[English] 日本語
Yorodumi
- PDB-5fgh: Yeast 20S proteasome beta5-K33A mutant (propeptide expressed in t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fgh
TitleYeast 20S proteasome beta5-K33A mutant (propeptide expressed in trans) in complex with MG132
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex / Proteasome / Mutant / Inhibitor / Binding Analysis
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
PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form / Chem-ALD / 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 ...PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form / Chem-ALD / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035/A2 Germany
CitationJournal: Nat Commun / Year: 2016
Title: A unified mechanism for proteolysis and autocatalytic activation in the 20S proteasome.
Authors: Huber, E.M. / Heinemeyer, W. / Li, X. / Arendt, C.S. / Hochstrasser, M. / Groll, M.
History
DepositionDec 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Structure summary
Revision 1.2Mar 29, 2017Group: Database references
Revision 1.3Jun 20, 2018Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 27, 2018Group: Data collection / Structure summary / Category: pdbx_molecule_features
Revision 1.5Oct 24, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.pdbx_mutation / _entity.src_method
Revision 1.6Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

-
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
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
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
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)734,13746
Polymers730,93528
Non-polymers3,20218
Water4,666259
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.920, 299.860, 145.980
Angle α, β, γ (deg.)90.00, 113.13, 90.00
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
1111A1 - 300
2111O1 - 300
1121B1 - 300
2121P1 - 300
1131C1 - 300
2131Q1 - 300
1141D1 - 300
2141R1 - 300
1151E1 - 300
2151S1 - 300
1161F1 - 300
2161T1 - 300
1171G1 - 300
2171U1 - 300
1181H1 - 300
2181V1 - 300
1191I1 - 300
2191W1 - 300
11101J1 - 300
21101X1 - 300
11111K1 - 300
21111Y1 - 300
11121L1 - 300
21121Z1 - 300
11131M1 - 300
21131a1 - 300
11141N1 - 300
21141b1 - 300

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999722, -0.002027, 0.023484), (-0.00212, -0.984531, -0.1752), (0.023476, -0.175201, 0.984253)68.33469, -288.27899, -25.9136

-
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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: 23267.148 Da / Num. of mol.: 2 / Mutation: K33A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Production host: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
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: 27200.893 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38624, proteasome endopeptidase complex

-
Non-polymers , 4 types, 277 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#16: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#17: Chemical
ChemComp-ALD / N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-1-hydroxy-4-methylpentan-2-yl]-L-leucinamide


Type: Peptide-like / Class: Inhibitor / Mass: 477.637 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C26H43N3O5 / Source: (synth.) synthetic construct (others) / References: PHQ-Leu-Leu-Leu-aldehyde MG-132, bound form
#18: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 3.67 Å3/Da / Density % sol: 66.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 20 mM MgAC2, 13% MPD, 0.1 M MES / PH range: 6.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2015
RadiationMonochromator: LN2 COOLED FIXED-EXIT. SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 257992 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.7
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 3 / % possible all: 98

