1YAR

Structure of Archeabacterial 20S proteasome mutant D9S- PA26 complex

> Summary

Summary for 1YAR

Related1YA7 1YAU
DescriptorProteasome alpha subunit (E.C.3.4.25.1), Proteasome beta subunit (E.C.3.4.25.1), proteasome activator protein PA26
Functional Keywordsproteasome 20s, pa26 proteasome activator 11s, hydrolase-hydrolase activator complex, hydrolase/hydrolase activator
Biological sourceThermoplasma acidophilum
More
Cellular locationCytoplasm (By similarity) P25156 P28061
Total number of polymer chains21
Total molecular weight533879.96
Authors
Forster, A.,Masters, E.I.,Whitby, F.G.,Robinson, H.,Hill, C.P. (deposition date: 2004-12-17, release date: 2005-07-26, Last modification date: 2011-07-13)
Primary citation
Forster, A.,Masters, E.I.,Whitby, F.G.,Robinson, H.,Hill, C.P.
The 1.9 A structure of a proteasome-11S activator complex and implications for proteasome-PAN/PA700 interactions.
Mol.Cell, 18:589-599, 2005
PubMed: 15916965
DOI: 10.1016/j.molcel.2005.04.016
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.9 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.21360.4%2.4%5.3%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1yar
no rotation
Molmil generated image of 1yar
rotated about x axis by 90°
Molmil generated image of 1yar
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 1yar
no rotation
Molmil generated image of 1yar
rotated about x axis by 90°
Molmil generated image of 1yar
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (1yar.pdb1.gz [1.54 MB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D, E...Proteasome alpha subunitpolymer23325801.67
UniProt (P25156)
Pfam (PF00227)
Pfam (PF10584)
Thermoplasma acidophilumMulticatalytic endopeptidase complex alpha subunit
H, I, J, K, L...Proteasome beta subunitpolymer21723998.87
UniProt (P28061)
Pfam (PF00227)
Thermoplasma acidophilumMulticatalytic endopeptidase complex beta subunit
O, P, Q, R, S...proteasome activator protein PA26polymer23726087.87
GenBank (AAD50581)
Pfam (PF02252)
UniProt (by SIFTS) (Q9U8G2)
Trypanosoma brucei@PDBj
SULFATE IONnon-polymer96.121
GLYCEROLnon-polymer92.17
waterwater18.03470

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains21
Total molecular weight531218.1
Non-Polymers*Number of molecules28
Total molecular weight2661.9
All*Total molecular weight533880.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)

Cell axes254.874127.512181.182
Cell angles90.0092.4590.00
SpacegroupC 1 2 1
Resolution limits47.30 - 1.90
the highest resolution shell value1.949 - 1.899
R-factor0.18196
R-work0.18185
the highest resolution shell value0.237
R-free0.21624
the highest resolution shell value0.263
RMSD bond length0.012
RMSD bond angle1.271

Data Collection Statistics

Resolution limits20.00 - 1.90
the highest resolution shell value -
Number of reflections442007
Rmerge_l_obs0.063
the highest resolution shell value0.497
Completeness97.4
Redundancy5
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP4.2273

