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- PDB-5u4p: Protein-protein complex between 26S proteasome regulatory subunit... -

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Basic information

Entry
Database: PDB / ID: 5u4p
TitleProtein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31
Components
  • 26S proteasome regulatory subunit RPN11
  • 26S proteasome regulatory subunit RPN8
  • Ubiquitin-40S ribosomal protein S31
KeywordsPROTEIN BINDING / Complex / Ubiquitin / Proteasome
Function / homology
Function and homology information


Metalloprotease DUBs / proteasome storage granule assembly / peroxisome fission / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway ...Metalloprotease DUBs / proteasome storage granule assembly / peroxisome fission / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / Ribosomal scanning and start codon recognition / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / proteasome storage granule / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / protein deubiquitination / Ub-specific processing proteases / proteasome assembly / Neutrophil degranulation / proteasome complex / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / metallopeptidase activity / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cytoplasmic translation / cysteine-type deubiquitinase activity / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / mitochondrion / zinc ion binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S27a-like superfamily ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-ribosomal protein eS31 fusion protein / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWorden, E.J. / Dong, K.C. / Martin, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) United States
National Science Foundation (NSF, United States) United States
CitationJournal: Mol. Cell / Year: 2017
Title: An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.
Authors: Worden, E.J. / Dong, K.C. / Martin, A.
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN8
B: 26S proteasome regulatory subunit RPN11
C: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2504
Polymers53,1853
Non-polymers651
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-81 kcal/mol
Surface area18970 Å2
MethodPISA
2
A: 26S proteasome regulatory subunit RPN8
B: 26S proteasome regulatory subunit RPN11
C: Ubiquitin-40S ribosomal protein S31
hetero molecules

A: 26S proteasome regulatory subunit RPN8
B: 26S proteasome regulatory subunit RPN11
C: Ubiquitin-40S ribosomal protein S31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5008
Polymers106,3696
Non-polymers1312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area14250 Å2
ΔGint-175 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.210, 126.210, 139.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-226-

HOH

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Components

#1: Protein 26S proteasome regulatory subunit RPN8


Mass: 20154.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN8, YOR261C, O5360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08723
#2: Protein 26S proteasome regulatory subunit RPN11 / Ubiquitin carboxyl-terminal hydrolase RPN11 / Protein MPR1


Mass: 24461.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN11, MPR1, YFR004W / Production host: Escherichia coli (E. coli) / References: UniProt: P43588, ubiquitinyl hydrolase 1
#3: Protein Ubiquitin-40S ribosomal protein S31


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPS31, RPS37, UBI3, YLR167W, L9470.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P05759
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 1.5 M ammonium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.5→109.301 Å / Num. obs: 23105 / % possible obs: 99 % / Redundancy: 19.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08667 / Net I/σ(I): 30.3
Reflection shell
Lowest resolution (Å)Diffraction-ID
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109.3011

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8X, 2ZNV, 4BOZ, 4JQW, 4K1R, rMSM, 4UN2

4o8x

2znv

4boz

4jqw

4k1r

4un2


Resolution: 2.5→109.301 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1156 5 %
Rwork0.2113 --
obs0.2125 23100 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→109.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 1 63 3314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153307
X-RAY DIFFRACTIONf_angle_d1.1984460
X-RAY DIFFRACTIONf_dihedral_angle_d17.1971232
X-RAY DIFFRACTIONf_chiral_restr0.06516
X-RAY DIFFRACTIONf_plane_restr0.007568
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)
14.03291.3532-1.38255.5024-2.73656.5122-0.0875-0.0831-0.1034-0.22510.0329-0.2780.7704-0.13130.06240.475-0.07120.13940.32-0.06420.4695-3.9943-49.713518.8511
24.43611.5802-1.91915.2574-2.44397.4635-0.20530.91220.7779-0.48050.12510.06390.3717-0.35280.02550.4556-0.00350.15390.55470.19480.66971.968-31.9797-0.5931
31.888-1.16291.37052.69131.34073.621-0.31751.9714-0.6268-1.52760.0308-0.47811.564-0.55010.3281.9743-0.56870.35011.9484-0.14070.7471-0.0595-47.7716-20.9391
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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