[English] 日本語
Yorodumi
- PDB-4ltc: Crystal structure of yeast 20S proteasome in complex with enone c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ltc
TitleCrystal structure of yeast 20S proteasome in complex with enone carmaphycin analogue 6
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHydrolase/Hydrolase Inhibitor / proteasome / inhibitor / carmaphycin / epoxyketone / vinylketone / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex ...proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / proteasome storage granule / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / mRNA binding / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / 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
N-HEXANOYL-L-VALYL-N~1~-[(4S,5S,6R)-5-HYDROXY-2,6-DIMETHYLOCTAN-4-YL]-N~5~,N~5~-DIMETHYL-L-GLUTAMAMIDE / Chem-EC6 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 ...N-HEXANOYL-L-VALYL-N~1~-[(4S,5S,6R)-5-HYDROXY-2,6-DIMETHYLOCTAN-4-YL]-N~5~,N~5~-DIMETHYL-L-GLUTAMAMIDE / Chem-EC6 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStein, M. / Trivella, D.B.B. / Groll, M.
CitationJournal: Chem.Biol. / Year: 2014
Title: Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor.
Authors: Trivella, D.B. / Pereira, A.R. / Stein, M.L. / Kasai, Y. / Byrum, T. / Valeriote, F.A. / Tantillo, D.J. / Groll, M. / Gerwick, W.H. / Moore, B.S.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-3
C: Proteasome subunit alpha type-4
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-6
F: Probable proteasome subunit alpha type-7
G: Proteasome subunit alpha type-1
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-3
Q: Proteasome subunit alpha type-4
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-6
T: Probable proteasome subunit alpha type-7
U: Proteasome subunit alpha type-1
H: Proteasome subunit beta type-2
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-4
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-6
M: Proteasome subunit beta type-7
N: Proteasome subunit beta type-1
V: Proteasome subunit beta type-2
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-4
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)729,33130
Polymers728,27828
Non-polymers1,0542
Water46,9652607
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area118690 Å2
ΔGint-357 kcal/mol
Surface area216220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.170, 300.230, 144.380
Angle α, β, γ (deg.)90.000, 112.790, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 500
2114O1 - 500
1124B1 - 500
2124P1 - 500
1134C1 - 500
2134Q1 - 500
1144D1 - 500
2144R1 - 500
1154E1 - 500
2154S1 - 500
1164F1 - 500
2164T1 - 500
1174G1 - 500
2174U1 - 500
1184H1 - 500
2184V1 - 500
1194I1 - 500
2194W1 - 500
11104J1 - 500
21104X1 - 500
11114K1 - 500
21114Y1 - 500
11124L1 - 500
21124Z1 - 500
11134M1 - 500
21134a1 - 500
11144N1 - 500
21144b1 - 500

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

-
Components

-
Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQDRESGU

#1: Protein Proteasome subunit alpha type-2 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-3 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-4 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-6 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-1 / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P21243, proteasome endopeptidase complex

-
Protein , 1 types, 2 molecules FT

#6: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31443.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P21242, proteasome endopeptidase complex

-
Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-2 / PSMB2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 25114.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / PSMB3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-4 / PSMB4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / PSMB5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component ...Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component ...Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-1 / PSMB1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component ...Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288c
References: UniProt: P38624, proteasome endopeptidase complex