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0019773cellular_componentproteasome core complex, alpha-subunit complex
A0004175molecular_functionendopeptidase activity
A0004298molecular_functionthreonine-type endopeptidase activity
A0010498biological_processproteasomal protein catabolic process
A0006511biological_processubiquitin-dependent protein catabolic process
B0005737cellular_componentcytoplasm
B0019773cellular_componentproteasome core complex, alpha-subunit complex
B0004175molecular_functionendopeptidase activity
B0004298molecular_functionthreonine-type endopeptidase activity
B0010498biological_processproteasomal protein catabolic process
B0006511biological_processubiquitin-dependent protein catabolic process
C0005737cellular_componentcytoplasm
C0019773cellular_componentproteasome core complex, alpha-subunit complex
C0004175molecular_functionendopeptidase activity
C0004298molecular_functionthreonine-type endopeptidase activity
C0010498biological_processproteasomal protein catabolic process
C0006511biological_processubiquitin-dependent protein catabolic process
D0005737cellular_componentcytoplasm
D0019773cellular_componentproteasome core complex, alpha-subunit complex
D0004175molecular_functionendopeptidase activity
D0004298molecular_functionthreonine-type endopeptidase activity
D0010498biological_processproteasomal protein catabolic process
D0006511biological_processubiquitin-dependent protein catabolic process
E0005737cellular_componentcytoplasm
E0019773cellular_componentproteasome core complex, alpha-subunit complex
E0004175molecular_functionendopeptidase activity
E0004298molecular_functionthreonine-type endopeptidase activity
E0010498biological_processproteasomal protein catabolic process
E0006511biological_processubiquitin-dependent protein catabolic process
F0005737cellular_componentcytoplasm
F0019773cellular_componentproteasome core complex, alpha-subunit complex
F0004175molecular_functionendopeptidase activity
F0004298molecular_functionthreonine-type endopeptidase activity
F0010498biological_processproteasomal protein catabolic process
F0006511biological_processubiquitin-dependent protein catabolic process
G0005737cellular_componentcytoplasm
G0019773cellular_componentproteasome core complex, alpha-subunit complex
G0004175molecular_functionendopeptidase activity
G0004298molecular_functionthreonine-type endopeptidase activity
G0010498biological_processproteasomal protein catabolic process
G0006511biological_processubiquitin-dependent protein catabolic process
H0005737cellular_componentcytoplasm
H0019774cellular_componentproteasome core complex, beta-subunit complex
H0004175molecular_functionendopeptidase activity
H0004298molecular_functionthreonine-type endopeptidase activity
H0010498biological_processproteasomal protein catabolic process
I0005737cellular_componentcytoplasm
I0019774cellular_componentproteasome core complex, beta-subunit complex
I0004175molecular_functionendopeptidase activity
I0004298molecular_functionthreonine-type endopeptidase activity
I0010498biological_processproteasomal protein catabolic process
J0005737cellular_componentcytoplasm
J0019774cellular_componentproteasome core complex, beta-subunit complex
J0004175molecular_functionendopeptidase activity
J0004298molecular_functionthreonine-type endopeptidase activity
J0010498biological_processproteasomal protein catabolic process
K0005737cellular_componentcytoplasm
K0019774cellular_componentproteasome core complex, beta-subunit complex
K0004175molecular_functionendopeptidase activity
K0004298molecular_functionthreonine-type endopeptidase activity
K0010498biological_processproteasomal protein catabolic process
L0005737cellular_componentcytoplasm
L0019774cellular_componentproteasome core complex, beta-subunit complex
L0004175molecular_functionendopeptidase activity
L0004298molecular_functionthreonine-type endopeptidase activity
L0010498biological_processproteasomal protein catabolic process
M0005737cellular_componentcytoplasm
M0019774cellular_componentproteasome core complex, beta-subunit complex
M0004175molecular_functionendopeptidase activity
M0004298molecular_functionthreonine-type endopeptidase activity
M0010498biological_processproteasomal protein catabolic process
N0005737cellular_componentcytoplasm
N0019774cellular_componentproteasome core complex, beta-subunit complex
N0004175molecular_functionendopeptidase activity
N0004298molecular_functionthreonine-type endopeptidase activity
N0010498biological_processproteasomal protein catabolic process
O0008537cellular_componentproteasome activator complex
O0006508biological_processproteolysis
O0061136biological_processregulation of proteasomal protein catabolic process
P0008537cellular_componentproteasome activator complex
P0006508biological_processproteolysis
P0061136biological_processregulation of proteasomal protein catabolic process
Q0008537cellular_componentproteasome activator complex
Q0006508biological_processproteolysis
Q0061136biological_processregulation of proteasomal protein catabolic process
R0008537cellular_componentproteasome activator complex
R0006508biological_processproteolysis
R0061136biological_processregulation of proteasomal protein catabolic process
S0008537cellular_componentproteasome activator complex
S0006508biological_processproteolysis
S0061136biological_processregulation of proteasomal protein catabolic process
T0008537cellular_componentproteasome activator complex
T0006508biological_processproteolysis
T0061136biological_processregulation of proteasomal protein catabolic process
U0008537cellular_componentproteasome activator complex
U0006508biological_processproteolysis
U0061136biological_processregulation of proteasomal protein catabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC17BINDING SITE FOR RESIDUE SO4 A 4001
ChainResidue
AGLU110
ALYS114
AHOH4049
BILE64
BGLU65
BGLN68
HARG71

