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- PDB-3m9d: Crystal structure of the prokaryotic ubiquintin-like protein Pup ... -

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Basic information

Entry
Database: PDB / ID: 3m9d
TitleCrystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the hexameric proteasomal ATPase Mpa which includes the amino terminal coiled coil domain and the inter domain
Components
  • Prokaryotic ubiquitin-like protein pup
  • Proteasome-associated ATPase
KeywordsCHAPERONE / alpha helix coil coil / 5 beta-strand barrel / ATP-binding / Nucleotide-binding / Proteasome / S-nitrosylation / Virulence / Isopeptide bond / Ubl conjugation pathway
Function / homology
Function and homology information


ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / retrograde protein transport, ER to cytosol / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process ...ubiquitin-like protein reader activity / symbiont defense to host-produced reactive oxygen species / protein pupylation / proteasome-activating nucleotidase complex / symbiont-mediated perturbation of host defenses / response to nitrosative stress / cell wall / retrograde protein transport, ER to cytosol / ATP-dependent peptidase activity / proteasomal ubiquitin-independent protein catabolic process / proteasome binding / protein unfolding / cellular response to nitric oxide / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / peptidoglycan-based cell wall / modification-dependent protein catabolic process / protein tag activity / molecular adaptor activity / ATP hydrolysis activity / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Prokaryotic ubiquitin-like protein Pup / Pup-like protein / Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) ...Prokaryotic ubiquitin-like protein Pup / Pup-like protein / Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Prokaryotic ubiquitin-like protein Pup / Proteasome-associated ATPase / Prokaryotic ubiquitin-like protein Pup / Proteasome-associated ATPase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.5 Å
AuthorsLi, H. / Wang, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.
Authors: Wang, T. / Darwin, K.H. / Li, H.
History
DepositionMar 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase
G: Prokaryotic ubiquitin-like protein pup
H: Prokaryotic ubiquitin-like protein pup
I: Prokaryotic ubiquitin-like protein pup
J: Proteasome-associated ATPase
K: Proteasome-associated ATPase
L: Proteasome-associated ATPase
M: Proteasome-associated ATPase
N: Proteasome-associated ATPase
O: Proteasome-associated ATPase
P: Prokaryotic ubiquitin-like protein pup
Q: Prokaryotic ubiquitin-like protein pup
R: Prokaryotic ubiquitin-like protein pup


Theoretical massNumber of molelcules
Total (without water)374,09618
Polymers374,09618
Non-polymers00
Water00
1
A: Proteasome-associated ATPase
B: Proteasome-associated ATPase
C: Proteasome-associated ATPase
D: Proteasome-associated ATPase
E: Proteasome-associated ATPase
F: Proteasome-associated ATPase
G: Prokaryotic ubiquitin-like protein pup
H: Prokaryotic ubiquitin-like protein pup
I: Prokaryotic ubiquitin-like protein pup


Theoretical massNumber of molelcules
Total (without water)187,0489
Polymers187,0489
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17900 Å2
ΔGint-114 kcal/mol
Surface area62190 Å2
2
J: Proteasome-associated ATPase
K: Proteasome-associated ATPase
L: Proteasome-associated ATPase
M: Proteasome-associated ATPase
N: Proteasome-associated ATPase
O: Proteasome-associated ATPase
P: Prokaryotic ubiquitin-like protein pup
Q: Prokaryotic ubiquitin-like protein pup
R: Prokaryotic ubiquitin-like protein pup


Theoretical massNumber of molelcules
Total (without water)187,0489
Polymers187,0489
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17830 Å2
ΔGint-113 kcal/mol
Surface area62160 Å2
Unit cell
Length a, b, c (Å)176.580, 176.960, 176.610
Angle α, β, γ (deg.)90.00, 89.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12A
22C
32E
13B
23D
33F
14G
24H
34I
15J
25K
35L
45M
55N
65O
16J
26L
36N
17K
27M
37O
18P
28Q
38R