-
Non-polymers , 2 types, 2609 molecules

#15: Chemical ChemComp-EC6 / N-hexanoyl-L-valyl-N~1~-[(4S,5S,6R)-5-hydroxy-2,6-dimethyloctan-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide / Double bound form of enone carmaphycin analogue 6, (S)-N1-((S,Z)-2,6-dimethyl-5-oxooct-6-en-4-yl)-2-((S)-2-hexanamido-3-methylbutanamido)-N5,N5-dimethylpentanediamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 526.752 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H54N4O5
Details: Originated from (S)-N1-((S,Z)-2,6-dimethyl-5-oxooct-6-en-4-yl)-2-((S)-2-hexanamido-3-methylbutanamido)-N5,N5-dimethylpentanediamide that reacts with N-terminal Thr of the protein, opening ...Details: Originated from (S)-N1-((S,Z)-2,6-dimethyl-5-oxooct-6-en-4-yl)-2-((S)-2-hexanamido-3-methylbutanamido)-N5,N5-dimethylpentanediamide that reacts with N-terminal Thr of the protein, opening double bonds of the original compound and making two covalent linkages with the amino group and side chain hydroxyl of the Thr. The PRD represents the bound form.
References: N-HEXANOYL-L-VALYL-N~1~-[(4S,5S,6R)-5-HYDROXY-2,6-DIMETHYLOCTAN-4-YL]-N~5~,N~5~-DIMETHYL-L-GLUTAMAMIDE
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2607 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 7.5
Details: 30 mM of magnesium acetate, 100 mM of MES (pH 7.2) and 12% of MPD, vapor diffusion, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 5, 2013
RadiationMonochromator: Double Multilayer Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 354256 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 55.34 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.60.5381.711036553932597.5
2.6-2.70.3712.44902893380997.6
2.7-2.80.2773.29820852917297.8
2.8-2.90.214.33703402533197.7
2.9-30.1765.17604502213697.8
3-3.10.1396.46501451921597.6
3.1-3.20.1118.12448081689597.5
3.2-40.05417.032195888213596.8
4-50.02535.821095924179196
5-60.02239.01488181862796.8
6-100.01552.09553832025897.3
10-200.01167.2413057494397.2
20-300.01279.69147550797.5
300.01779.3230411249.1