AC27BINDING SITE FOR RESIDUE SO4 B 4002
ChainResidue
BGLU110
BLYS114
BHOH4086
CILE64
CGLU65
CGLN68
IARG71

AC36BINDING SITE FOR RESIDUE SO4 C 4003
ChainResidue
CGLU110
CLYS114
DILE64
DGLU65
DGLN68
JARG71

AC45BINDING SITE FOR RESIDUE SO4 D 4004
ChainResidue
DGLU110
DLYS114
EILE64
EGLU65
EGLN68

AC58BINDING SITE FOR RESIDUE SO4 F 4005
ChainResidue
EGLU110
ELYS114
FSER63
FILE64
FGLU65
FGLN68
FHOH4072
LARG71

AC68BINDING SITE FOR RESIDUE SO4 F 4006
ChainResidue
FGLU110
FLYS114
GSER63
GILE64
GGLU65
GGLN68
GHOH4101
MARG71

AC76BINDING SITE FOR RESIDUE SO4 G 4007
ChainResidue
ASER63
AGLU65
GGLU110
GLYS114
GHOH4049
NARG71

AC87BINDING SITE FOR RESIDUE SO4 H 4008
ChainResidue
HTHR1
HGLY47
HGLY128
HSER129
HHOH5063
HHOH5074
HHOH5097

AC98BINDING SITE FOR RESIDUE SO4 N 4009
ChainResidue
NTHR1
NGLY47
NGLY128
NSER129
NHOH5062
NHOH5122
NHOH5173
NHOH5177

BC17BINDING SITE FOR RESIDUE SO4 M 4010
ChainResidue
MTHR1
MGLY47
MGLY128
MSER129
MHOH5147
MHOH5151
MHOH5153

BC29BINDING SITE FOR RESIDUE SO4 I 4011
ChainResidue
ITHR1
IALA46
IGLY47
IGLY128
ISER129
IHOH5073
IHOH5074
IHOH5078
IHOH5158

BC37BINDING SITE FOR RESIDUE SO4 J 4012
ChainResidue
JTHR1
JALA46
JGLY47
JGLY128
JSER129
JHOH5064
JHOH5140

BC49BINDING SITE FOR RESIDUE SO4 K 4013
ChainResidue
KTHR1
KALA46
KGLY47
KGLY128
KSER129
KHOH5066
KHOH5106
KHOH5111
KHOH5163

BC56BINDING SITE FOR RESIDUE SO4 L 4014
ChainResidue
LTHR1
LGLY47
LGLY128
LSER129
LHOH5088
LHOH5107

BC66BINDING SITE FOR RESIDUE SO4 H 4015
ChainResidue
ATYR103
AARG115
HARG70
HHOH5013
HHOH5044
HHOH5067

BC77BINDING SITE FOR RESIDUE SO4 B 4016
ChainResidue
BTYR103
BARG115
BHOH4045
BHOH4056
BHOH4141
IGLN69
IARG70

BC86BINDING SITE FOR RESIDUE SO4 J 4017
ChainResidue
CTYR103
CARG115
JARG70
JHOH5021
JHOH5036
JHOH5097

BC97BINDING SITE FOR RESIDUE SO4 K 4018
ChainResidue
DTYR103
DARG115
KGLN69
KARG70
KHOH5028
KHOH5048
KHOH5073

CC16BINDING SITE FOR RESIDUE SO4 L 4019
ChainResidue
ETYR103
EARG115
LARG70
LHOH5047
LHOH5054
LHOH5154

CC26BINDING SITE FOR RESIDUE SO4 M 4020
ChainResidue
FTYR103
FARG115
MARG70
MHOH5028
MHOH5086
MHOH5097

CC37BINDING SITE FOR RESIDUE SO4 N 4021
ChainResidue
GTYR103
GARG115
NGLN69
NARG70
NHOH5033
NHOH5093
NHOH5110

CC46BINDING SITE FOR RESIDUE GOL L 5001
ChainResidue
LGLN53
LARG57
LLYS60
LHOH5056
LHOH5137
LHOH5139

CC56BINDING SITE FOR RESIDUE GOL M 5002
ChainResidue
MGLN53
MARG57
MLYS60
MHOH5034
MHOH5107
NHOH5089

CC66BINDING SITE FOR RESIDUE GOL N 5003
ChainResidue
NGLN53
NVAL56
NARG57
NLYS60
NHOH5058
NHOH5092

CC76BINDING SITE FOR RESIDUE GOL H 5004
ChainResidue
HGLN53
HARG57
HLYS60
HHOH5043
HHOH5156
IHOH5069

CC87BINDING SITE FOR RESIDUE GOL I 5005
ChainResidue
IGLN53
IVAL56
IARG57
ILYS60
IHOH5046
IHOH5072
IHOH5131

CC97BINDING SITE FOR RESIDUE GOL J 5006
ChainResidue
JGLN53
JVAL56
JARG57
JLYS60
JHOH5092
JHOH5099
KHOH5088

DC17BINDING SITE FOR RESIDUE GOL K 5007
ChainResidue
KGLN53
KVAL56
KARG57
KLYS60
KHOH5064
KHOH5097
LHOH5135

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
GOL_1yar_H_50046GLYCEROL binding site
ChainResidueligand
HPHE35GOL: GLYCEROL
HGLN53GOL: GLYCEROL
HVAL56-ARG57GOL: GLYCEROL
HLYS60GOL: GLYCEROL
ITHR81GOL: GLYCEROL

