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- PDB-5lf1: Human 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom -

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Basic information

Entry
Database: PDB / ID: 5lf1
TitleHuman 20S proteasome complex with Dihydroeponemycin at 2.0 Angstrom
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
KeywordsHYDROLASE / Proteasome / Multicatalytic Proteinase / NTN-Hydrolase
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / CD8-positive, alpha-beta T cell homeostasis / Antigen processing: Ub, ATP-independent proteasomal degradation / T-helper 1 cell differentiation / negative regulation of regulatory T cell differentiation / cellular response to type I interferon / Regulation of ornithine decarboxylase (ODC) / proteasome core complex ...purine ribonucleoside triphosphate binding / CD8-positive, alpha-beta T cell differentiation / thymic T cell selection / CD8-positive, alpha-beta T cell homeostasis / Antigen processing: Ub, ATP-independent proteasomal degradation / T-helper 1 cell differentiation / negative regulation of regulatory T cell differentiation / cellular response to type I interferon / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / T-helper 17 cell differentiation / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / flagellated sperm motility / myofibril / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / SPOP-mediated proteasomal degradation of PD-L1(CD274) / proteasomal ubiquitin-independent protein catabolic process / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / proteasome storage granule / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / immune system process / regulation of G1/S transition of mitotic cell cycle / ciliary tip / response to type II interferon / positive regulation of interleukin-2 production / regulation of proteasomal protein catabolic process / : / proteasome complex / sarcomere / proteasomal protein catabolic process / Regulation of activated PAK-2p34 by proteasome mediated degradation / sperm end piece / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / negative regulation of inflammatory response to antigenic stimulus / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / lipopolysaccharide binding / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / P-body / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / meiotic cell cycle / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Hedgehog 'on' state / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / MAPK6/MAPK4 signaling / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / response to virus / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / nuclear matrix / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Interleukin-1 signaling / positive regulation of type II interferon production / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of tumor necrosis factor production / Separation of Sister Chromatids / UCH proteinases / KEAP1-NFE2L2 pathway / peptidase activity
Similarity search - Function
Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 ...Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / 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 B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6VC / : / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 ...Chem-6VC / : / Proteasome subunit alpha type-7 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSchrader, J. / Henneberg, F. / Mata, R. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationCH1098/1-1 Germany
German Research FoundationSFB860-TP A5 Germany
Bundesministerium fuer Bildung und Forschung05K2013-624 Germany
CitationJournal: Science / Year: 2016
Title: The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.
Authors: Schrader, J. / Henneberg, F. / Mata, R.A. / Tittmann, K. / Schneider, T.R. / Stark, H. / Bourenkov, G. / Chari, A.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.type / _database_2.pdbx_DOI ..._chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _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
Revision 2.0Oct 1, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha type-2
B: Proteasome subunit alpha type-4
C: Proteasome subunit alpha type-7
D: Proteasome subunit alpha type-5
E: Proteasome subunit alpha type-1
F: Proteasome subunit alpha type-3
G: Proteasome subunit alpha type-6
H: Proteasome subunit beta type-7
I: Proteasome subunit beta type-3
J: Proteasome subunit beta type-2
K: Proteasome subunit beta type-5
L: Proteasome subunit beta type-1
M: Proteasome subunit beta type-4
N: Proteasome subunit beta type-6
O: Proteasome subunit alpha type-2
P: Proteasome subunit alpha type-4
Q: Proteasome subunit alpha type-7
R: Proteasome subunit alpha type-5
S: Proteasome subunit alpha type-1
T: Proteasome subunit alpha type-3
U: Proteasome subunit alpha type-6
V: Proteasome subunit beta type-7
W: Proteasome subunit beta type-3
X: Proteasome subunit beta type-2
Y: Proteasome subunit beta type-5
Z: Proteasome subunit beta type-1
a: Proteasome subunit beta type-4
b: Proteasome subunit beta type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)726,015115
Polymers718,98128
Non-polymers7,03587
Water65,2323621
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area126380 Å2
ΔGint-1130 kcal/mol
Surface area210060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.890, 203.490, 316.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21O
12B
22P
13C
23Q
14D
24R
15E
25S
16F
26T
17G
27U
18H
28V
19I
29W
110J
210X
111K
211Y
112L
212Z
113M
213a
114N
214b

