.35 Å / Num. obs: 47926 / % possible obs: 81.44 % / Redundancy: 2.9 % / Biso Wilson estimate: 93.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0886 / Rsym value: 0.1047 / Net I/av σ(I): 6.75 / Net I/σ(I): 8.6
Reflection shellResolution: 3.5→3.549 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.41 / CC1/2: 0.85 / % possible all: 78

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XDSMay 1, 2016data reduction
Aimless0.5.26data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LFP
Resolution: 3.503→45.35 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 39.21
RfactorNum. reflection% reflection
Rfree0.3013 3739 7.8 %
Rwork0.2423 --
obs0.2469 47926 80.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 448.59 Å2 / Biso mean: 106.81 Å2 / Biso min: 37.24 Å2
Refinement stepCycle: final / Resolution: 3.503→45.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13856 0 0 0 13856
Num. residues----1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00514032
X-RAY DIFFRACTIONf_angle_d0.70719040
X-RAY DIFFRACTIONf_chiral_restr0.0412256
X-RAY DIFFRACTIONf_plane_restr0.0052544
X-RAY DIFFRACTIONf_dihedral_angle_d9.4948720
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8025X-RAY DIFFRACTION8.384TORSIONAL
12B8025X-RAY DIFFRACTION8.384TORSIONAL
13C8025X-RAY DIFFRACTION8.384TORSIONAL
14D8025X-RAY DIFFRACTION8.384TORSIONAL
15E8025X-RAY DIFFRACTION8.384TORSIONAL
16F8025X-RAY DIFFRACTION8.384TORSIONAL
17G8025X-RAY DIFFRACTION8.384TORSIONAL
18H8025X-RAY DIFFRACTION8.384TORSIONAL
19I8025X-RAY DIFFRACTION8.384TORSIONAL
110J8025X-RAY DIFFRACTION8.384TORSIONAL
111K8025X-RAY DIFFRACTION8.384TORSIONAL
112L8025X-RAY DIFFRACTION8.384TORSIONAL
113M8025X-RAY DIFFRACTION8.384TORSIONAL
114N8025X-RAY DIFFRACTION8.384TORSIONAL
115O8025X-RAY DIFFRACTION8.384TORSIONAL
116P8025X-RAY DIFFRACTION8.384TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5029-3.54720.34991220.36651544166676
3.5472-3.59390.43341190.34231580169976
3.5939-3.64310.38841380.34991532167077
3.6431-3.69510.4471390.36431542168177
3.6951-3.75020.38651230.34911477160071
3.7502-3.80880.35121330.29961522165576
3.8088-3.87120.38691370.30991615175279
3.8712-3.93790.3481280.31181618174681
3.9379-4.00950.37911600.29581631179182
4.0095-4.08660.31891360.26191632176880
4.0866-4.16990.35191440.27281697184183
4.1699-4.26050.30271460.24371650179681
4.2605-4.35960.26511320.24041693182583
4.3596-4.46850.29561410.24181572171380
4.4685-4.58920.35211150.2731673178878
4.5892-4.72410.43491310.25321558168980
4.7241-4.87640.29741530.22391650180381
4.8764-5.05050.26141320.21431704183683
5.0505-5.25240.32821470.25451778192586
5.2524-5.49110.28921290.22491709183886
5.4911-5.78010.38811420.27111766190886
5.7801-6.14140.28951370.26071640177782
6.1414-6.61420.32971400.2211783192386
6.6142-7.27740.26651690.20911824199390
7.2774-8.32480.22931570.16691737189487
8.3248-10.46710.19781700.14861646181682
10.4671-45.35460.22671160.1971417153369
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)
16.8143-0.6369-0.82034.21390.02433.0158-0.3326-0.15740.3320.23250.04770.27560.10160.7407-0.00530.56790.0010.03970.7806-0.09630.9145-44.452264.6177177.8825
23.2881-1.3111.84527.58310.17562.0196-0.0138-0.5167-0.23260.5486-0.1652-0.43660.4476-0.17490.00870.5017-0.0865-0.04550.7427-0.09990.9075-14.893323.1635177.9946