GOL_1yar_N_50036GLYCEROL binding site
ChainResidueligand
HTHR81GOL: GLYCEROL
NPHE35GOL: GLYCEROL
NGLN53GOL: GLYCEROL
NVAL56-ARG57GOL: GLYCEROL
NLYS60GOL: GLYCEROL

GOL_1yar_I_50056GLYCEROL binding site
ChainResidueligand
IPHE35GOL: GLYCEROL
IGLN53GOL: GLYCEROL
IVAL56-ARG57GOL: GLYCEROL
ILYS60GOL: GLYCEROL
JTHR81GOL: GLYCEROL

GOL_1yar_J_50066GLYCEROL binding site
ChainResidueligand
JPHE35GOL: GLYCEROL
JGLN53GOL: GLYCEROL
JVAL56-ARG57GOL: GLYCEROL
JLYS60GOL: GLYCEROL
KTHR81GOL: GLYCEROL

GOL_1yar_K_50077GLYCEROL binding site
ChainResidueligand
KPHE35GOL: GLYCEROL
KGLN53GOL: GLYCEROL
KVAL56-ARG57GOL: GLYCEROL
KLYS60GOL: GLYCEROL
LTHR81GOL: GLYCEROL
LSER119GOL: GLYCEROL

GOL_1yar_L_50016GLYCEROL binding site
ChainResidueligand
LPHE35GOL: GLYCEROL
LGLN53GOL: GLYCEROL
LVAL56-ARG57GOL: GLYCEROL
LLYS60GOL: GLYCEROL
MTHR81GOL: GLYCEROL

GOL_1yar_M_50026GLYCEROL binding site
ChainResidueligand
MPHE35GOL: GLYCEROL
MGLN53GOL: GLYCEROL
MVAL56-ARG57GOL: GLYCEROL
MLYS60GOL: GLYCEROL
NTHR81GOL: GLYCEROL

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11Nucleophile.
ChainResidueDetails
HTHR9

SWS_FT_FI21Nucleophile.
ChainResidueDetails
ITHR9

SWS_FT_FI31Nucleophile.
ChainResidueDetails
JTHR9

SWS_FT_FI41Nucleophile.
ChainResidueDetails
KTHR9

SWS_FT_FI51Nucleophile.
ChainResidueDetails
LTHR9

SWS_FT_FI61Nucleophile.
ChainResidueDetails
MTHR9

SWS_FT_FI71Nucleophile.
ChainResidueDetails
NTHR9

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA14Annotated By Reference To The Literature 1pma
ChainResidueDetails
HGLY47
HLYS33
HTHR1
HSER129

CSA24Annotated By Reference To The Literature 1pma
ChainResidueDetails
IGLY47
ILYS33
ITHR1
ISER129

CSA34Annotated By Reference To The Literature 1pma
ChainResidueDetails
JGLY47
JLYS33
JTHR1
JSER129

CSA44Annotated By Reference To The Literature 1pma
ChainResidueDetails
KGLY47
KLYS33
KTHR1
KSER129

CSA54Annotated By Reference To The Literature 1pma
ChainResidueDetails
LGLY47
LLYS33
LTHR1
LSER129

CSA64Annotated By Reference To The Literature 1pma
ChainResidueDetails
MGLY47
MLYS33
MTHR1
MSER129

CSA74Annotated By Reference To The Literature 1pma
ChainResidueDetails
NGLY47
NLYS33
NTHR1
NSER129

CSA84Annotated By Reference To The Literature 1pma
ChainResidueDetails
AGLY80
ASER35
ASER167
ALYS66

CSA94Annotated By Reference To The Literature 1pma
ChainResidueDetails
BGLY80
BSER35
BSER167
BLYS66

CSA104Annotated By Reference To The Literature 1pma
ChainResidueDetails
CGLY80
CSER35
CSER167
CLYS66

CSA114Annotated By Reference To The Literature 1pma
ChainResidueDetails
DGLY80
DSER35
DSER167
DLYS66

CSA124Annotated By Reference To The Literature 1pma
ChainResidueDetails
EGLY80
ESER35
ESER167
ELYS66

CSA134Annotated By Reference To The Literature 1pma
ChainResidueDetails
FGLY80
FSER35
FSER167
FLYS66

CSA144Annotated By Reference To The Literature 1pma
ChainResidueDetails
GGLY80
GSER35
GSER167
GLYS66

> Sequence Neighbor

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