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- PDB-4v7o: Proteasome Activator Complex -

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Basic information

Entry
Database: PDB / ID: 4v7o
TitleProteasome Activator Complex
Components
  • (Proteasome activator ...) x 3
  • (Proteasome component ...) x 14
KeywordsHYDROLASE / 20S Proteasome BLM10 / Nucleus / Phosphoprotein / Protease / Proteasome / Threonine protease / Isopeptide bond / Zymogen
Function / homology
Function and homology information


proteasome core complex import into nucleus / proteasome storage granule assembly => GO:1902906 / : / UCH proteinases / peptidase activator activity / 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 ...proteasome core complex import into nucleus / proteasome storage granule assembly => GO:1902906 / : / UCH proteinases / peptidase activator activity / 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 binding / 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 / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / proteasomal protein catabolic process / lysine-acetylated histone binding / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / DNA repair / mRNA binding / DNA damage response / endoplasmic reticulum membrane / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / Domain of unknown function (DUF3437) / Proteasome-substrate-size regulator, mid region / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 ...Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / Domain of unknown function (DUF3437) / Proteasome-substrate-size regulator, mid region / 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 / Armadillo-type fold
Similarity search - Domain/homology
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 ...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 / Proteasome activator BLM10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.005 Å
AuthorsHill, C.P. / Whitby, F.G.
CitationJournal: Mol.Cell / Year: 2010
Title: Structure of a Blm10 complex reveals common mechanisms for proteasome binding and gate opening.
Authors: Sadre-Bazzaz, K. / Whitby, F.G. / Robinson, H. / Formosa, T. / Hill, C.P.
History
DepositionDec 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 1VSY, 3L5Q
Revision 1.1Dec 10, 2014Group: Other
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Proteasome component C7-alpha
AG: Proteasome component Y7
AH: Proteasome component Y13
AI: Proteasome component PRE6
AJ: Proteasome component PUP2
AK: Proteasome component PRE5
AL: Proteasome component C1
AB: Proteasome component PRE3
AM: Proteasome component PUP1
AN: Proteasome component PUP3
AO: Proteasome component C11
AP: Proteasome component PRE2
AQ: Proteasome component C5
AR: Proteasome component PRE4
AC: Proteasome component C7-alpha
AS: Proteasome component Y7
AT: Proteasome component Y13
AU: Proteasome component PRE6
AV: Proteasome component PUP2
AW: Proteasome component PRE5
AX: Proteasome component C1
AD: Proteasome component PRE3
AY: Proteasome component PUP1
AZ: Proteasome component PUP3
A1: Proteasome component C11
A2: Proteasome component PRE2
A3: Proteasome component C5
A4: Proteasome component PRE4
AE: Proteasome activator BLM10
A5: Proteasome activator BLM10
A6: Proteasome activator BLM10
AF: Proteasome activator BLM10
A7: Proteasome activator BLM10
A8: Proteasome activator BLM10
BA: Proteasome component C7-alpha
BB: Proteasome component Y7
BC: Proteasome component Y13
BD: Proteasome component PRE6
BE: Proteasome component PUP2
BF: Proteasome component PRE5
BG: Proteasome component C1
BH: Proteasome component PRE3
BI: Proteasome component PUP1
BJ: Proteasome component PUP3
BK: Proteasome component C11
BL: Proteasome component PRE2
BM: Proteasome component C5
BN: Proteasome component PRE4
BO: Proteasome component C7-alpha
BP: Proteasome component Y7
BQ: Proteasome component Y13
BR: Proteasome component PRE6
BS: Proteasome component PUP2
BT: Proteasome component PRE5
BU: Proteasome component C1
BV: Proteasome component PRE3
BW: Proteasome component PUP1
BX: Proteasome component PUP3
BY: Proteasome component C11
BZ: Proteasome component PRE2
B1: Proteasome component C5
B2: Proteasome component PRE4
B3: Proteasome activator BLM10
B4: Proteasome activator BLM10
B5: Proteasome activator BLM10
B6: Proteasome activator BLM10
B7: Proteasome activator BLM10
B8: Proteasome activator BLM10


Theoretical massNumber of molelcules
Total (without water)2,258,05568
Polymers2,258,05568
Non-polymers00
Water0
1
AA: Proteasome component C7-alpha
AG: Proteasome component Y7
AH: Proteasome component Y13
AI: Proteasome component PRE6
AJ: Proteasome component PUP2
AK: Proteasome component PRE5
AL: Proteasome component C1
AB: Proteasome component PRE3
AM: Proteasome component PUP1
AN: Proteasome component PUP3
AO: Proteasome component C11
AP: Proteasome component PRE2
AQ: Proteasome component C5
AR: Proteasome component PRE4
AC: Proteasome component C7-alpha
AS: Proteasome component Y7
AT: Proteasome component Y13
AU: Proteasome component PRE6
AV: Proteasome component PUP2
AW: Proteasome component PRE5
AX: Proteasome component C1
AD: Proteasome component PRE3
AY: Proteasome component PUP1
AZ: Proteasome component PUP3
A1: Proteasome component C11
A2: Proteasome component PRE2
A3: Proteasome component C5
A4: Proteasome component PRE4
AE: Proteasome activator BLM10
A5: Proteasome activator BLM10
A6: Proteasome activator BLM10
AF: Proteasome activator BLM10
A7: Proteasome activator BLM10
A8: Proteasome activator BLM10


