[English] 日本語
Yorodumi
- PDB-3ipm: Crystal Structure of Archaeal 20S Proteasome in Complex with the ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ipm
TitleCrystal Structure of Archaeal 20S Proteasome in Complex with the C-terminus of PAN
Components
  • Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / Proteasome / proteasomal ATPase / protein degradation / AAA ATPase / electron cryomicroscopy / Hydrolase / Protease / Threonine protease / HYDROLASE-HYDROLASE ACTIVATOR COMPLEX
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / CTPase activity / proteasome activator complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process ...proteasome-activating nucleotidase complex / CTPase activity / proteasome activator complex / cytosolic proteasome complex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein unfolding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasomal protein catabolic process / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of proteasomal protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / GTPase activity / ATP hydrolysis activity / proteolysis / ATP binding / cytoplasm / cytosol
Similarity search - Function
Proteasome activator pa28, C-terminal domain / Proteasome-activating nucleotidase PAN / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain ...Proteasome activator pa28, C-terminal domain / Proteasome-activating nucleotidase PAN / Proteasome activator PA28, C-terminal domain / Proteasome activator superfamily / Proteasome activator PA28, C-terminal domain superfamily / Proteasome activator PA28, C-terminal / Peptidase T1A, proteasome beta-subunit, archaeal / Proteasome alpha subunit, archaeal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / 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 / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / Four Helix Bundle (Hemerythrin (Met), subunit A) / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 4-Layer Sandwich / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Proteasome subunit alpha / Proteasome subunit beta / Proteasome activator protein PA26 / Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
Trypanosoma brucei brucei (eukaryote)
Methanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsYu, Y. / Cheng, Y.
CitationJournal: EMBO J / Year: 2010
Title: Interactions of PAN's C-termini with archaeal 20S proteasome and implications for the eukaryotic proteasome-ATPase interactions.
Authors: Yadong Yu / David M Smith / Ho Min Kim / Victor Rodriguez / Alfred L Goldberg / Yifan Cheng /
Abstract: Protein degradation in the 20S proteasome is regulated in eukaryotes by the 19S ATPase complex and in archaea by the homologous PAN ATPase ring complex. Subunits of these hexameric ATPases contain on ...Protein degradation in the 20S proteasome is regulated in eukaryotes by the 19S ATPase complex and in archaea by the homologous PAN ATPase ring complex. Subunits of these hexameric ATPases contain on their C-termini a conserved hydrophobic-tyrosine-X (HbYX) motif that docks into pockets in the 20S to stimulate the opening of a gated substrate entry channel. Here, we report the crystal structure of the archaeal 20S proteasome in complex with the C-terminus of the archaeal proteasome regulatory ATPase, PAN. This structure defines the detailed interactions between the critical C-terminal HbYX motif and the 20S alpha-subunits and indicates that the intersubunit pocket in the 20S undergoes an induced-fit conformational change on binding of the HbYX motif. This structure together with related mutagenesis data suggest how in eukaryotes certain proteasomal ATPases bind to specific pockets in an asymmetrical manner to regulate gate opening.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Oct 13, 2021Group: Database references / Source and taxonomy / Structure summary
Category: database_2 / entity_name_com ...database_2 / entity_name_com / entity_src_gen / pdbx_database_related / struct_ref / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_related.content_type / _struct_ref.db_code / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
P: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
Q: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
R: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
S: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
T: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
U: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein


Theoretical massNumber of molelcules
Total (without water)533,09321
Polymers533,09321
Non-polymers00
Water00
1
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
P: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
Q: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
R: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
S: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
T: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
U: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein

A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit beta
I: Proteasome subunit beta
J: Proteasome subunit beta
K: Proteasome subunit beta
L: Proteasome subunit beta
M: Proteasome subunit beta
N: Proteasome subunit beta
O: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
P: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
Q: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
R: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
S: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
T: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein
U: Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein


Theoretical massNumber of molelcules
Total (without water)1,066,18642
Polymers1,066,18642
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area182430 Å2
ΔGint-667 kcal/mol
Surface area315100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.890, 166.890, 412.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

-
Components

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PsmA


Mass: 25829.447 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmA, Ta1288 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P25156, proteasome endopeptidase complex
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PsmB


Mass: 23998.691 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: psmB, Ta0612 / Plasmid: pRSET-A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P28061, proteasome endopeptidase complex
#3: Protein
Proteasome activator PA26, Proteasome-activating nucleotidase fusion protein


Mass: 26327.992 Da / Num. of mol.: 7 / Fragment: PA26 residues 2-223, PAN residues 424-430 / Mutation: E102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote), (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: Tb10.70.3660 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q38BM8, UniProt: Q58576

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.1 M MES pH6.8, 20% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2007
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 4→89.5 Å / Num. all: 50164 / Num. obs: 48850 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 53.1 Å2 / Rmerge(I) obs: 0.226 / Net I/σ(I): 2.9
Reflection shellResolution: 4→4.22 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7045 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YA7

1ya7


Resolution: 4→89.51 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2435 -random
Rwork0.249 ---
all0.25 50164 --
obs0.25 48849 98.4 %-
Displacement parametersBiso mean: 92.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.63 Å0.56 Å
Luzzati d res low-8 Å
Luzzati sigma a0.82 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 4→89.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35133 0 0 0 35133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.008
LS refinement shellResolution: 4→4.14 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.351 252 -
Rwork0.326 --
obs-4779 98.1 %

+
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://pdbjlvh1.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