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROAA98 - 23798 - 237
21PROPROPROPROBB98 - 23798 - 237
31PROPROPROPROCC98 - 23798 - 237
41PROPROPROPRODD98 - 23798 - 237
51PROPROPROPROEE98 - 23798 - 237
61PROPROPROPROFF98 - 23798 - 237
12SERSERPROPROAA52 - 9752 - 97
22SERSERPROPROCC52 - 9752 - 97
32SERSERPROPROEE52 - 9752 - 97
13SERSERPROPROBB52 - 9752 - 97
23SERSERPROPRODD52 - 9752 - 97
33SERSERPROPROFF52 - 9752 - 97
14SERSERALAALAGG21 - 5125 - 55
24SERSERALAALAHH21 - 5125 - 55
34SERSERALAALAII21 - 5125 - 55
15PROPROPROPROJJ98 - 23798 - 237
25PROPROPROPROKK98 - 23798 - 237
35PROPROPROPROLL98 - 23798 - 237
45PROPROPROPROMM98 - 23798 - 237
55PROPROPROPRONN98 - 23798 - 237
65PROPROPROPROOO98 - 23798 - 237
16SERSERPROPROJJ52 - 9752 - 97
26SERSERPROPROLL52 - 9752 - 97
36SERSERPROPRONN52 - 9752 - 97
17SERSERPROPROKK52 - 9752 - 97
27SERSERPROPROMM52 - 9752 - 97
37SERSERPROPROOO52 - 9752 - 97
18SERSERALAALAPP21 - 5125 - 55
28SERSERALAALAQQ21 - 5125 - 55
38SERSERALAALARR21 - 5125 - 55

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
Proteasome-associated ATPase / AAA ATPase forming ring-shaped complexes / ARC / Mycobacterial proteasome ATPase


Mass: 27491.785 Da / Num. of mol.: 12 / Fragment: Coil Coil inter domain (UNP residues: 1-234)
Source method: isolated from a genetically manipulated source
Details: IPTG inducible expression / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: mpa, MT2175 / Plasmid: pET-24b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P63345, UniProt: P9WQN5*PLUS
#2: Protein
Prokaryotic ubiquitin-like protein pup / Bacterial ubiquitin-like modifier


Mass: 7365.744 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: IPTG inducible expression / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: pup, MT2171 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O33246, UniProt: P9WHN5*PLUS