Theoretical massNumber of molelcules
Total (without water)1,129,02834
Polymers1,129,02834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BA: Proteasome component C7-alpha
BB: Proteasome component Y7
BC: Proteasome component Y13
BD: Proteasome component PRE6
BE: Proteasome component PUP2
BF: Proteasome component PRE5
BG: Proteasome component C1
BH: Proteasome component PRE3
BI: Proteasome component PUP1
BJ: Proteasome component PUP3
BK: Proteasome component C11
BL: Proteasome component PRE2
BM: Proteasome component C5
BN: Proteasome component PRE4
BO: Proteasome component C7-alpha
BP: Proteasome component Y7
BQ: Proteasome component Y13
BR: Proteasome component PRE6
BS: Proteasome component PUP2
BT: Proteasome component PRE5
BU: Proteasome component C1
BV: Proteasome component PRE3
BW: Proteasome component PUP1
BX: Proteasome component PUP3
BY: Proteasome component C11
BZ: Proteasome component PRE2
B1: Proteasome component C5
B2: Proteasome component PRE4
B3: Proteasome activator BLM10
B4: Proteasome activator BLM10
B5: Proteasome activator BLM10
B6: Proteasome activator BLM10
B7: Proteasome activator BLM10
B8: Proteasome activator BLM10


Theoretical massNumber of molelcules
Total (without water)1,129,02834
Polymers1,129,02834
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.116, 127.739, 532.668
Angle α, β, γ (deg.)90.000, 102.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21F
31K
41L
12A
22C
32G
42I
13B
23D
33H
43J

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AE or chain A5 or chain A6AE79 - 154
121chain AE or chain A5 or chain A6A5239 - 1037
131chain AE or chain A5 or chain A6A61147 - 2143
211chain AF or chain A7 or chain A8AF79 - 154
221chain AF or chain A7 or chain A8A7239 - 1037
231chain AF or chain A7 or chain A8A81147 - 2143
311chain B3 or chain B4 or chain B5B379 - 154
321chain B3 or chain B4 or chain B5B4239 - 1037
331chain B3 or chain B4 or chain B5B51147 - 2143
411chain B6 or chain B7 or chain B8B679 - 154
421chain B6 or chain B7 or chain B8B7239 - 1037
431chain B6 or chain B7 or chain B8B81147 - 2143
112chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAA1010 - 1252
122chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAG2020 - 2250
132chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAH3014 - 3245
142chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAI4017 - 4243
152chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAJ5001 - 5250
162chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAK6001 - 6234
172chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK or chain ALAL7004 - 7247
212chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAC1010 - 1252
222chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAS - AT2020 - 2250
232chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAT3014 - 3245
242chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAU4017 - 4243
252chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAV5001 - 5250
262chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAW6001 - 6234
272chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AXAX7004 - 7247
312chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBA1010 - 1252
322chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBB2020 - 2250
332chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBC3014 - 3245
342chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBD4017 - 4243
352chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBE5001 - 5250
362chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBF6001 - 6234
372chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BGBG7004 - 7247
412chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBO1010 - 1252
422chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBP2020 - 2250
432chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBQ3014 - 3245
442chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBR4017 - 4243
452chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBS5001 - 5250
462chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBT6001 - 6234
472chain BO or chain BP or chain BQ or chain BR or chain BS or chain BT or chain BUBU7004 - 7247
113chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAB1001 - 1196
123chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAM2001 - 2222
133chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAN3001 - 3196
143chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAO4001 - 4197
153chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAP5001 - 5212
163chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAQ6001 - 6213
173chain AB or chain AM or chain AN or chain AO or chain AP or chain AQ or chain ARAR7001 - 7225
213chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4AD1001 - 1196
223chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4AY2001 - 2222
233chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4AZ3001 - 3196
243chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4A14001 - 4197
253chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4A25001 - 5212
263chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4A36001 - 6213
273chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4A47001 - 7225
313chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBH1001 - 1196
323chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBI2001 - 2222
333chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBJ3001 - 3196
343chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBK4001 - 4197
353chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBL5001 - 5212
363chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBM6001 - 6213
373chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BNBN7001 - 7225
413chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2BV1001 - 1196
423chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2BW2001 - 2222
433chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2BX3001 - 3196
443chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2BY4001 - 4197
453chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2BZ5001 - 5212
463chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2B16001 - 6213
473chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2B27001 - 7225

NCS ensembles :
ID
1
2
3
DetailsOne BLM10 molecule caps each end of the 20S proteasome. BLM10 comprises a single polypeptide chain of about 2000 residues.

