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- PDB-5yk3: human Ragulator complex -

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Basic information

Entry
Database: PDB / ID: 5yk3
Titlehuman Ragulator complex
Components(Ragulator complex protein ...) x 11
KeywordsSIGNALING PROTEIN / cellular signal transduction
Function / homology
Function and homology information


regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / TORC1 signaling ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / protein localization to lysosome / TORC1 signaling / endosome organization / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / protein localization to membrane / kinase activator activity / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / lysosome organization / RHOJ GTPase cycle / RHOQ GTPase cycle / mTORC1-mediated signalling / cellular response to nutrient levels / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / specific granule membrane / protein-membrane adaptor activity / positive regulation of TORC1 signaling / RAC1 GTPase cycle / viral genome replication / guanyl-nucleotide exchange factor activity / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / cholesterol homeostasis / regulation of cell growth / TP53 Regulates Metabolic Genes / cellular response to amino acid stimulus / response to virus / MAP2K and MAPK activation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein localization / positive regulation of protein localization to nucleus / late endosome / GTPase binding / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / molecular adaptor activity / lysosome / endosome membrane / membrane raft / lysosomal membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR2-like ...LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR2-like / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsWu, G. / Mu, Z.
CitationJournal: Cell Discov / Year: 2017
Title: Structural insight into the Ragulator complex which anchors mTORC1 to the lysosomal membrane
Authors: Mu, Z. / Wang, L. / Deng, W. / Wang, J. / Wu, G.
History
DepositionOct 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
m: Ragulator complex protein LAMTOR3
l: Ragulator complex protein LAMTOR2
o: Ragulator complex protein LAMTOR5
n: Ragulator complex protein LAMTOR4
k: Ragulator complex protein LAMTOR1
C: Ragulator complex protein LAMTOR3
B: Ragulator complex protein LAMTOR2
E: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4
A: Ragulator complex protein LAMTOR1
H: Ragulator complex protein LAMTOR3
G: Ragulator complex protein LAMTOR2
J: Ragulator complex protein LAMTOR5
I: Ragulator complex protein LAMTOR4
F: Ragulator complex protein LAMTOR1


Theoretical massNumber of molelcules
Total (without water)169,17315
Polymers169,17315
Non-polymers00
Water00
1
m: Ragulator complex protein LAMTOR3
l: Ragulator complex protein LAMTOR2
o: Ragulator complex protein LAMTOR5
n: Ragulator complex protein LAMTOR4
k: Ragulator complex protein LAMTOR1


Theoretical massNumber of molelcules
Total (without water)55,7045
Polymers55,7045
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ragulator complex protein LAMTOR3
B: Ragulator complex protein LAMTOR2
E: Ragulator complex protein LAMTOR5
D: Ragulator complex protein LAMTOR4
A: Ragulator complex protein LAMTOR1


Theoretical massNumber of molelcules
Total (without water)56,3645
Polymers56,3645
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: Ragulator complex protein LAMTOR3
G: Ragulator complex protein LAMTOR2
J: Ragulator complex protein LAMTOR5
I: Ragulator complex protein LAMTOR4
F: Ragulator complex protein LAMTOR1


Theoretical massNumber of molelcules
Total (without water)57,1055
Polymers57,1055
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.644, 126.644, 614.005
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
31k
12B
22G
32l
13C
23H
33m
14D
24I
34n
15E
25J
35o

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A78 - 161
2114F78 - 161
3114k78 - 161
1124B1 - 125
2124G1 - 125
3124l1 - 125
1134C1 - 124
2134H1 - 124
3134m1 - 124
1144D1 - 99
2144I1 - 99
3144n1 - 99
1154E1 - 91
2154J1 - 91
3154o1 - 91

NCS ensembles :
ID
1
2
3
4
5

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.479927, 0.862961, -0.158013), (-0.876527, -0.479256, 0.044866), (-0.037011, 0.160035, 0.986417)-94.813492, 16.3323, -6.80229
3given(-0.49393, -0.868665, -0.038144), (0.860714, -0.494689, 0.12023), (-0.123309, 0.026555, 0.992013)-32.50119, 92.749702, -5.8089
4given(1), (1), (1)
5given(-0.48015, 0.864117, -0.150857), (-0.877124, -0.475022, 0.070769), (-0.010508, 0.1663, 0.986019)-95.147346, 15.19015, -5.59752
6given(-0.516729, -0.855945, -0.018692), (0.841765, -0.511912, 0.1714), (-0.156278, 0.072834, 0.985024)-34.35947, 90.238113, -8.19798
7given(1), (1), (1)
8given(-0.486942, 0.853461, -0.185722), (-0.871401, -0.4892, 0.036661), (-0.059566, 0.17969, 0.981918)-94.060638, 17.09296, -9.25313
9given(-0.487276, -0.871353, -0.057499), (0.859787, -0.490241, 0.142933), (-0.152733, 0.020211, 0.988061)-31.249241, 91.827919, -7.38036
10given(1), (1), (1)
11given(-0.426219, 0.895635, -0.127185), (-0.899545, -0.404746, 0.164318), (0.095691, 0.184443, 0.978174)-95.642632, 2.61388, 1.26721
12given(-0.531735, -0.842858, -0.082749), (0.832534, -0.538134, 0.131523), (-0.155385, 0.001044, 0.987853)-33.270401, 89.243393, -7.1264
13given(1), (1), (1)
14given(-0.427271, 0.89248, -0.144633), (-0.904117, -0.422383, 0.064542), (-0.003488, 0.158342, 0.987378)-94.979637, 8.94703, -4.4711
15given(-0.54473, -0.83646, -0.060036), (0.830508, -0.548011, 0.099706), (-0.1163, 0.004453, 0.993204)-35.48637, 91.374367, -4.99643

