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- PDB-2fhg: Crystal Structure of Mycobacterial Tuberculosis Proteasome -

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Basic information

Entry
Database: PDB / ID: 2fhg
TitleCrystal Structure of Mycobacterial Tuberculosis Proteasome
Components
  • 20S proteasome, alpha and beta subunitsProteasome
  • proteasome, beta subunit
KeywordsHYDROLASE / multi-protein / multi-subunit complex / protease / proteasome
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta ...Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / Proteasome subunit beta / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsHu, G. / Lin, G. / Wang, M. / Dick, L. / Xu, R.M. / Nathan, C. / Li, H.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate.
Authors: Hu, G. / Lin, G. / Wang, M. / Dick, L. / Xu, R.M. / Nathan, C. / Li, H.
History
DepositionDec 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 20S proteasome, alpha and beta subunits
H: proteasome, beta subunit
B: 20S proteasome, alpha and beta subunits
C: proteasome, beta subunit
D: 20S proteasome, alpha and beta subunits
E: proteasome, beta subunit
F: 20S proteasome, alpha and beta subunits
G: proteasome, beta subunit
I: 20S proteasome, alpha and beta subunits
J: proteasome, beta subunit
K: 20S proteasome, alpha and beta subunits
L: proteasome, beta subunit
M: 20S proteasome, alpha and beta subunits
N: proteasome, beta subunit
O: 20S proteasome, alpha and beta subunits
P: proteasome, beta subunit
Q: 20S proteasome, alpha and beta subunits
R: proteasome, beta subunit
S: 20S proteasome, alpha and beta subunits
T: proteasome, beta subunit
U: 20S proteasome, alpha and beta subunits
V: proteasome, beta subunit
W: 20S proteasome, alpha and beta subunits
X: proteasome, beta subunit
Y: 20S proteasome, alpha and beta subunits
Z: proteasome, beta subunit
1: 20S proteasome, alpha and beta subunits
2: proteasome, beta subunit


Theoretical massNumber of molelcules
Total (without water)733,41128
Polymers733,41128
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area79750 Å2
ΔGint-69 kcal/mol
Surface area224060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.327, 113.802, 200.133
Angle α, β, γ (deg.)90.00, 113.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41F
51I
61K
71M
81O
91Q
101S
111U
121W
131Y
1411
12H
22C
32E
42G
52J
62L
72N
82P
92R
102T
112V
122X
132Z
1422

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLNGLNAA8 - 23710 - 239
21SERSERGLNGLNBC8 - 23710 - 239
31SERSERGLNGLNDE8 - 23710 - 239
41SERSERGLNGLNFG8 - 23710 - 239
51SERSERGLNGLNII8 - 23710 - 239
61SERSERGLNGLNKK8 - 23710 - 239
71SERSERGLNGLNMM8 - 23710 - 239
81SERSERGLNGLNOO8 - 23710 - 239
91SERSERGLNGLNQQ8 - 23710 - 239
101SERSERGLNGLNSS8 - 23710 - 239
111SERSERGLNGLNUU8 - 23710 - 239
121SERSERGLNGLNWW8 - 23710 - 239
131SERSERGLNGLNYY8 - 23710 - 239
141SERSERGLNGLN1AA8 - 23710 - 239
12THRTHRSERSERHB301 - 5221 - 222
22THRTHRSERSERCD301 - 5221 - 222
32THRTHRSERSEREF301 - 5221 - 222
42THRTHRSERSERGH301 - 5221 - 222
52THRTHRSERSERJJ301 - 5221 - 222
62THRTHRSERSERLL301 - 5221 - 222
72THRTHRSERSERNN301 - 5221 - 222
82THRTHRSERSERPP301 - 5221 - 222
92THRTHRSERSERRR301 - 5221 - 222
102THRTHRSERSERTT301 - 5221 - 222
112THRTHRSERSERVV301 - 5221 - 222
122THRTHRSERSERXX301 - 5221 - 222
132THRTHRSERSERZZ301 - 5221 - 222
142THRTHRSERSER2BA301 - 5221 - 222