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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: 7.4 Å3/Da / Density % sol: 83.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30%v/v Tacsimate (1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium ...Details: 30%v/v Tacsimate (1.8305 M Malonic acid, 0.25 M Ammonium citrate tribasic, 0.12 M Succinic acid, 0.3 M DL-Malic acid, 0.4 M Sodium acetate trihydrate, 0.5 M Sodium formate, 0.16 M Ammonium tartrate dibasic), pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 4.5→25 Å / Num. obs: 78737 / % possible obs: 99 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.095
Reflection shellResolution: 4.5→4.61 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementResolution: 4.5→25 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.89 / SU B: 117.604 / SU ML: 0.638 / Cross valid method: THROUGHOUT / ESU R: 1.693 / ESU R Free: 0.701 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29208 3428 5 %RANDOM
Rwork0.26389 ---
obs0.26534 65041 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 153.999 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0.49 Å2
2---0.56 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 4.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18636 0 0 0 18636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02218882
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.851.99625614
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5152400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.92524.133900
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.992153330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.44915204
X-RAY DIFFRACTIONr_chiral_restr0.1230.23018
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114304
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A560TIGHT POSITIONAL0.490.05
12B560TIGHT POSITIONAL0.520.05
13C560TIGHT POSITIONAL0.510.05
14D560TIGHT POSITIONAL0.50.05
15E560TIGHT POSITIONAL0.540.05
16F560TIGHT POSITIONAL0.510.05
11A504MEDIUM POSITIONAL0.880.5
12B504MEDIUM POSITIONAL0.920.5
13C504MEDIUM POSITIONAL0.880.5
14D504MEDIUM POSITIONAL0.870.5
15E504MEDIUM POSITIONAL0.870.5
16F504MEDIUM POSITIONAL0.890.5
21A184TIGHT POSITIONAL0.020.05
22C184TIGHT POSITIONAL0.020.05
23E184TIGHT POSITIONAL0.020.05
21A184MEDIUM POSITIONAL0.030.5
22C184MEDIUM POSITIONAL0.020.5
23E184MEDIUM POSITIONAL0.020.5
31B184TIGHT POSITIONAL0.020.05
32D184TIGHT POSITIONAL0.020.05
33F184TIGHT POSITIONAL0.020.05
31B184MEDIUM POSITIONAL0.020.5
32D184MEDIUM POSITIONAL0.020.5
33F184MEDIUM POSITIONAL0.020.5
41G124TIGHT POSITIONAL0.020.05
42H124TIGHT POSITIONAL0.010.05
43I124TIGHT POSITIONAL0.010.05
41G120MEDIUM POSITIONAL0.020.5
42H120MEDIUM POSITIONAL0.020.5
43I120MEDIUM POSITIONAL0.020.5
51J560TIGHT POSITIONAL0.490.05
52K560TIGHT POSITIONAL0.490.05
53L560TIGHT POSITIONAL0.510.05
54M560TIGHT POSITIONAL0.50.05
55N560TIGHT POSITIONAL0.460.05
56O560TIGHT POSITIONAL0.50.05
51J504MEDIUM POSITIONAL0.830.5
52K504MEDIUM POSITIONAL0.910.5
53L504MEDIUM POSITIONAL0.80.5
54M504MEDIUM POSITIONAL0.820.5
55N504MEDIUM POSITIONAL0.80.5
56O504MEDIUM POSITIONAL0.860.5
61J184TIGHT POSITIONAL0.020.05
62L184TIGHT POSITIONAL0.020.05
63N184TIGHT POSITIONAL0.020.05
61J184MEDIUM POSITIONAL0.020.5
62L184MEDIUM POSITIONAL0.020.5
63N184MEDIUM POSITIONAL0.020.5
71K184TIGHT POSITIONAL0.020.05
72M184TIGHT POSITIONAL0.020.05
73O184TIGHT POSITIONAL0.020.05
71K184MEDIUM POSITIONAL0.020.5
72M184MEDIUM POSITIONAL0.020.5
73O184MEDIUM POSITIONAL0.020.5
81P124TIGHT POSITIONAL0.020.05
82Q124TIGHT POSITIONAL0.020.05
83R124TIGHT POSITIONAL0.010.05
81P120MEDIUM POSITIONAL0.020.5
82Q120MEDIUM POSITIONAL0.020.5
83R120MEDIUM POSITIONAL0.020.5
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)