34.3556-1.321-1.51714.79641.18241.49050.0617-0.4206-0.53970.68590.277-0.01840.21710.0257-0.00491.0185-0.05520.08870.9837-0.00460.8447-33.740145.663274.1503
43.30040.0823-1.46751.492-1.96923.1211-0.0794-0.4889-0.47570.90830.49640.0906-0.7064-0.46660.00171.1323-0.03970.00531.08080.08880.6404-22.989330.37174.2024
54.4907-1.5219-1.78221.0182-0.06192.679-0.6313-0.4748-0.49840.24980.0554-0.1328-0.5391-0.2669-0.0891.11310.0338-0.14391.09530.18890.8367-5.973922.723874.2181
60.91740.0962-1.49065.26350.25063.5765-0.2236-0.52630.48240.36750.37110.61980.160.97470.01431.01420.05240.02811.2208-0.03640.7837-35.509464.177374.2625
73.0874-1.42561.82366.2401-1.86892.5334-0.1556-0.30870.26860.17940.4733-0.0433-0.03630.1679-0.00560.45720.1144-0.04590.6438-0.05010.7104-16.684941.6817177.9024
85.85121.09081.1513.40432.914.8979-0.1527-0.53750.27580.67060.2453-0.50380.30911.09260.01110.65190.1227-0.02080.4926-0.10660.7261-27.454356.9798177.915
93.6042-2.7709-1.28733.36532.39082.0149-0.0070.14450.4141-0.5249-0.20050.6763-0.0005-0.3138-0.06991.1109-0.099-0.00211.0573-0.10510.78-27.762535.3145129.0787
102.35760.88972.60434.0681-0.10613.1840.42020.7017-0.0592-0.9307-0.21670.58281.16370.431-0.01311.03770.0855-0.04641.16230.09970.6818-35.61552.2232129.05
113.10480.3491-0.71815.95750.76223.25710.04540.2067-0.3712-0.5907-0.0615-0.265-0.39840.4207-0.00830.6099-0.0949-0.0040.7103-0.05710.8256-16.706316.530425.3307
125.4575-1.4637-1.98454.4435-2.81034.41640.00960.47150.1934-0.6764-0.05920.09130.4019-0.21170.01070.5241-0.046-0.12540.57490.07390.8687-37.828162.86825.2721
132.26140.74030.72484.92920.55243.6143-0.11210.0210.2876-0.7682-0.17530.10570.49770.2359-0.0631.2419-0.07210.02061.19620.12160.7174-33.748770.7823129.0119
144.4696-2.0598-1.00192.73211.06233.3908-0.08260.1001-0.6055-0.66030.1102-0.0098-1.11850.1310.00211.1254-0.14070.05991.0626-0.08990.7033-12.592224.4822128.9345
156.4143-2.25350.0374.8836-2.3334.9094-0.08850.3425-0.1056-0.24490.2447-0.5883-0.67990.49760.28580.6180.03480.10590.40240.10760.7281-22.689752.005125.3427
162.70941.1166-3.57314.1558-0.22385.08580.28920.58450.3352-0.41370.0125-1.1579-1.3417-0.35030.04080.61270.11850.11360.535-0.07010.8153-14.839435.095825.2905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 37 through 149)A37 - 149
2X-RAY DIFFRACTION2(chain 'B' and resid 37 through 149)B37 - 149
3X-RAY DIFFRACTION3(chain 'C' and resid 37 through 149)C37 - 149
4X-RAY DIFFRACTION4(chain 'D' and resid 37 through 149)D37 - 149
5X-RAY DIFFRACTION5(chain 'E' and resid 37 through 149)E37 - 149
6X-RAY DIFFRACTION6(chain 'F' and resid 37 through 149)F37 - 149
7X-RAY DIFFRACTION7(chain 'G' and resid 37 through 149)G37 - 149
8X-RAY DIFFRACTION8(chain 'H' and resid 37 through 149)H37 - 149
9X-RAY DIFFRACTION9(chain 'I' and resid 37 through 149)I37 - 149
10X-RAY DIFFRACTION10(chain 'J' and resid 37 through 149)J37 - 149
11X-RAY DIFFRACTION11(chain 'K' and resid 37 through 149)K37 - 149
12X-RAY DIFFRACTION12(chain 'L' and resid 37 through 149)L37 - 149
13X-RAY DIFFRACTION13(chain 'M' and resid 37 through 149)M37 - 149
14X-RAY DIFFRACTION14(chain 'N' and resid 37 through 149)N37 - 149
15X-RAY DIFFRACTION15(chain 'O' and resid 37 through 149)O37 - 149
16X-RAY DIFFRACTION16(chain 'P' and resid 37 through 149)P37 - 149

+
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://pdbjlvh1.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