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- PDB-4u0g: Crystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist -

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Basic information

Entry
Database: PDB / ID: 4u0g
TitleCrystal Structure of M. tuberculosis ClpP1P2 bound to ADEP and agonist
Components
  • (ATP-dependent Clp protease proteolytic subunit ...) x 2
  • ADEP-2B5Me
Keywordshydrolase/antibiotic / hydrolase / peptidase / hydrolase-antibiotic complex
Function / homology
Function and homology information


endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / peptidoglycan-based cell wall / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytosol
Similarity search - Function
ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...ClpP, Ser active site / Endopeptidase Clp serine active site. / ClpP, histidine active site / Endopeptidase Clp histidine active site. / ATP-dependent Clp protease proteolytic subunit / Clp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADEP-2B5Me / N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine / ATP-dependent Clp protease proteolytic subunit 2 / ATP-dependent Clp protease proteolytic subunit 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1978 Å
AuthorsSchmitz, K.R. / Carney, D.W. / Sello, J.K. / Sauer, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-101988 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery.
Authors: Schmitz, K.R. / Carney, D.W. / Sello, J.K. / Sauer, R.T.
History
DepositionJul 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_peptide_omega / pdbx_validate_torsion / refine_hist / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
c: ADEP-2B5Me
i: ADEP-2B5Me
d: ADEP-2B5Me
e: ADEP-2B5Me
f: ADEP-2B5Me
g: ADEP-2B5Me
h: ADEP-2B5Me
j: ADEP-2B5Me
k: ADEP-2B5Me
l: ADEP-2B5Me
m: ADEP-2B5Me
n: ADEP-2B5Me
o: ADEP-2B5Me
p: ADEP-2B5Me
hetero molecules


Theoretical massNumber of molelcules
Total (without water)638,038120
Polymers622,90742
Non-polymers15,13178
Water52229
1
A: ATP-dependent Clp protease proteolytic subunit 2
B: ATP-dependent Clp protease proteolytic subunit 2
C: ATP-dependent Clp protease proteolytic subunit 2
D: ATP-dependent Clp protease proteolytic subunit 2
E: ATP-dependent Clp protease proteolytic subunit 2
F: ATP-dependent Clp protease proteolytic subunit 2
G: ATP-dependent Clp protease proteolytic subunit 2
H: ATP-dependent Clp protease proteolytic subunit 1
I: ATP-dependent Clp protease proteolytic subunit 1
J: ATP-dependent Clp protease proteolytic subunit 1
K: ATP-dependent Clp protease proteolytic subunit 1
L: ATP-dependent Clp protease proteolytic subunit 1
M: ATP-dependent Clp protease proteolytic subunit 1
N: ATP-dependent Clp protease proteolytic subunit 1
c: ADEP-2B5Me
i: ADEP-2B5Me
d: ADEP-2B5Me
e: ADEP-2B5Me
f: ADEP-2B5Me
g: ADEP-2B5Me
h: ADEP-2B5Me
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,01060
Polymers311,45421
Non-polymers7,55739
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: ATP-dependent Clp protease proteolytic subunit 2
P: ATP-dependent Clp protease proteolytic subunit 2
Q: ATP-dependent Clp protease proteolytic subunit 2
R: ATP-dependent Clp protease proteolytic subunit 2
S: ATP-dependent Clp protease proteolytic subunit 2
T: ATP-dependent Clp protease proteolytic subunit 2
U: ATP-dependent Clp protease proteolytic subunit 2
V: ATP-dependent Clp protease proteolytic subunit 1
W: ATP-dependent Clp protease proteolytic subunit 1
X: ATP-dependent Clp protease proteolytic subunit 1
Y: ATP-dependent Clp protease proteolytic subunit 1
Z: ATP-dependent Clp protease proteolytic subunit 1
a: ATP-dependent Clp protease proteolytic subunit 1
b: ATP-dependent Clp protease proteolytic subunit 1
j: ADEP-2B5Me
k: ADEP-2B5Me
l: ADEP-2B5Me
m: ADEP-2B5Me
n: ADEP-2B5Me
o: ADEP-2B5Me
p: ADEP-2B5Me
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,02860
Polymers311,45421
Non-polymers7,57539
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.748, 187.673, 294.029
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain O
91chain P
101chain Q
111chain R
121chain S
131chain T
141chain U
12chain H
22chain I
32chain J
42chain K
52chain L
62chain M
72chain N
82chain V
92chain W
102chain X
112chain Y
122chain Z
132chain a
142chain b

