[English] 日本語
Yorodumi
- PDB-4fzc: 20S yeast proteasome in complex with cepafungin I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fzc
Title20S yeast proteasome in complex with cepafungin I
Components
  • (Proteasome component ...) x 14
  • Cepafungin I
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ubiquitin / proteasome / drug development / inhibitor / natural product / N-terminal nucleophilic hydrolase / protein degradation / 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
Cepafungin I / 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 ...Cepafungin I / 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: 2.8 Å
AuthorsStein, M. / Beck, P. / Kaiser, M. / Dudler, R. / Becker, C.F.W. / Groll, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: One-shot NMR analysis of microbial secretions identifies highly potent proteasome inhibitor.
Authors: Stein, M.L. / Beck, P. / Kaiser, M. / Dudler, R. / Becker, C.F. / Groll, M.
History
DepositionJul 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 2.0May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_distant_solvent_atoms / struct_conn
Item: _chem_comp.mon_nstd_flag / _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
a: Proteasome component PRE4
b: Proteasome component PRE3
c: Cepafungin I
d: Cepafungin I
e: Cepafungin I
f: Cepafungin I


Theoretical massNumber of molelcules
Total (without water)706,42532
Polymers706,42532
Non-polymers00
Water23,7801320
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.680, 301.020, 144.830
Angle α, β, γ (deg.)90.00, 112.86, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Proteasome component ... , 14 types, 28 molecules AOBPCQDRESFTGUHVIWJXKYLZMaNb

#1: Protein Proteasome component Y7 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit 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: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#2: Protein Proteasome component Y13 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteinase YSCE subunit 13


Mass: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#3: Protein Proteasome component PRE6 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteinase YSCE subunit PRE6


Mass: 26903.330 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#4: Protein Proteasome component PUP2 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteinase YSCE subunit PUP2


Mass: 26544.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#5: Protein Proteasome component PRE5 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteinase YSCE subunit PRE5


Mass: 25502.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex
#6: Protein Proteasome component C1 / / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteinase YSCE subunit 1


Mass: 26892.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex
#7: Protein Proteasome component C7-alpha / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 27316.037 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#8: Protein Proteasome component PUP1 / / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteinase YSCE subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome component PUP3 / / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#10: Protein Proteasome component C11 / / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit 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: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#11: Protein Proteasome component PRE2 / / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit 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: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex
#12: Protein Proteasome component C5 / / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#13: Protein Proteasome component PRE4 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit 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: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#14: Protein Proteasome component PRE3 / / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit 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: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex

-
Protein/peptide / Non-polymers , 2 types, 1324 molecules cdef

#15: Protein/peptide
Cepafungin I


Type: Peptide-like / Class: Inhibitor / Mass: 554.719 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: ATCC 204508 / S288c / References: Cepafungin I
#16: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1320 / 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: 3.86 Å3/Da / Density % sol: 68.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 100 mM MES; 20 mM MgAc2; 12% MPD, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2011
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→25 Å / Num. obs: 256455 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.4 / % possible all: 99

-
Processing

Software
NameClassification
XDSdata scaling
CNSrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementResolution: 2.8→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 6450863.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 12718 5 %RANDOM
Rwork0.214 ---
obs0.214 255126 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.2007 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 67.2 Å2
Baniso -1Baniso -2Baniso -3
1-24.18 Å20 Å2-13.75 Å2
2---33.54 Å20 Å2
3---9.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.76 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49700 0 0 1320 51020
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.931.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.332.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.409 2138 5 %
Rwork0.394 40772 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4lum.par

+
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