NCS ensembles :
ID
1
2

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Components

#1: Protein
20S proteasome, alpha and beta subunits / Proteasome


Mass: 27112.221 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PrcA / Plasmid: prcA-prcB-His6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 76783992, UniProt: P9WHU1*PLUS
#2: Protein
proteasome, beta subunit /


Mass: 25274.264 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: PrcB / Plasmid: pACYCDuet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 13881852, UniProt: P9WHT9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 8% PEG 6000, 50 mM sodium citrate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 1, 2005
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 86867 / Num. obs: 91407 / % possible obs: 80.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.9
Reflection shellResolution: 3.2→3.31 Å / % possible all: 0.544

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q5Q
Resolution: 3.23→50 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.892 / SU B: 83.377 / SU ML: 0.578 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.692 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26611 4537 5 %RANDOM
Rwork0.24337 ---
all0.244 91407 --
obs0.24448 86867 79.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.863 Å2
Baniso -1Baniso -2Baniso -3
1-2.58 Å20 Å20.4 Å2
2--2.13 Å20 Å2
3----4.38 Å2
Refinement stepCycle: LAST / Resolution: 3.23→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46620 0 0 226 46846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02247334
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.96964092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55556146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.50623.0462114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57157672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.52715476
X-RAY DIFFRACTIONr_chiral_restr0.070.27294
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0236218
X-RAY DIFFRACTIONr_nbd_refined0.2530.224120
X-RAY DIFFRACTIONr_nbtor_refined0.3080.233337
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.21882
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5990.2256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5560.215
X-RAY DIFFRACTIONr_mcbond_it01.531138
X-RAY DIFFRACTIONr_mcangle_it0248510
X-RAY DIFFRACTIONr_scbond_it0317897
X-RAY DIFFRACTIONr_scangle_it04.515582
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1693tight positional0.040.05
12H1693tight positional0.030.05
13C1693tight positional0.030.05
14E1693tight positional0.030.05
15I1693tight positional0.030.05
16K1693tight positional0.020.05
17M1693tight positional0.030.05
18O1693tight positional0.020.05
19Q1693tight positional0.020.05
110S1693tight positional0.020.05
111U1693tight positional0.020.05
112W1693tight positional0.030.05
113Y1693tight positional0.030.05
11411693tight positional0.020.05
21G1639tight positional0.040.05
22B1639tight positional0.030.05
23D1639tight positional0.040.05
24F1639tight positional0.030.05
25J1639tight positional0.030.05
26L1639tight positional0.040.05
27N1639tight positional0.030.05
28P1639tight positional0.030.05
29R1639tight positional0.030.05
210T1639tight positional0.030.05
211V1639tight positional0.030.05
