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- PDB-4ady: Crystal structure of 26S proteasome subunit Rpn2 -

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Basic information

Entry
Database: PDB / ID: 4ady
TitleCrystal structure of 26S proteasome subunit Rpn2
Components26S PROTEASOME REGULATORY SUBUNIT RPN2
KeywordsPROTEIN BINDING / RPN1 / PC REPEAT
Function / homology
Function and homology information


proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process ...proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome assembly / Ub-specific processing proteases / enzyme regulator activity / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin protein ligase binding / nucleus
Similarity search - Function
: / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...: / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / HEAT repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
26S proteasome regulatory subunit RPN2
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsKulkarni, K. / He, J. / Da Fonseca, P.C.A. / Krutauz, D. / Glickman, M.H. / Barford, D. / Morris, E.P.
CitationJournal: Structure / Year: 2012
Title: The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings.
Authors: Jun He / Kiran Kulkarni / Paula C A da Fonseca / Dasha Krutauz / Michael H Glickman / David Barford / Edward P Morris /
Abstract: The 26S proteasome proteolyses ubiquitylated proteins and is assembled from a 20S proteolytic core and two 19S regulatory particles (19S-RP). The 19S-RP scaffolding subunits Rpn1 and Rpn2 function to ...The 26S proteasome proteolyses ubiquitylated proteins and is assembled from a 20S proteolytic core and two 19S regulatory particles (19S-RP). The 19S-RP scaffolding subunits Rpn1 and Rpn2 function to engage ubiquitin receptors. Rpn1 and Rpn2 are characterized by eleven tandem copies of a 35-40 amino acid repeat motif termed the proteasome/cyclosome (PC) repeat. Here, we reveal that the eleven PC repeats of Rpn2 form a closed toroidal structure incorporating two concentric rings of α helices encircling two axial α helices. A rod-like N-terminal domain consisting of 17 stacked α helices and a globular C-terminal domain emerge from one face of the toroid. Rpn13, an ubiquitin receptor, binds to the C-terminal 20 residues of Rpn2. Rpn1 adopts a similar conformation to Rpn2 but differs in the orientation of its rod-like N-terminal domain. These findings have implications for understanding how 19S-RPs recognize, unfold, and deliver ubiquitylated substrates to the 20S core.
History
DepositionJan 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S PROTEASOME REGULATORY SUBUNIT RPN2
B: 26S PROTEASOME REGULATORY SUBUNIT RPN2


Theoretical massNumber of molelcules
Total (without water)214,7002
Polymers214,7002
Non-polymers00
Water1,06359
1
A: 26S PROTEASOME REGULATORY SUBUNIT RPN2


Theoretical massNumber of molelcules
Total (without water)107,3501
Polymers107,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 26S PROTEASOME REGULATORY SUBUNIT RPN2


Theoretical massNumber of molelcules
Total (without water)107,3501
Polymers107,3501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.960, 148.660, 114.030
Angle α, β, γ (deg.)90.00, 107.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN2 / RPN2