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEALAALAchain AAA15 - 2113 - 199
21TYRTYRSERSERchain BBB14 - 2102 - 198
31ILEILESERSERchain CCC15 - 2103 - 198
41ILEILELEULEUchain DDD15 - 2093 - 197
51ILEILEALAALAchain EEE15 - 2113 - 199
61ILEILESERSERchain FFF15 - 2103 - 198
71ILEILESERSERchain GGG15 - 2103 - 198
81ILEILESERSERchain OOO15 - 2103 - 198
91ILEILELYSLYSchain PPP15 - 2083 - 196
101ILEILELEULEUchain QQQ15 - 2093 - 197
111ILEILESERSERchain RRR15 - 2103 - 198
121ILEILESERSERchain SSS15 - 2103 - 198
131ILEILESERSERchain TTT15 - 2103 - 198
141ILEILESERSERchain UUU15 - 2103 - 198
12THRTHRILEILEchain HHH17 - 19011 - 184
22SERSERILEILEchain III19 - 19013 - 184
32ASPASPARGARGchain JJJ18 - 19212 - 186
42SERSERILEILEchain KKK19 - 19013 - 184
52ASPASPTHRTHRchain LLL18 - 19112 - 185
62SERSERTHRTHRchain MMM19 - 19113 - 185
72ASPASPTHRTHRchain NNN18 - 19112 - 185
82ASPASPARGARGchain VVV18 - 19212 - 186
92ASPASPARGARGchain WWW18 - 19212 - 186
102ASPASPARGARGchain XXX18 - 19212 - 186
112ASPASPTHRTHRchain YYY18 - 19112 - 185
122THRTHRTHRTHRchain ZZZ17 - 19111 - 185
132ASPASPTHRTHRchain aaAA18 - 19112 - 185
142THRTHRTHRTHRchain bbBA17 - 19111 - 185

NCS ensembles :
ID
1
2

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Components

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ATP-dependent Clp protease proteolytic subunit ... , 2 types, 28 molecules ABCDEFGOPQRSTUHIJKLMNVWXYZab

#1: Protein
ATP-dependent Clp protease proteolytic subunit 2 / Endopeptidase Clp 2


Mass: 22235.328 Da / Num. of mol.: 14 / Fragment: mature enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: clpP2, Rv2460c, MTV008.16c / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC3, endopeptidase Clp
#2: Protein
ATP-dependent Clp protease proteolytic subunit 1 / Endopeptidase Clp 1


Mass: 21441.100 Da / Num. of mol.: 14 / Fragment: mature enzyme
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: clpP1, clpP, Rv2461c, MTV008.17c / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPC5, endopeptidase Clp

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Protein/peptide , 1 types, 14 molecules cidefghjklmnop

#3: Protein/peptide
ADEP-2B5Me


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 816.931 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: ADEP-2B5Me

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Non-polymers , 4 types, 107 molecules

#4: Chemical...
ChemComp-ZIL / N-[(benzyloxy)carbonyl]-L-isoleucyl-L-leucine / Z-Ile-Leu