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Components

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Proteasome component ... , 14 types, 56 molecules AAACBABOAGASBBBPAHATBCBQAIAUBDBRAJAVBEBSAKAWBFBTALAXBGBUABAD...

#1: Protein
Proteasome component C7-alpha / / Macropain subunit C7-alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / ...Macropain subunit C7-alpha / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex C7 / Proteasome component Y8 / SCL1 suppressor protein


Mass: 27316.037 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#2: Protein
Proteasome component Y7 / / Macropain subunit Y7 / Proteinase YSCE subunit 7 / Multicatalytic endopeptidase complex subunit Y7


Mass: 25112.486 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#3: Protein
Proteasome component Y13 / / Macropain subunit Y13 / Proteinase YSCE subunit 13 / Multicatalytic endopeptidase complex subunit Y13


Mass: 25606.820 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#4: Protein
Proteasome component PRE6 / / Macropain subunit PRE6 / Proteinase YSCE subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6


Mass: 25384.691 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#5: Protein
Proteasome component PUP2 / / Macropain subunit PUP2 / Proteinase YSCE subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2


Mass: 27573.982 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#6: Protein
Proteasome component PRE5 / / Macropain subunit PRE5 / Proteinase YSCE subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P40302, proteasome endopeptidase complex
#7: Protein
Proteasome component C1 / / Macropain subunit C1 / Proteinase YSCE subunit 1 / Multicatalytic endopeptidase complex subunit C1


Mass: 26892.482 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#8: Protein
Proteasome component PRE3 / / Macropain subunit PRE3 / Proteinase YSCE subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3


Mass: 21487.158 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P38624, proteasome endopeptidase complex
#9: Protein
Proteasome component PUP1 / / Macropain subunit PUP1 / Proteinase YSCE subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1


Mass: 23987.254 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#10: Protein
Proteasome component PUP3 / / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3


Mass: 22496.645 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#11: Protein
Proteasome component C11 / / Macropain subunit C11 / Proteinase YSCE subunit 11 / Multicatalytic endopeptidase complex subunit C11


Mass: 22545.676 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#12: Protein
Proteasome component PRE2 / / Macropain subunit PRE2 / Proteinase YSCE subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2


Mass: 23353.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#13: Protein
Proteasome component C5 / / Multicatalytic endopeptidase complex subunit C5


Mass: 24883.928 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#14: Protein
Proteasome component PRE4 / / Macropain subunit PRE4 / Proteinase YSCE subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4


Mass: 25945.496 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P30657, proteasome endopeptidase complex

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Proteasome activator ... , 3 types, 12 molecules AEAFB3B6A5A7B4B7A6A8B5B8

#15: Protein
Proteasome activator BLM10 / Bleomycin resistance protein BLM10


Mass: 9103.230 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43583
#16: Protein
Proteasome activator BLM10 / Bleomycin resistance protein BLM10


Mass: 92568.531 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43583
#17: Protein
Proteasome activator BLM10 / Bleomycin resistance protein BLM10


Mass: 114622.109 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43583

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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: 3.47 Å3/Da / Density % sol: 64.54 % / Mosaicity: 0.357 °
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. all: 416217 / Num. obs: 416217 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.103 / Χ2: 1.058 / Net I/σ(I): 8.3
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.314 / Num. unique all: 37221 / Χ2: 0.896 / % possible all: 88.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å30.02 Å
Translation4 Å30.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
PHENIX(phenix.refine)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: yeast 20S proteasome