Mass: 107349.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: P32565
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.82 Å3/Da / Density % sol: 56.4 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION IN HANGING DROPS AT 18 C. PROTEIN AT A CONCENTRATION OF 18 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 100 MM BIS-TRIS ...Details: CRYSTALS WERE GROWN BY VAPOUR DIFFUSION IN HANGING DROPS AT 18 C. PROTEIN AT A CONCENTRATION OF 18 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 100 MM BIS-TRIS PROPANE PH 7.0, 200 MM POTASSIUM SODIUM TARTRATE AND 16-18% (W/V) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→74.33 Å / Num. obs: 64456 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 56.74 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
PHENIX1.7.2_869refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→70.579 Å / SU ML: 0.75 / σ(F): 1.37 / Phase error: 27.08 / Stereochemistry target values: ML
Details: RESIDUES A1-A3, A788-A859, A926-945, B1-B57, B790-B855, AND B926-B945 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2402 1322 2 %
Rwork0.1827 --
obs0.1839 64344 99.74 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.351 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 79.55 Å2
Baniso -1Baniso -2Baniso -3
1-20.9353 Å20 Å211.2515 Å2
2---2.456 Å20 Å2
3----18.4793 Å2
Refinement stepCycle: LAST / Resolution: 2.7→70.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12522 0 0 59 12581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812732
X-RAY DIFFRACTIONf_angle_d1.19217265
X-RAY DIFFRACTIONf_dihedral_angle_d17.5024564
X-RAY DIFFRACTIONf_chiral_restr0.0852032
X-RAY DIFFRACTIONf_plane_restr0.0072211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.80820.34461690.30146915X-RAY DIFFRACTION99
2.8082-2.9360.3091380.2666973X-RAY DIFFRACTION100
2.936-3.09080.29071450.23637018X-RAY DIFFRACTION100
3.0908-3.28440.2891350.21816981X-RAY DIFFRACTION100
3.2844-3.5380.29221580.19446991X-RAY DIFFRACTION100
3.538-3.8940.24771420.16867004X-RAY DIFFRACTION100
3.894-4.45740.21841280.13247035X-RAY DIFFRACTION100
4.4574-5.61550.18961630.15587024X-RAY DIFFRACTION100
5.6155-70.60360.20321440.17757081X-RAY DIFFRACTION99
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)
10.85450.2227-0.17953.42690.55211.46260.20340.01690.0755-0.48580.0177-0.0886-0.59060.2013-0.05480.7835-0.02030.11150.3788-0.09620.4967-27.9216-60.4929-48.8713
20.75320.0787-0.79591.87821.27351.49690.0551-0.1377-0.0904-0.0964-0.15030.21650.17660.07240.03560.65670.04740.03940.5569-0.11990.5886-43.9836-37.3995-18.7422
30.8509-0.2025-0.39210.73510.33231.52870.1694-0.1320.23180.2129-0.09830.0915-0.4799-0.14170.0130.8599-0.01620.16150.591-0.15660.5379-40.96243.78741.5198
45.8832-1.96030.99346.25920.40341.4761-0.08240.14720.3624-0.1420.18730.2839-0.3775-0.11550.07841.28360.1920.29490.8507-0.09220.9812-53.162716.7694-1.1279
51.7559-0.0879-1.54111.19120.30433.17610.1730.24230.06920.0988-0.17020.1769-0.1334-0.52180.00280.3471-0.0034-0.02490.5267-0.09650.4491-38.2606-2.2992-17.5011
61.35480.1063-0.43771.4982-0.38231.87630.0055-0.3716-0.20150.3778-0.1991-0.0190.32480.37020.19090.71420.04550.07530.5335-0.00630.3888-34.5151-15.2137.7973
72.0029-0.5619-7.50946.3425-6.32919.7909-0.0865-0.63730.39060.2576-0.23560.3231-0.0387-0.18930.03941.3236-0.2570.13930.99120.24510.9455-49.9106-4.764516.1422
88.9714-1.79074.66870.3553-0.93282.43130.1132-0.0338-0.48230.0608-0.0223-0.12730.44830.088-0.07051.5871-0.09340.28891.60210.03991.1396-12.8117-38.81597.3653
92.1936-0.0729-0.69360.7963-0.39571.3813-0.0193-0.1385-0.39350.1729-0.20140.10.151-0.39190.2081.00220.04680.16741.01260.00640.9412-5.017-38.7898-13.3549
10-0.09160.59990.7730.128-0.11520.9513-0.1319-0.2066-0.2116-0.05850.0166-0.30030.63410.22250.02651.09890.37790.20781.00670.03090.72457.7028-39.1501-45.8355
111.53490.1423-0.69570.9905-0.19212.9255-0.1305-0.09680.0097-0.0978-0.0048-0.24490.32850.38330.09080.31440.0177-0.01080.37440.0550.3824-3.3667-13.3415-53.243
121.48650.74370.50072.13270.13531.6811-0.25520.1236-0.4606-0.33930.0797-0.07721.0551-0.02870.20880.9344-0.0640.20270.4191-0.00960.4782-10.629-33.7713-60.056
131.54460.2871-1.55390.0593-0.28971.549-0.3363-0.0354-0.3292-0.01560.1150.150.7623-0.56220.21051.97470.11730.10620.5797-0.04521.5844-4.9396-55.2658-62.478
142.32870.2398-0.43742.0448-0.41481.9797-0.09060.3562-0.4087-0.22630.3707-0.70010.52430.0492-0.07191.25620.13080.14910.6474-0.10240.9610.8448-46.128-64.6678
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:75)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 76:276)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 277:388)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 389:396)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 397:734)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 735:919)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 920:925)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 58:64)
9X-RAY DIFFRACTION9(CHAIN B AND RESID 65:186)
10X-RAY DIFFRACTION10(CHAIN B AND RESID 187:306)
11X-RAY DIFFRACTION11(CHAIN B AND RESID 307:732)
12X-RAY DIFFRACTION12(CHAIN B AND RESID 733:885)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 886:892)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 893:925)

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