10.20440.6627-0.34715.2602-2.71371.5105-0.07890.12480.0579-0.1570.0045-0.22980.0520.07880.07440.2085-0.15060.09560.22610.01170.1656-5.871-532.94382.0101
20.7798-0.91080.47754.1266-3.8424.1643-0.0557-0.00410.15410.0729-0.038-0.1107-0.18710.13620.09370.156-0.13610.07910.1299-0.11140.2045-2.3488-517.821611.7138
31.78470.35843.02330.20760.58115.54280.0502-0.0199-0.0395-0.0708-0.09780.11240.2849-0.08360.04770.2159-0.08250.03190.1884-0.15270.1816-42.0942-551.835119.4351
44.4337-0.55783.94010.8435-1.07144.18470.06850.236-0.1141-0.0821-0.06220.01920.02890.0965-0.00630.2339-0.0730.10610.1726-0.14460.1318-32.3714-555.42754.3573
55.9619-2.9126-0.44251.60130.2530.16040.0572-0.22710.23190.05130.0196-0.0869-0.1232-0.0802-0.07680.2252-0.00890.14360.1984-0.08930.1591-24.7008-515.494838.2772
64.0037-3.55130.91453.8073-0.48230.7329-0.0234-0.0058-0.06430.14890.03680.2305-0.0033-0.1144-0.01330.1489-0.11390.14530.2177-0.07960.1508-39.795-525.259341.7798
716.90919.8365-27.894228.2442-37.915854.23460.4131-0.2915-0.1375-0.42960.51881.05380.35650.309-0.93180.4681-0.1341-0.04470.49850.06760.6488-20.9986-504.0242-8.1897
833.014-42.5167-21.717456.744429.147717.13190.32030.60580.53960.5174-0.6166-0.47470.37920.27180.29630.45890.00790.10560.61810.02710.4857-53.5144-505.26122.8166
952.6726.384839.503415.874620.12330.6162-0.6066-0.3246-0.50140.43180.3074-0.3564-0.4676-0.30930.29920.60310.0002-0.00810.5014-0.09810.5249-51.9184-536.3655-9.5864
105.84262.95870.90221.56370.45420.23070.08620.1179-0.1819-0.036-0.004-0.03640.106-0.0531-0.08230.20420.0287-0.1510.1649-0.08510.166963.5973-511.445550.0869
114.52523.9466-1.02024.0837-0.57890.6182-0.09090.090.0288-0.18240.08950.21230.0676-0.10930.00130.1470.0972-0.14710.2362-0.08520.161748.5179-501.70846.5464
120.3039-1.04230.53975.3121-2.61831.4427-0.0943-0.118-0.04170.08620.08-0.0966-0.03860.03630.01430.18890.1595-0.07260.2152-0.00730.137382.4833-493.951986.2659
130.69030.8436-0.45843.8628-3.70154.212-0.0399-0.0245-0.1109-0.1013-0.0458-0.04520.24050.13840.08570.15820.1419-0.08250.1353-0.11040.222386.0457-509.069476.5679
141.3889-0.4732-2.50410.25270.96935.21710.02820.07610.08880.0501-0.05490.0805-0.0648-0.1710.02670.15510.1165-0.0020.1869-0.11910.191646.2975-475.123368.8783
154.39070.5894-3.90820.8124-1.12674.24170.0797-0.22560.14940.0556-0.05160.0297-0.0140.1036-0.0280.22160.0878-0.08890.1604-0.14510.132556.0044-471.508983.9423
1629.13238.605918.78253.416726.247815.04770.4049-0.3941-0.486-0.2837-0.5-0.4955-0.39080.38310.0950.4582-0.0009-0.08570.57390.05480.552334.5203-521.337665.4142
1750.8013-25.2678-37.018714.753118.381628.2375-0.50190.09170.7577-0.34830.4666-0.51460.468-0.2220.03530.6097-0.02370.01860.5209-0.11990.491236.0548-490.206997.622
1814.1568-17.137524.089927.1077-35.849551.34260.44810.61630.34350.46440.15370.753-0.53271.0341-0.60180.51740.07340.02580.52330.0470.614566.9849-522.777796.3206
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A52 - 237
2X-RAY DIFFRACTION2B52 - 237
3X-RAY DIFFRACTION3C52 - 237
4X-RAY DIFFRACTION4D52 - 237
5X-RAY DIFFRACTION5E52 - 237
6X-RAY DIFFRACTION6F52 - 237
7X-RAY DIFFRACTION7G21 - 51
8X-RAY DIFFRACTION8H21 - 51
9X-RAY DIFFRACTION9I21 - 51
10X-RAY DIFFRACTION10J52 - 237
11X-RAY DIFFRACTION11K52 - 237
12X-RAY DIFFRACTION12L52 - 237
13X-RAY DIFFRACTION13M52 - 237
14X-RAY DIFFRACTION14N52 - 237
15X-RAY DIFFRACTION15O52 - 237
16X-RAY DIFFRACTION16P21 - 51
17X-RAY DIFFRACTION17Q21 - 51
18X-RAY DIFFRACTION18R21 - 51

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  • 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

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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

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