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- PDB-1g0u: A GATED CHANNEL INTO THE PROTEASOME CORE PARTICLE -

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Basic information

Entry
Database: PDB / ID: 1g0u
TitleA GATED CHANNEL INTO THE PROTEASOME CORE PARTICLE
Components(PROTEASOME COMPONENT ...) x 14
KeywordsHYDROLASE / proteasome / ubiquitin / degradation / protease / Ntn-hydrolase
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
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 ...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 / Resolution: 2.4 Å
AuthorsGroll, M. / Bajorek, M. / Kohler, A. / Moroder, L. / Rubin, D.M. / Huber, R. / Glickman, M.H. / Finley, D.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: A gated channel into the proteasome core particle.
Authors: Groll, M. / Bajorek, M. / Kohler, A. / Moroder, L. / Rubin, D.M. / Huber, R. / Glickman, M.H. / Finley, D.
History
DepositionOct 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASOME COMPONENT Y7
B: PROTEASOME COMPONENT Y13
C: PROTEASOME COMPONENT PRE6
D: PROTEASOME COMPONENT PUP2
E: PROTEASOME COMPONENT PRE5
F: PROTEASOME COMPONENT C1
G: PROTEASOME COMPONENT C7-ALPHA
H: PROTEASOME COMPONENT PUP1
I: PROTEASOME COMPONENT PUP3
J: PROTEASOME COMPONENT C11
K: PROTEASOME COMPONENT PRE2
L: PROTEASOME COMPONENT C5
M: PROTEASOME COMPONENT PRE4
N: PROTEASOME COMPONENT PRE3
O: PROTEASOME COMPONENT Y7
P: PROTEASOME COMPONENT Y13
Q: PROTEASOME COMPONENT PRE6
R: PROTEASOME COMPONENT PUP2
S: PROTEASOME COMPONENT PRE5
T: PROTEASOME COMPONENT C1
U: PROTEASOME COMPONENT C7-ALPHA
V: PROTEASOME COMPONENT PUP1
W: PROTEASOME COMPONENT PUP3
X: PROTEASOME COMPONENT C11
Y: PROTEASOME COMPONENT PRE2
Z: PROTEASOME COMPONENT C5
1: PROTEASOME COMPONENT PRE4
2: PROTEASOME COMPONENT PRE3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,94448
Polymers718,45828
Non-polymers48620
Water52,3882908
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area112920 Å2
ΔGint-510 kcal/mol
Surface area217200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.18, 301.1, 144.1
Angle α, β, γ (deg.)90., 113., 90.
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
DetailsThe biological assembly is a multisubunit complex composed of 28 subunits, whereas 14 subunits are different.

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Components

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PROTEASOME COMPONENT ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZM1N2

#1: Protein PROTEASOME COMPONENT Y7 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT Y7 / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y7


Mass: 27191.828 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23639, EC: 3.4.99.46
#2: Protein PROTEASOME COMPONENT Y13 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT Y13 / PROTEINASE YSCE SUBUNIT 13 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT Y13


Mass: 27181.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23638, EC: 3.4.99.46
#3: Protein PROTEASOME COMPONENT PRE6 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE6 / PROTEINASE YSCE SUBUNIT PRE6 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE6


Mass: 27121.605 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P40303, EC: 3.4.99.46
#4: Protein PROTEASOME COMPONENT PUP2 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP2 / PROTEINASE YSCE SUBUNIT PUP2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP2


Mass: 26453.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P32379, EC: 3.4.99.46
#5: Protein PROTEASOME COMPONENT PRE5 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE5 / PROTEINASE YSCE SUBUNIT PRE5 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE5


Mass: 25541.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P40302, EC: 3.4.99.46
#6: Protein PROTEASOME COMPONENT C1 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT C1 / PROTEINASE YSCE SUBUNIT 1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C1


Mass: 27325.020 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P21242, EC: 3.4.99.46
#7: Protein PROTEASOME COMPONENT C7-ALPHA / / E.C.3.4.99.46 / MACROPAIN SUBUNIT C7-ALPHA / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / ...MACROPAIN SUBUNIT C7-ALPHA / PROTEINASE YSCE SUBUNIT 7 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX C7 / COMPONENT Y8 / SCL1 SUPPRESSOR PROTEIN


Mass: 28033.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P21243, EC: 3.4.99.46
#8: Protein PROTEASOME COMPONENT PUP1 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP1 / PROTEINASE YSCE SUBUNIT PUP1 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P25043, EC: 3.4.99.46
#9: Protein PROTEASOME COMPONENT PUP3 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PUP3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P25451, EC: 3.4.99.46
#10: Protein PROTEASOME COMPONENT C11 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT C11 / PROTEINASE YSCE SUBUNIT 11 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C11


Mass: 22545.676 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P22141, EC: 3.4.99.46
#11: Protein PROTEASOME COMPONENT PRE2 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE2 / PROTEINASE YSCE SUBUNIT PRE2 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE2


Mass: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P30656, EC: 3.4.99.46
#12: Protein PROTEASOME COMPONENT C5 / / E.C.3.4.99.46 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT C5


Mass: 26905.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P23724, EC: 3.4.99.46
#13: Protein PROTEASOME COMPONENT PRE4 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE4 / PROTEINASE YSCE SUBUNIT PRE4 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P30657, EC: 3.4.99.46
#14: Protein PROTEASOME COMPONENT PRE3 / / E.C.3.4.99.46 / MACROPAIN SUBUNIT PRE3 / PROTEINASE YSCE SUBUNIT PRE3 / MULTICATALYTIC ENDOPEPTIDASE COMPLEX SUBUNIT PRE3


Mass: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PART OF 20S SUBUNIT / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Variant: SUB61 / References: UniProt: P38624, EC: 3.4.99.46

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Non-polymers , 2 types, 2928 molecules

#15: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2908 / 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: 3.76 Å3/Da / Density % sol: 67.25 %
Crystal growTemperature: 297 K / Method: hanging drop vapor-diffusion / pH: 6.7
Details: 22mM Magnesium acetate, 4% Dimethylsulfoxide, 100mM morpholinoethanesulfonic acid, 11% methylpentanediol, pH 6.7, hanging drop vapour-diffusion, temperature 297K
Crystal grow
*PLUS
Temperature: 24 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMEDTA1drop
422 mMmagnesium acetate1reservoir
55 %(v/v)dimethylsulfoxide1reservoir
6100 mMmorpholino-ethane-sulphonic1reservoir
711 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 378678 / Num. obs: 378678 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.161 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 0.2 % / Rmerge(I) obs: 0.396 / % possible all: 85.4
Reflection
*PLUS
Num. measured all: 1017653
Reflection shell
*PLUS
Rmerge(I) obs: 0.42

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.303 18933 5 %random
Rwork0.25 ---
all0.263 378678 --
obs0.26 378678 --
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48906 0 20 2908 51834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.878
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.25 / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS

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