212X1639tight positional0.030.05
213Z1639tight positional0.030.05
21421639tight positional0.030.05
11A1693tight thermal00.5
12H1693tight thermal00.5
13C1693tight thermal00.5
14E1693tight thermal00.5
15I1693tight thermal00.5
16K1693tight thermal00.5
17M1693tight thermal00.5
18O1693tight thermal00.5
19Q1693tight thermal00.5
110S1693tight thermal00.5
111U1693tight thermal00.5
112W1693tight thermal00.5
113Y1693tight thermal00.5
11411693tight thermal00.5
21G1639tight thermal00.5
22B1639tight thermal00.5
23D1639tight thermal00.5
24F1639tight thermal00.5
25J1639tight thermal00.5
26L1639tight thermal00.5
27N1639tight thermal00.5
28P1639tight thermal00.5
29R1639tight thermal00.5
210T1639tight thermal00.5
211V1639tight thermal00.5
212X1639tight thermal00.5
213Z1639tight thermal00.5
21421639tight thermal00.5
LS refinement shellResolution: 3.227→3.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 206 -
Rwork0.41 3727 -
obs--46.79 %
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)
13.73220.4390.46523.27320.78974.55580.0707-0.70410.10390.4999-0.22460.2696-0.3328-0.04790.1539-0.5923-0.10930.1091-0.1483-0.224-0.328445.05975.342316.1705
23.62250.0140.03213.6868-0.88333.78590.1224-0.9998-0.39640.9735-0.18430.27470.2567-0.18120.062-0.1459-0.19310.2078-0.0594-0.0817-0.186139.8478-26.038616.6348
31.7460.296-0.26692.9102-0.88533.4479-0.00660.3311-0.2720.00060.0299-0.74610.37040.9879-0.0232-0.21480.32250.25040.68360.0463-0.2458128.0714-34.139-55.6201
42.77960.00790.09413.7137-0.6774.4386-0.02020.96830.4698-1.2406-0.093-0.2144-0.84560.61570.11310.6663-0.2713-0.0251-0.13490.0792-0.422592.41915.2628-103.902
53.0028-0.1290.68574.3525-0.07883.36120.0308-0.752-0.56870.41870.07220.80550.6512-0.8523-0.103-0.3809-0.28360.22060.23660.00370.212321.0369-43.4431-2.5208
62.59680.2014-0.38032.63650.13523.03330.08280.00870.1762-0.1633-0.3918-0.9792-0.39641.38990.309-0.0114-0.22240.07881.21880.4038-0.0941129.1161-2.1211-59.5704
72.8791-0.301-0.08153.960.35943.05270.05290.00020.33-0.26240.0453-0.5064-0.40940.9275-0.0983-0.0093-0.31740.27290.2461-0.0069-0.3512112.727114.9098-81.0429
82.73070.9892-0.6563.457-0.83234.09290.2795-0.41940.76450.5716-0.07660.7733-1.6697-0.5771-0.20290.45110.34310.1402-0.0453-0.30930.153232.322627.874-3.3059
94.2366-0.88540.13175.0296-0.67931.5122-0.34450.0195-1.0486-0.53530.0554-0.63160.77880.80730.28920.35490.53820.37630.1620.0393-0.1213110.1205-56.4412-70.8886
103.8401-0.3313-0.07894.21980.70154.34890.016-0.3722-0.4740.1983-0.31171.04370.5904-1.11350.2956-0.4559-0.1511-0.01270.2968-0.20680.41111.7248-33.7308-26.2666
113.07860.1754-0.82052.88880.73663.76570.0681-0.00040.45670.0808-0.10790.7669-0.974-1.03230.0399-0.01420.4821-0.12810.1339-0.24330.39811.003923.4022-27.2207
125.411-0.266-0.69782.66640.04415.414-0.3040.9739-0.5893-0.9271-0.0119-0.05560.50220.30510.31590.3207-0.0958-0.0118-0.363-0.1154-0.347982.3348-24.2829-110.2317
134.3898-0.92630.89013.81550.5963.44030.11121.5147-0.9955-0.8594-0.13920.04320.87010.45630.0280.70840.42550.12920.0373-0.1797-0.217189.6207-52.4231-95.2727
142.4398-0.38220.1113.0050.20833.224-0.09440.09630.1166-0.0890.0380.917-0.078-1.07080.0565-0.290.216-0.27650.4088-0.26650.6908-2.6913-3.7392-37.5613
155.441.2032-3.2682.5935-1.10563.47830.1302-0.5450.1961-0.17880.0080.31150.04790.565-0.1383-0.6366-0.01660.0469-0.1357-0.2101-0.580676.7111-6.5486-5.1834