Mass: 378.463 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C20H30N2O5
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 3.49 Å3/Da / Density % sol: 64.77 % / Description: 100x100x200 micron rectangular
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 mixture of reservoir (1.5 M (NH4)2SO4, 0.1 M MES) and protein solution (2.5 mg/mL ClpP1, 2.5 mg/mL ClpP2, 0.2 mM ADEP-2B5Me, 0.5 mM Z-Ile-Leu, 10 mM HEPES, 50 mM NaCl, 0.5 mM TCEP, 15% DMSO)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1978→50 Å / Num. obs: 141536 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 49.62 Å2 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Rrim(I) all: 0.165 / Χ2: 1.01 / Net I/av σ(I): 13.5 / Net I/σ(I): 4.4 / Num. measured all: 965776
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1978-3.267.10.5569240.8780.2210.5930.992100
3.26-3.317.10.46170170.9110.1860.4980.995100
3.31-3.387.10.41570350.9260.1670.4480.998100
3.38-3.4570.37169770.9420.150.41.004100
3.45-3.5270.33670320.950.1370.3631.001100
3.52-3.670.28370210.9620.1150.3061.007100
3.6-3.696.90.2470260.9730.0980.261100
3.69-3.796.80.20870120.9790.0860.2251.007100
3.79-3.916.70.18770220.9810.0780.2031.019100
3.91-4.036.40.15470270.9860.0660.1671.0199.9
4.03-4.1860.13370540.9880.0590.1451.023100
4.18-4.347.10.12470400.9920.050.1341.018100
4.34-4.547.20.10770670.9940.0430.1161.011100
4.54-4.787.10.10470810.9940.0420.1131.021100
4.78-5.0870.10970920.9930.0440.1181.016100
5.08-5.476.80.11870790.9920.0490.1281.005100
5.47-6.026.20.11971270.990.0520.131.025100
6.02-6.896.70.1171620.9930.0460.1191.028100
6.89-8.676.90.07472510.9970.030.080.982100
8.67-506.40.0574900.9980.0210.0541.04799.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.2 Å49.91 Å
Translation3.2 Å49.91 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1760)refinement
HKL-2000data scaling
HKL-20002.5.5data reduction
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1978→49.913 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 7075 5.02 %random selection
Rwork0.1903 133824 --
obs0.1919 140899 99.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 221.26 Å2 / Biso mean: 36.0093 Å2 / Biso min: 1.83 Å2
Refinement stepCycle: final / Resolution: 3.1978→49.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40064 0 3503 29 43596
Biso mean--55.11 17.83 -
Num. residues----5180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441682
X-RAY DIFFRACTIONf_angle_d0.70256424
X-RAY DIFFRACTIONf_chiral_restr0.036521
X-RAY DIFFRACTIONf_plane_restr0.0047624
X-RAY DIFFRACTIONf_dihedral_angle_d11.50315895
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16135X-RAY DIFFRACTION2.382TORSIONAL
12B16135X-RAY DIFFRACTION2.382TORSIONAL
13C16135X-RAY DIFFRACTION2.382TORSIONAL
14D16135X-RAY DIFFRACTION2.382TORSIONAL
15E16135X-RAY DIFFRACTION2.382TORSIONAL
16F16135X-RAY DIFFRACTION2.382TORSIONAL
17G16135X-RAY DIFFRACTION2.382TORSIONAL
18O16135X-RAY DIFFRACTION2.382TORSIONAL
19P16135X-RAY DIFFRACTION2.382TORSIONAL
110Q16135X-RAY DIFFRACTION2.382TORSIONAL
111R16135X-RAY DIFFRACTION2.382TORSIONAL
112S16135X-RAY DIFFRACTION2.382TORSIONAL
113T16135X-RAY DIFFRACTION2.382TORSIONAL
114U16135X-RAY DIFFRACTION2.382TORSIONAL
21H13003X-RAY DIFFRACTION2.382TORSIONAL
22I13003X-RAY DIFFRACTION2.382TORSIONAL
23J13003X-RAY DIFFRACTION2.382TORSIONAL
24K13003X-RAY DIFFRACTION2.382TORSIONAL
25L13003X-RAY DIFFRACTION2.382TORSIONAL
26M13003X-RAY DIFFRACTION2.382TORSIONAL
27N13003X-RAY DIFFRACTION2.382TORSIONAL
28V13003X-RAY DIFFRACTION2.382TORSIONAL
29W13003X-RAY DIFFRACTION2.382TORSIONAL
210X13003X-RAY DIFFRACTION2.382TORSIONAL
211Y13003X-RAY DIFFRACTION2.382TORSIONAL
212Z13003X-RAY DIFFRACTION2.382TORSIONAL
213a13003X-RAY DIFFRACTION2.382TORSIONAL
214b13003X-RAY DIFFRACTION2.382TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1978-3.23420.35362370.3014295453297
3.2342-3.27220.3442110.27744348455999
3.2722-3.31210.31182290.27814396462599
3.3121-3.3540.29362170.26624471468899
3.354-3.39820.30281990.24554357455699
3.3982-3.44470.26192370.24054424466199
3.4447-3.49390.27672470.24224402464999
3.4939-3.5460.24712380.226544014639100
3.546-3.60140.24572440.2254447469199
3.6014-3.66050.25042440.219143864630100
3.6605-3.72360.23942430.212344374680100
3.7236-3.79120.23442380.196944434681100
3.7912-3.86410.2642490.195144144663100
3.8641-3.9430.22372370.182244464683100
3.943-4.02870.20222360.173344294665100
4.0287-4.12240.19462650.168844094674100
4.1224-4.22540.18292190.157844714690100
4.2254-4.33960.20752430.160544664709100
4.3396-4.46720.1742260.147644824708100
4.4672-4.61130.15792260.138944804706100
4.6113-4.7760.18042230.141445064729100
4.776-4.9670.1872330.159745034736100
4.967-5.19290.2192230.172644854708100
5.1929-5.46630.20512390.177544814720100
5.4663-5.80830.23422530.194444944747100
5.8083-6.2560.21182430.194345314774100
6.256-6.88410.22622250.188745184743100
6.8841-7.87690.19792620.16745564818100
7.8769-9.91130.17322350.158846164851100
9.9113-49.91940.20712540.1944730498499

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