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- PDB-3whk: Crystal structure of PAN-Rpt5C chimera -

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Basic information

Entry
Database: PDB / ID: 3whk
TitleCrystal structure of PAN-Rpt5C chimera
ComponentsProteasome-activating nucleotidase, 26S protease regulatory subunit 6A
KeywordsHYDROLASE / Four-helix bundle / Proteasome ATPase subunit / ATP Binding
Function / homology
Function and homology information


proteasome-activating nucleotidase complex / proteasome regulatory particle assembly / proteasome-activating activity / 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 ...proteasome-activating nucleotidase complex / proteasome regulatory particle assembly / proteasome-activating activity / 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 / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / protein unfolding / proteasomal protein catabolic process / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) ...Proteasome-activating nucleotidase PAN / Helicase, Ruva Protein; domain 3 - #60 / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome regulatory subunit 6A / Proteasome-activating nucleotidase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSatoh, T. / Saeki, Y. / Hiromoto, T. / Wang, Y.-H. / Uekusa, Y. / Yagi, H. / Yoshihara, H. / Yagi-Utsumi, M. / Mizushima, T. / Tanaka, K. / Kato, K.
CitationJournal: Structure / Year: 2014
Title: Structural basis for proteasome formation controlled by an assembly chaperone nas2.
Authors: Satoh, T. / Saeki, Y. / Hiromoto, T. / Wang, Y.H. / Uekusa, Y. / Yagi, H. / Yoshihara, H. / Yagi-Utsumi, M. / Mizushima, T. / Tanaka, K. / Kato, K.
History
DepositionAug 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
B: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
C: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
D: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
E: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
F: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
G: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
H: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,24416
Polymers240,1868
Non-polymers4,0578
Water1,49583
1
A: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5302
Polymers30,0231
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.04, 85.76, 105.26
Angle α, β, γ (deg.)90.04, 90.03, 89.89
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAAA168 - 4244 - 260
21ALAALABB168 - 4244 - 260
12LYSLYSAA168 - 4284 - 264
22LYSLYSCC168 - 4284 - 264
13LYSLYSAA168 - 4264 - 262
23LYSLYSDD168 - 4264 - 262
14SERSERAA168 - 4294 - 265
24SERSEREE168 - 4294 - 265
15ALAALAAA168 - 4244 - 260
25ALAALAFF168 - 4244 - 260
16LYSLYSAA168 - 4284 - 264
26LYSLYSGG168 - 4284 - 264
17LYSLYSAA168 - 4264 - 262
27LYSLYSHH168 - 4264 - 262
18ALAALABB168 - 4244 - 260
28ALAALACC168 - 4244 - 260
19ALAALABB168 - 4244 - 260
29ALAALADD168 - 4244 - 260
110ALAALABB168 - 4244 - 260
210ALAALAEE168 - 4244 - 260
111ARGARGBB168 - 4254 - 261
211ARGARGFF168 - 4254 - 261
112ALAALABB168 - 4244 - 260
212ALAALAGG168 - 4244 - 260
113ALAALABB168 - 4244 - 260
213ALAALAHH168 - 4244 - 260
114SERSERCC168 - 4274 - 263
214SERSERDD168 - 4274 - 263
115LYSLYSCC168 - 4284 - 264
215LYSLYSEE168 - 4284 - 264
116ALAALACC168 - 4244 - 260
216ALAALAFF168 - 4244 - 260
117LYSLYSCC168 - 4284 - 264
217LYSLYSGG168 - 4284 - 264
118SERSERCC168 - 4274 - 263
218SERSERHH168 - 4274 - 263
119SERSERDD168 - 4274 - 263
219SERSEREE168 - 4274 - 263
120ALAALADD168 - 4244 - 260
220ALAALAFF168 - 4244 - 260
121SERSERDD168 - 4274 - 263
221SERSERGG168 - 4274 - 263
122SERSERDD168 - 4274 - 263
222SERSERHH168 - 4274 - 263
123ALAALAEE168 - 4244 - 260
223ALAALAFF168 - 4244 - 260
124LYSLYSEE168 - 4284 - 264
224LYSLYSGG168 - 4284 - 264
125LYSLYSEE168 - 4264 - 262
225LYSLYSHH168 - 4264 - 262
126ALAALAFF168 - 4244 - 260
226ALAALAGG168 - 4244 - 260
127ALAALAFF168 - 4244 - 260
227ALAALAHH168 - 4244 - 260
128SERSERGG168 - 4274 - 263
228SERSERHH168 - 4274 - 263

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Proteasome-activating nucleotidase, 26S protease regulatory subunit 6A / PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle / Tat- ...PAN / Proteasomal ATPase / Proteasome regulatory ATPase / Proteasome regulatory particle / Tat-binding protein homolog 1 / TBP-1


Mass: 30023.271 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Fusion protein of residues 125-309 FROM Proteasome-activating nucleotidase (PAN, UNP Q8U4H3), linker (EF), and residues 356-434 from 26S protease regulatory subunit 6A (Rpt5, UNP P33297).
Source: (gene. exp.) Pyrococcus furiosus (archaea), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: DSM 3638, S288c / Gene: pan, PF0115, O3258, RPT5, YOR117W, YOR3258W, YTA1 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q8U4H3, UniProt: P33297
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8% PEG3350, 0.1M Bis-Tris (pH6.0), 0.1M magnesium formate, 3mM CHAPSO, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 18, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 76400 / Num. obs: 73505 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3769 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H4M

3h4m


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.921 / SU B: 13.635 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R: 0.968 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 3681 5 %RANDOM
Rwork0.242 ---
all0.243 69725 --
obs0.243 69725 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.513 Å2
Baniso -1Baniso -2Baniso -3
1-7.03 Å2-0.18 Å2-0.76 Å2
2---0.55 Å2-0.67 Å2
3----6.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15342 0 248 83 15673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01915846
X-RAY DIFFRACTIONr_bond_other_d0.0040.0215537
X-RAY DIFFRACTIONr_angle_refined_deg1.4712.00321448
X-RAY DIFFRACTIONr_angle_other_deg1.075335789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85551940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.92224.563732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.312152845
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.89315127
X-RAY DIFFRACTIONr_chiral_restr0.0810.22426
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117571
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023344
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A157200.04
12B157200.04
21A158420.04
22C158420.04
31A157490.05
32D157490.05
41A161020
42E161020
51A157090.04
52F157090.04
61A158860.04
62G158860.04
71A158990.04
72H158990.04
81B155710.04
82C155710.04
91B155880.04
92D155880.04
101B156650.03
102E156650.03
111B159680.01
112F159680.01
121B156120.03
122G156120.03
131B157450.03
132H157450.03
141C157450.05
142D157450.05
151C157850.04
152E157850.04
161C155600.04
162F155600.04
171C159490.03
172G159490.03
181C158510.03
182H158510.03
191D157160.05
192E157160.05
201D155810.04
202F155810.04
211D157320.04
212G157320.04
221D158440.04
222H158440.04
231E156540.04
232F156540.04
241E158300.03
242G158300.03
251E158420.04
252H158420.04
261F156030.03
262G156030.03
271F157360.03
272H157360.03
281G158080.03
282H158080.03
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 256 -
Rwork0.343 4977 -
obs--95.28 %

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