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 1 / SU B: 21.293 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.338 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 17633 5 %RANDOM
Rwork0.2041 ---
obs0.2055 352662 96.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.79 Å2 / Biso mean: 57.9261 Å2 / Biso min: 16.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å2-0 Å20.19 Å2
2--0.03 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49538 0 74 2607 52219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950526
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248322
X-RAY DIFFRACTIONr_angle_refined_deg0.911.96568358
X-RAY DIFFRACTIONr_angle_other_deg0.6953111274
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33956338
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68324.4082264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.056158778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.93215288
X-RAY DIFFRACTIONr_chiral_restr0.0660.27702
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257358
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211326
X-RAY DIFFRACTIONr_mcbond_it1.1124.225436
X-RAY DIFFRACTIONr_mcbond_other1.1124.225435
X-RAY DIFFRACTIONr_mcangle_it2.0226.29231746
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3795MEDIUM POSITIONAL0.080.5
1A3795MEDIUM THERMAL42
2B3757MEDIUM POSITIONAL0.090.5
2B3757MEDIUM THERMAL3.542
3C3746MEDIUM POSITIONAL0.070.5
3C3746MEDIUM THERMAL4.572
4D3666MEDIUM POSITIONAL0.090.5
4D3666MEDIUM THERMAL2.662
5E3553MEDIUM POSITIONAL0.070.5
5E3553MEDIUM THERMAL4.32
6F3756MEDIUM POSITIONAL0.080.5
6F3756MEDIUM THERMAL4.782
7G3792MEDIUM POSITIONAL0.10.5
7G3792MEDIUM THERMAL3.052
8H3337MEDIUM POSITIONAL0.070.5
8H3337MEDIUM THERMAL1.862
9I3119MEDIUM POSITIONAL0.070.5
9I3119MEDIUM THERMAL2.622
10J3144MEDIUM POSITIONAL0.070.5
10J3144MEDIUM THERMAL3.012
11K3188MEDIUM POSITIONAL0.070.5
11K3188MEDIUM THERMAL1.682
12L3439MEDIUM POSITIONAL0.070.5
12L3439MEDIUM THERMAL1.922
13M3618MEDIUM POSITIONAL0.070.5
13M3618MEDIUM THERMAL2.582
14N2949MEDIUM POSITIONAL0.070.5
14N2949MEDIUM THERMAL1.462
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 1274 -
Rwork0.351 24219 -
all-25493 -
obs--97.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4861-0.20150.22780.6392-0.13390.4366-0.04460.06940.01330.05720.0258-0.146-0.06760.01840.01880.0816-0.03920.04660.1603-0.03480.170266.9158-92.091445.8658
20.655-0.04150.05580.3710.17010.4708-0.03720.0069-0.01-0.1095-0.0225-0.0337-0.14110.12520.05970.1812-0.05420.08910.1850.05670.110259.4999-87.843516.3015
30.32630.19530.08670.3679-0.06510.4163-0.08560.0570.0563-0.14510.06030.0505-0.06710.07760.02540.2177-0.02110.00550.15990.07720.090932.19-87.28810.8602
40.36040.07790.04110.54810.01120.3339-0.0492-0.01880.0666-0.0790.00790.2592-0.06660.03420.04130.09230.0545-0.07450.11710.05720.24513.4237-90.404414.1087
50.40570.06260.20410.1955-0.03270.689-0.049-0.02080.02480.07510.04030.2385-0.1088-0.13750.00870.05790.05870.09990.1878-0.00510.3535-3.0358-94.23545.6194
60.55140.16930.2420.4551-0.04610.1467-0.0027-0.08720.07620.118-0.02480.1057-0.0166-0.06060.02750.25650.01780.16720.1891-0.06830.146115.2593-95.027169.7483
70.22390.01130.08390.6395-0.0310.4782-0.00270.04080.00730.1938-0.043-0.0784-0.0519-0.03650.04570.2574-0.02150.01350.1162-0.04790.044947.6643-93.313971.0066
80.4161-0.1993-0.16510.47290.29860.5298-0.02760.0284-0.01230.02760.01120.12990.1328-0.07150.01640.095-0.0731-0.0480.10540.05480.22432.1825-206.568436.7712
90.35560.15860.27610.67880.00610.4503-0.0401-0.07370.0164-0.15330.02710.0270.0505-0.0990.0130.1279-0.0084-0.08450.1244-0.0610.14358.6926-205.5696.7078
100.55110.34080.24340.488-0.17150.7290.07920.0943-0.0794-0.23220.03980.11230.14630.0813-0.1190.38350.0584-0.18060.0756-0.10820.196735.9577-203.5996-9.3414