166.76110.9104-1.68441.39080.42831.3871-0.1534-0.8352-0.1603-0.0997-0.0990.31680.38610.35990.2524-0.38190.15360.1462-0.22950.1229-0.505566.6877-38.5852-10.3619
175.08081.9628-1.9373.498-1.98494.9546-0.1643-0.07820.1268-0.36830.06770.00880.18170.82740.0965-0.63020.30230.10470.0697-0.0188-0.6172102.3903-22.5107-26.7168
181.8792-2.2863-2.37053.52482.96384.2670.35430.3528-0.1418-1.0745-0.62860.3644-1.1858-0.54910.27430.2140.318-0.4687-0.4661-0.1044-0.261358.29355.5109-83.6473
196.4167-1.1275-1.90892.23650.26361.7558-0.1359-0.2173-0.2493-0.2378-0.15350.38110.4474-0.22860.2894-0.119-0.03980.0678-0.5637-0.0487-0.274444.5641-50.9943-33.3475
202.1312-0.2248-1.89480.8255-0.06854.68980.1152-0.05620.2254-0.3041-0.1177-0.0523-0.60470.97130.0025-0.2777-0.35040.04060.0885-0.0382-0.447898.880710.1623-36.9444
212.2626-0.1175-2.35282.22322.12996.010.10870.06280.1799-0.3072-0.02350.0991-0.69860.2738-0.08520.0084-0.1292-0.067-0.62890.0312-0.374979.203522.3067-62.4939
222.59751.2406-2.96012.6893-1.32514.74290.0888-0.48440.1219-0.0383-0.10140.2511-0.67740.1130.0126-0.1118-0.1141-0.09-0.4181-0.1346-0.370867.026421.785-22.0074
236.30130.629-1.73912.0125-0.09871.7905-0.20110.0234-0.1102-0.2347-0.0716-0.06050.49670.61370.2727-0.14860.38340.1843-0.33920.0907-0.420686.716-50.4391-39.1922
243.0592-1.8188-1.6292.52060.38612.172-0.1538-0.00890.1563-0.1212-0.03230.29040.2796-0.73810.1861-0.215-0.1297-0.2069-0.2544-0.162-0.091926.6982-34.2797-57.6713
252.2349-0.4318-2.05661.58250.70476.60920.43630.08810.1698-0.1358-0.21910.3933-0.6043-0.4081-0.21720.03930.2016-0.2768-0.6107-0.088-0.170944.971524.3257-48.1913
265.0175-1.7315-1.07792.13991.20912.1125-0.32440.27970.2101-0.56270.0880.12850.2022-0.21990.2363-0.0038-0.2285-0.287-0.56880.0453-0.326951.4553-27.9636-84.8525
277.6145-0.26-1.3291.54130.01721.2781-0.24840.0934-0.1527-0.3241-0.0869-0.03480.5867-0.05070.33540.24160.0830.0474-0.6681-0.1101-0.434863.8944-53.1195-64.8715
282.2768-0.1377-2.23150.43991.04314.09790.17750.262-0.0375-0.2885-0.13890.7858-0.4498-0.7281-0.0387-0.02850.3671-0.649-0.0019-0.28090.318427.1847-0.3028-64.0798
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 23710 - 239
2X-RAY DIFFRACTION2BC8 - 23710 - 239
3X-RAY DIFFRACTION3DE8 - 23710 - 239
4X-RAY DIFFRACTION4FG8 - 23710 - 239
5X-RAY DIFFRACTION5II8 - 23710 - 239
6X-RAY DIFFRACTION6KK8 - 23710 - 239
7X-RAY DIFFRACTION7MM8 - 23710 - 239
8X-RAY DIFFRACTION8OO8 - 23710 - 239
9X-RAY DIFFRACTION9QQ8 - 23710 - 239
10X-RAY DIFFRACTION10SS8 - 23710 - 239
11X-RAY DIFFRACTION11UU8 - 23710 - 239
12X-RAY DIFFRACTION12WW8 - 23710 - 239
13X-RAY DIFFRACTION13YY8 - 23710 - 239
14X-RAY DIFFRACTION141AA8 - 23710 - 239
15X-RAY DIFFRACTION15HB301 - 5221 - 222
16X-RAY DIFFRACTION16CD301 - 5221 - 222
17X-RAY DIFFRACTION17EF301 - 5221 - 222
18X-RAY DIFFRACTION18GH301 - 5221 - 222
19X-RAY DIFFRACTION19JJ301 - 5221 - 222
20X-RAY DIFFRACTION20LL301 - 5221 - 222
21X-RAY DIFFRACTION21NN301 - 5221 - 222
22X-RAY DIFFRACTION22PP301 - 5221 - 222
23X-RAY DIFFRACTION23RR301 - 5221 - 222
24X-RAY DIFFRACTION24TT301 - 5221 - 222
25X-RAY DIFFRACTION25VV301 - 5221 - 222
26X-RAY DIFFRACTION26XX301 - 5221 - 222
27X-RAY DIFFRACTION27ZZ301 - 5221 - 222
28X-RAY DIFFRACTION282BA301 - 5221 - 222

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