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RYP

1ryp


Resolution: 2.8→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 24.691 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 12900 5 %RANDOM
Rwork0.178 ---
obs0.18 245092 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å2-0.63 Å2
2---5.3 Å20 Å2
3---1.83 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49358 0 216 259 49833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01950487
X-RAY DIFFRACTIONr_bond_other_d0.0010.0248289
X-RAY DIFFRACTIONr_angle_refined_deg0.8551.96868301
X-RAY DIFFRACTIONr_angle_other_deg0.6823111177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.83456316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.93324.4212253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.136158745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.03615284
X-RAY DIFFRACTIONr_chiral_restr0.0490.27705
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0257255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211321
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_it3.0346.30125348
X-RAY DIFFRACTIONr_mcbond_other3.0346.30125347
X-RAY DIFFRACTIONr_mcangle_it4.0499.43631633
X-RAY DIFFRACTIONr_mcangle_other4.0499.43631634
X-RAY DIFFRACTIONr_scbond_it3.0286.81625139
X-RAY DIFFRACTIONr_scbond_other3.0286.81625139
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.80210.04136667
X-RAY DIFFRACTIONr_long_range_B_refined4.70149.43853616
X-RAY DIFFRACTIONr_long_range_B_other4.68649.43553590
X-RAY DIFFRACTIONr_rigid_bond_restr1.306398776
X-RAY DIFFRACTIONr_sphericity_free30.795165
X-RAY DIFFRACTIONr_sphericity_bonded16.7597976
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A3099tight positional0.010.05
1A3264tight positional00.05
1A3423tight positional00.05
1A3618tight positional00.05
1A3024tight positional00.05
1A3795tight thermal6.380.5
2B3756tight thermal5.060.5
3C3729tight thermal10.890.5
4D3578tight thermal8.460.5
5E3509tight thermal5.510.5
6F3749tight thermal5.750.5
7G3770tight thermal4.560.5
8H3478tight thermal4.70.5
9I3119tight thermal3.920.5
10J3099tight thermal3.50.5
11K3264tight thermal4.530.5
12L3423tight thermal3.620.5
13M3618tight thermal3.10.5
14N3024tight thermal3.560.5
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 868 -
Rwork0.283 16488 -
obs--91.89 %
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)
10.0765-0.0022-0.00520.0554-0.00120.0029-0.00070.0038-0.0105-0.00580.0025-0.0194-0.0049-0.0087-0.00180.0755-0.00420.00440.0395-0.00760.077767.5245-91.73646.4887
20.0810.0187-0.03020.01050.00720.0669-0.01130.0027-0.0091-0.01230.00240.0082-0.00640.0150.00890.0819-0.00730.01570.04290.00530.067660.2233-87.441116.8049
30.0670.0359-0.00590.0211-0.00470.0046-0.00220.0113-0.002-0.00410.01180.00950.00090.0058-0.00960.094-0.00020.00060.04250.00840.066132.8525-86.76121.4289
40.0018-0.0037-0.00530.01420.01710.0261-0.0098-0.0019-0.0025-0.00430.0010.0237-0.00430.01110.00880.06930.0084-0.01370.03720.01550.09773.5207-89.491613.9465
50.00480.0023-0.00790.0045-0.00760.01720.00790.0006-0.00470.00570.00390.0163-0.0153-0.0037-0.01180.05530.00990.01150.03470.00490.1112-2.7837-93.946645.9959
60.0014-0.00080.00020.0011-0.00040.00110.00290.0028-0.0080.0037-0.00510.00640.00390.00560.00220.08940.0020.02430.0373-0.00650.074415.6592-94.704370.2366
70.0080.0116-0.00540.028-0.00960.03220.00940.0068-0.00730.0296-0.0109-0.0139-0.005-0.00490.00150.0946-0.00250.00610.032-0.00930.060848.2196-93.211571.5784
80.0023-0.0026-0.00760.00980.0070.03130.0040.0070.00360.0064-0.0058-0.0251-0.0007-0.03080.00180.0672-0.0038-0.00440.0309-0.00590.082768.154-129.303447.6336
90.0984-0.0473-0.01260.1519-0.01050.00730.005-0.0023-0.00760.0033-0.0135-0.019-0.01410.00280.00850.0672-0.00080.0180.0422-0.00080.073768.8352-126.96121.2691