110.47160.14510.13220.8735-0.06910.17790.0643-0.03910.0276-0.2601-0.0988-0.14840.07340.01680.03440.22510.09630.10370.1586-0.0780.187564.9584-202.7413.8272
120.24290.2218-0.30440.3069-0.16180.68060.03950.0533-0.12560.07310.0897-0.32770.11850.0952-0.12910.09690.1033-0.14110.1126-0.13890.518272.1287-204.296335.2315
130.93260.4180.09180.25180.05590.4130.1726-0.0773-0.26250.1953-0.0535-0.22810.0755-0.0509-0.11910.2851-0.0177-0.25340.0360.05640.273854.3502-207.685659.4706
140.22870.1277-0.12070.5017-0.04770.39410.03170.0087-0.01520.15970.00790.07350.03450.0419-0.03960.2598-0.0351-0.06890.06520.06890.126822.0664-209.823361.0898
150.19620.0628-0.05750.22250.02930.03290.0710.03540.03760.0989-0.0163-0.17360.0106-0.0022-0.05470.1158-0.0034-0.02550.1698-0.02610.210367.6774-129.962148.2277
160.22560.0245-0.09390.98370.14740.33060.03560.0992-0.0093-0.0412-0.0162-0.2221-0.0662-0.0101-0.01940.08340.0040.10320.221-0.02570.188568.2946-127.437420.7895
170.6963-0.10360.37931.08220.0620.2214-0.01370.04270.0004-0.18970.02660.0141-0.03980.0188-0.01290.2239-0.0030.08840.19960.00730.043944.7175-126.7596-1.0203
180.50350.5758-0.1161.25220.15150.3016-0.00910.00440.0704-0.21770.04270.2529-0.02940.0413-0.03360.11310.031-0.09690.15960.04550.153610.9593-130.83722.1497
190.3384-0.06410.28520.6060.27950.5170.0393-0.046-0.0464-0.0571-0.0170.2343-0.02280.0088-0.02230.02570.0080.0350.19770.03310.3039-4.4622-134.464128.5254
200.2156-0.05330.13271.0808-0.010.10090.0617-0.0430.04730.1912-0.04490.19140.0092-0.0197-0.01690.1274-0.02060.14570.20750.00280.17597.8462-137.975660.3819
210.6081-0.002-0.06360.88550.0280.2490.08190.01510.0450.243-0.0505-0.0540.0101-0.0131-0.03140.2361-0.02370.01270.1586-0.0240.017339.8715-134.022870.8238
220.1341-0.04710.00310.3408-0.00680.02150.0557-0.0003-0.04320.0776-0.0260.22950.0389-0.0042-0.02970.1319-0.02960.00680.15430.05110.22131.5885-169.691245.5809
230.14610.140.05130.894-0.11920.32580.04690.02620.0196-0.1315-0.02070.22560.08980.0042-0.02620.0722-0.0048-0.08040.16070.00780.20490.3293-167.440218.0962
240.6489-0.0034-0.18191.2361-0.13580.3035-0.02840.025-0.0648-0.2140.07240.0516-0.00580.0213-0.0440.23240.0154-0.06610.1314-0.03440.047423.3935-164.3239-4.0568
250.59490.64860.21781.21080.00720.2915-0.00290.0322-0.0583-0.23830.0868-0.16050.05830.0736-0.08390.18790.03660.11710.209-0.06170.150657.2283-160.8199-0.9695
260.0460.03150.0230.3110.01080.05290.01540.0126-0.0162-0.0240.0206-0.12960.00660.0286-0.0360.02890.01750.04340.2169-0.02990.137956.4257-155.307328.9926
270.3206-0.1155-0.04371.00750.27780.09760.03210.0328-0.04740.2225-0.0009-0.21240.0404-0.0419-0.03120.15780.0112-0.10660.12310.00090.143661.7003-163.760557.5065
280.54280.03310.13160.8990.19590.56050.0807-0.0256-0.03920.1908-0.01610.05320.0432-0.0169-0.06450.2298-0.04110.01910.14250.05010.034829.9193-169.524467.8888
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8O-10 - 9999
9X-RAY DIFFRACTION9P-10 - 9999
10X-RAY DIFFRACTION10Q-10 - 9999
11X-RAY DIFFRACTION11R-10 - 9999
12X-RAY DIFFRACTION12S-10 - 9999
13X-RAY DIFFRACTION13T-10 - 9999
14X-RAY DIFFRACTION14U-10 - 9999
15X-RAY DIFFRACTION15H-10 - 9999
16X-RAY DIFFRACTION16I-10 - 9999
17X-RAY DIFFRACTION17J-10 - 9999
18X-RAY DIFFRACTION18K-10 - 9999
19X-RAY DIFFRACTION19L-10 - 9999
20X-RAY DIFFRACTION20M-10 - 9999
21X-RAY DIFFRACTION21N-10 - 9999
22X-RAY DIFFRACTION22V-10 - 9999
23X-RAY DIFFRACTION23W-10 - 9999
24X-RAY DIFFRACTION24X-10 - 9999
25X-RAY DIFFRACTION25Y-10 - 9999
26X-RAY DIFFRACTION26Z-10 - 9999
27X-RAY DIFFRACTION27a-10 - 9999
28X-RAY DIFFRACTION28b-10 - 9999

+
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://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