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Components

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Ragulator complex protein ... , 11 types, 15 molecules mHlGonkCBEJDAFI

#1: Protein Ragulator complex protein LAMTOR3 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / Mitogen-activated protein kinase kinase 1-interacting protein 1 / Mitogen-activated protein kinase scaffold protein 1


Mass: 13637.678 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHA4
#2: Protein Ragulator complex protein LAMTOR2 / Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late ...Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 2 / Mitogen-activated protein-binding protein-interacting protein / MAPBP-interacting protein / Roadblock domain-containing protein 3


Mass: 13517.450 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2Q5
#3: Protein Ragulator complex protein LAMTOR5 / Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal ...Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5


Mass: 9535.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504
#4: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 9495.797 Da / Num. of mol.: 1 / Mutation: Q7A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1
#5: Protein Ragulator complex protein LAMTOR1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / Protein associated with DRMs and endosomes / p27Kip1-releasing factor from RhoA / p27RF-Rho


Mass: 9516.825 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IAA8
#6: Protein Ragulator complex protein LAMTOR3 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 3 / MEK-binding partner 1 / Mp1 / Mitogen-activated protein kinase kinase 1-interacting protein 1 / Mitogen-activated protein kinase scaffold protein 1


Mass: 13490.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR3, MAP2K1IP1, MAPKSP1, PRO2783 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHA4
#7: Protein Ragulator complex protein LAMTOR2 / Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late ...Endosomal adaptor protein p14 / Late endosomal/lysosomal Mp1-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 2 / Mitogen-activated protein-binding protein-interacting protein / MAPBP-interacting protein / Roadblock domain-containing protein 3


Mass: 13285.083 Da / Num. of mol.: 1 / Mutation: V122A, S125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR2, MAPBPIP, ROBLD3, HSPC003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2Q5
#8: Protein Ragulator complex protein LAMTOR5 / Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal ...Hepatitis B virus X-interacting protein / HBX-interacting protein / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5


Mass: 9622.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR5, HBXIP, XIP / Production host: Escherichia coli (E. coli) / References: UniProt: O43504
#9: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 10391.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1
#10: Protein Ragulator complex protein LAMTOR1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / ...Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1 / Lipid raft adaptor protein p18 / Protein associated with DRMs and endosomes / p27Kip1-releasing factor from RhoA / p27RF-Rho


Mass: 9573.876 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR1, C11orf59, PDRO, PP7157 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IAA8
#11: Protein Ragulator complex protein LAMTOR4 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4


Mass: 10753.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMTOR4, C7orf59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0VGL1

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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: 4.2 Å3/Da / Density % sol: 70.72 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop
Details: 0.1M CHES, pH 9.5, 0.56 M sodium citrate tribasic, and 1.4 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.01→50 Å / Num. obs: 59234 / % possible obs: 99.9 % / Redundancy: 18 % / Net I/σ(I): 26

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.01→50 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.865 / SU B: 42.11 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.447 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28541 2569 5 %RANDOM
Rwork0.22504 ---
obs0.22809 48813 86.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.331 Å2
Baniso -1Baniso -2Baniso -3
1--5.36 Å2-2.68 Å20 Å2
2---5.36 Å20 Å2
3---8.05 Å2
Refinement stepCycle: 1 / Resolution: 3.01→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11608 0 0 0 11608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01911782
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.97116003
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84451534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45824.841471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.079151968
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2261561
X-RAY DIFFRACTIONr_chiral_restr0.0770.21926
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218720
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.371311781
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded45.506511608
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A613MEDIUM POSITIONAL0.860.5
12F613MEDIUM POSITIONAL1.150.5
13k613MEDIUM POSITIONAL1.050.5
11A613MEDIUM THERMAL21.382
12F613MEDIUM THERMAL18.922
13k613MEDIUM THERMAL28.792
21B853MEDIUM POSITIONAL0.50.5
22G853MEDIUM POSITIONAL0.490.5
23l853MEDIUM POSITIONAL0.520.5
21B853MEDIUM THERMAL10.542
22G853MEDIUM THERMAL16.212
23l853MEDIUM THERMAL14.642
31C920MEDIUM POSITIONAL0.460.5
32H920MEDIUM POSITIONAL0.450.5
33m920MEDIUM POSITIONAL0.430.5
31C920MEDIUM THERMAL14.312
32H920MEDIUM THERMAL17.712
33m920MEDIUM THERMAL192
41D532MEDIUM POSITIONAL0.860.5
42I532MEDIUM POSITIONAL1.270.5
43n532MEDIUM POSITIONAL1.030.5
41D532MEDIUM THERMAL33.192
42I532MEDIUM THERMAL23.492
43n532MEDIUM THERMAL44.952
51E652MEDIUM POSITIONAL0.560.5
52J652MEDIUM POSITIONAL0.620.5
53o652MEDIUM POSITIONAL0.470.5
51E652MEDIUM THERMAL17.622
52J652MEDIUM THERMAL17.152
53o652MEDIUM THERMAL26.332
LS refinement shellResolution: 3.011→3.089 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 52 -
Rwork0.313 917 -
obs--23.61 %

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