100.13330.01290.01710.09330.06550.05110.0105-0.00360.0134-0.02650.0003-0.0001-0.00320.0037-0.01080.09520.00230.01160.04120.00290.053845.2144-126.0226-0.3497
110.04560.083-0.00080.16080.0080.0108-0.0046-0.0090.0266-0.00560.00070.0595-0.00430.01870.0040.06870.0103-0.01690.03820.00460.0911.3822-130.29832.8392
120.0911-0.01320.07880.0405-0.00380.07420.0111-0.0049-0.00680.0099-0.00220.01880.00240.0014-0.00890.0530.00540.0010.03640.00960.0996-4.1211-133.84328.6763
130.0239-0.04380.01050.0909-0.01980.0050.00110.00040.00240.0155-0.00010.02370.00120.0038-0.0010.07120.00040.02080.0414-0.00310.08428.2456-137.539960.5043
140.06440.0396-0.06960.121-0.03770.07750.0130.01050.00930.03040.00290.006-0.002-0.0104-0.01590.09140-0.00160.0414-0.00460.054440.3827-133.907770.7281
150.0363-0.0043-0.00880.04920.03080.0222-0.00350.0170.00830.0044-0.00450.01010.0103-0.00220.0080.0688-0.0119-0.0070.02720.00820.08492.0939-206.185636.8092
160.0840.0370.05290.01790.01630.0638-0.01030.00360.0102-0.00480.00090.0024-0.0026-0.00320.00950.0849-0.0026-0.01650.0343-0.00740.08058.6483-204.97036.7193
170.00160.0012-0.00060.00540.00420.0072-0.0001-0.00440.0044-0.0226-0.00120.0061-0.01590.00650.00130.11270.0169-0.01360.0238-0.00670.056735.9409-203.1327-9.0918
180.0053-0.00540.00190.0121-0.00640.00540.0012-0.00690.0146-0.0259-0.0093-0.02150.01030.00440.00810.07630.01940.02450.0254-0.00940.060365.4676-202.66233.3749
190.005-0.00110.0020.00090.00060.00250.01350.00370.0047-0.0016-0.0011-0.00890.00880.0031-0.01240.05290.0175-0.00680.0156-0.01570.099172.4171-203.883435.4641
200.01280.0056-0.0070.003-0.00290.00940.0132-0.0019-0.01640.0043-0.0103-0.0098-0.0118-0.011-0.00290.0850.0054-0.01440.02770.01150.077354.3923-207.459859.7216
210.0051-0.0004-0.00790.0357-0.04120.0756-0.00430.00760.00330.0112-0.00020.01540.00190.00260.00450.0916-0.0024-0.0060.02890.00880.073421.9227-209.364661.2659
220.0117-0.0061-0.02280.01740.00740.04980.0017-0.002-0.00220.01140.00050.03310.0080.0119-0.00220.0646-0.00980.00250.02740.00890.08811.5996-169.499944.62
230.0848-0.0015-0.0080.0895-0.01240.00260.0055-0.00330.0161-0.0257-0.00030.01710.00430.0005-0.00520.0685-0.0007-0.01740.03720.00050.08680.4427-167.000218.2256
240.0393-0.0064-0.01770.0927-0.01680.01320.0079-0.0105-0.0126-0.0401-0.00250.01030.00030.0074-0.00540.09750.0036-0.01290.0411-0.00430.061723.6368-164.0223-3.625
250.06450.1122-0.00250.2002-0.00680.0018-0.00480.0012-0.0215-0.00720.0105-0.03130.0056-0.0026-0.00570.07280.00720.02140.0407-0.01290.068657.5529-160.4191-0.2187
260.0350.0521-0.02530.0807-0.03480.02710.0023-0.0026-0.01220.00510.0029-0.03220.0086-0.007-0.00520.05790.00990.00890.0444-0.00830.089173.4851-161.540625.53
270.0323-0.0078-0.02480.05250.01640.022-0.00290.0065-0.00580.01380.0024-0.0205-0.0005-0.00850.00050.07390.0058-0.01280.03780.00150.076361.7536-163.579957.7031
280.053-0.02780.03640.0565-0.00910.02830.01290.0002-0.00410.0279-0.00400.0122-0.0043-0.00890.0936-0.0040.01040.03940.00540.059529.8413-169.069567.6824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 250
2X-RAY DIFFRACTION2B1 - 244
3X-RAY DIFFRACTION3C1 - 240
4X-RAY DIFFRACTION4D1 - 242
5X-RAY DIFFRACTION5E3 - 233
6X-RAY DIFFRACTION6F2 - 244
7X-RAY DIFFRACTION7G2 - 242
8X-RAY DIFFRACTION8H1 - 226
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 195
11X-RAY DIFFRACTION11K1 - 212
12X-RAY DIFFRACTION12L1 - 222
13X-RAY DIFFRACTION13M1 - 233
14X-RAY DIFFRACTION14N1 - 196
15X-RAY DIFFRACTION15O1 - 250
16X-RAY DIFFRACTION16P1 - 244
17X-RAY DIFFRACTION17Q1 - 240
18X-RAY DIFFRACTION18R1 - 242
19X-RAY DIFFRACTION19S3 - 233
20X-RAY DIFFRACTION20T2 - 244
21X-RAY DIFFRACTION21U2 - 242
22X-RAY DIFFRACTION22V1 - 226
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 195
25X-RAY DIFFRACTION25Y1 - 212
26X-RAY DIFFRACTION26Z1 - 222
27X-RAY DIFFRACTION27a1 - 233
28X-RAY DIFFRACTION28b1 - 196

+
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