Resolution: 3.005→29.994 Å / WRfactor Rfree: 0.288 / WRfactor Rwork: 0.223 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.758 / SU ML: 0.36 / SU Rfree: 0.555 / σ(F): 1.34 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4963 1 %thin shells
Rwork0.196 ---
obs0.196 495778 80.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.918 Å2 / ksol: 0.268 e/Å3
Displacement parametersBiso max: 330.49 Å2 / Biso mean: 104.286 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1--20.819 Å20 Å26.618 Å2
2--5.826 Å20 Å2
3---14.993 Å2
Refinement stepCycle: LAST / Resolution: 3.005→29.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms79452 0 0 0 79452
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11AE15229X-RAY DIFFRACTIONPOSITIONAL0.043
12AF15229X-RAY DIFFRACTIONPOSITIONAL0.043
13AK15229X-RAY DIFFRACTIONPOSITIONAL0.043
14AL15229X-RAY DIFFRACTIONPOSITIONAL0.043
21AA12909X-RAY DIFFRACTIONPOSITIONAL0.042
22AC12909X-RAY DIFFRACTIONPOSITIONAL0.042
23AG12909X-RAY DIFFRACTIONPOSITIONAL0.044
24AI12909X-RAY DIFFRACTIONPOSITIONAL0.044
31AB11398X-RAY DIFFRACTIONPOSITIONAL0.045
32AD11398X-RAY DIFFRACTIONPOSITIONAL0.045
33AH11398X-RAY DIFFRACTIONPOSITIONAL0.047
34AJ11398X-RAY DIFFRACTIONPOSITIONAL0.046
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)
10.33990.0293-0.14880.0776-0.00570.23840.0445-0.1761-0.1030.0326-0.0644-0.1789-0.03630.19050.0620.1951-0.0414-0.08360.13960.10780.182850.4322-16.8684-205.4315
20.50860.0687-0.19180.0951-0.04720.1061-0.0146-0.228-0.15950.05470.00260.03390.0047-0.0351-0.03080.2670.0145-0.04490.10170.08980.084511.6533-23.7686-196.5726
30.33230.0726-0.22170.2209-0.04970.24460.0311-0.0435-0.11720.04480.00680.3073-0.0023-0.2849-0.16160.0591-0.03920.07910.15590.2470.3497-60.7712-35.5839-184.7331
40.46690.1379-0.1720.103-0.11880.1363-0.0111-0.1541-0.0980.03370.03910.0164-0.0159-0.04230.01390.20080.0404-0.00110.09540.11630.1389-21.7579-27.5171-191.2031
50.2402-0.1006-0.00050.1976-0.21590.26650.0376-0.24020.0466-0.00130.0648-0.2798-0.10590.31520.17150.2147-0.0662-0.19240.09380.1963-0.083391.08163.9714-210.0513
60.23690.0244-0.13680.0897-0.03250.2227-0.0475-0.0177-0.07390.01780.0169-0.00440.0482-0.1679-0.19460.2618-0.0520.00780.25390.2240.2467-99.4726-49.555-164.3876
70.5285-0.0004-0.16750.0728-0.0180.06940.0013-0.25780.07860.0683-0.04570.198-0.0169-0.276300.3237-0.0781-0.00381.3918-0.05370.3522-50.5514-63.3213-42.9555
80.63920.0296-0.26630.0593-0.00280.1147-0.0681-0.17780.06070.0361-0.02980.05320.035-0.065400.3769-0.1096-0.05061.10370.09950.2406-11.788-64.527-54.19
90.3664-0.0215-0.22750.0707-0.03560.1845-0.0082-0.2178-0.03790.0036-0.0127-0.14530.02470.1942-00.3119-0.14170.00820.9550.13480.288360.6561-68.228-70.5686
100.7176-0.062-0.17340.01480.04260.1087-0.0819-0.25220.07750.0271-0.00670.05470.0319-0.052100.3872-0.1587-0.0420.97750.13730.227121.6239-64.8733-60.7992
110.47110.0538-0.17290.05570.0480.2020.0036-0.21250.30220.10090.05030.2547-0.0637-0.09610.00010.5524-0.0647-0.02021.4987-0.1240.5067-91.2508-47.8248-28.1151
120.31920.0154-0.13680.07810.05340.2229-0.052-0.2433-0.05380.0467-0.0064-0.06860.03680.18460.00190.3574-0.10740.01740.66010.21720.130999.4657-69.4673-95.0834
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain AA or chain AG or chain AH or chain AI or chain AJ or chain AK
2X-RAY DIFFRACTION2chain AB or chain AM or chain AN or chain OO or chain AP or chain AQ or chain AR
3X-RAY DIFFRACTION3chain AC or chain AS or chain AT or chain AU or chain AV or chain AW or chain AX
4X-RAY DIFFRACTION4chain AD or chain AY or chain AZ or chain A1 or chain A2 or chain A3 or chain A4
5X-RAY DIFFRACTION5chain AE or chain A5 or chain A6
6X-RAY DIFFRACTION6chain AF or chain A7 or chain A8
7X-RAY DIFFRACTION7chain BA or chain BB or chain BC or chain BD or chain BE or chain BF or chain BG
8X-RAY DIFFRACTION8chain BH or chain BI or chain BJ or chain BK or chain BL or chain BM or chain BN
9X-RAY DIFFRACTION9chain BO or chain BP or chain BQ or chain BR or chain BS or chain BY or chain BU
10X-RAY DIFFRACTION10chain BV or chain BW or chain BX or chain BY or chain BZ or chain B1 or chain B2
11X-RAY DIFFRACTION11chain B3 or chain B4 or chain B5
12X-RAY DIFFRACTION12chain B6 or chain B7 or chain B8

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