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGILEILEAA3 - 2324 - 233
21ARGARGILEILEOO3 - 2324 - 233
12SERSERARGARGBB2 - 2492 - 249
22SERSERARGARGPP2 - 2492 - 249
13SERSERGLUGLUCC2 - 2372 - 237
23SERSERGLUGLUQQ2 - 2372 - 237
14ASPASPILEILEDD9 - 2419 - 241
24ASPASPILEILERR9 - 2419 - 241
15ASNASNLEULEUEE4 - 2364 - 236
25ASNASNLEULEUSS4 - 2364 - 236
16GLYGLYLEULEUFF6 - 2437 - 244
26GLYGLYLEULEUTT6 - 2437 - 244
17SERSERARGARGGG2 - 2452 - 245
27SERSERARGARGUU2 - 2452 - 245
18THRTHRGLUGLUHH1 - 2201 - 220
28THRTHRGLUGLUVV1 - 2201 - 220
19SERSERASPASPII1 - 2042 - 205
29SERSERASPASPWW1 - 2042 - 205
110METMETPHEPHEJJ1 - 1961 - 196
210METMETPHEPHEXX1 - 1961 - 196
111THRTHRTYRTYRKK1 - 1991 - 199
211THRTHRTYRTYRYY1 - 1991 - 199
112ARGARGASPASPLL1 - 2131 - 213
212ARGARGASPASPZZ1 - 2131 - 213
113THRTHRSERSERMM1 - 2161 - 216
213THRTHRSERSERaAA1 - 2161 - 216
114THRTHRTHRTHRNN1 - 2011 - 201
214THRTHRTHRTHRbBA1 - 2011 - 201

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14

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Components

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Proteasome subunit alpha type- ... , 7 types, 14 molecules AOBPCQDRESFTGU

#1: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25787, proteasome endopeptidase complex
#2: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25789, proteasome endopeptidase complex
#3: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27986.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: O14818, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28066, proteasome endopeptidase complex
#5: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29720.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25786, proteasome endopeptidase complex
#6: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P25788, proteasome endopeptidase complex
#7: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27739.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P60900, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYLZMaNb

#8: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: Q99436, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P49720, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22989.402 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P49721, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28074, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P20618, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28070, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HELA
References: UniProt: P28072, proteasome endopeptidase complex

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Non-polymers , 6 types, 3708 molecules

#15: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: Cl
#16: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#17: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#18: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#19: Chemical
ChemComp-6VC / ~{N}-[(2~{S})-1-[[(2~{S},3~{R},4~{S})-2,6-dimethyl-1,2,3-tris(oxidanyl)heptan-4-yl]amino]-3-oxidanyl-1-oxidanylidene-propan-2-yl]-6-methyl-heptanamide / Dihydroeponemycin bound form


Mass: 404.541 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H40N2O6
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3621 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris, 0.2 M Magnesium Chloride, 10 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 20, 2015 / Details: CRL Transfocator
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→171.09 Å / Num. obs: 464668 / % possible obs: 99.5 % / Redundancy: 9.43 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 1 / CC1/2: 0.39 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LE5

5le5


Resolution: 2→171.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 10.455 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21275 24379 5 %RANDOM
Rwork0.17788 ---
obs0.1796 464668 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.785 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0 Å20 Å2
2--0.74 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→171.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47874 0 384 3621 51879
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01949427
X-RAY DIFFRACTIONr_bond_other_d0.0050.0247001
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.97166879
X-RAY DIFFRACTIONr_angle_other_deg1.2833107865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09356302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97323.7112126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.403158262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.92915340
X-RAY DIFFRACTIONr_chiral_restr0.1090.27564
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0256165
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0211203
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_it1.0572.1425035
X-RAY DIFFRACTIONr_mcbond_other1.0572.1425034
X-RAY DIFFRACTIONr_mcangle_it1.7213.20231276
X-RAY DIFFRACTIONr_mcangle_other1.7213.20231277
X-RAY DIFFRACTIONr_scbond_it1.6942.36924392
X-RAY DIFFRACTIONr_scbond_other1.6942.36924392
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5093.46135564
X-RAY DIFFRACTIONr_long_range_B_refined8.13318.81256547
X-RAY DIFFRACTIONr_long_range_B_other8.13318.81356548
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)
11A258240.07
12O258240.07
21B275940.08
22P275940.08
31C249660.1
32Q249660.1
41D261780.08
42R261780.08
51E271700.08
52S271700.08
61F278760.08
62T278760.08
71G263700.09
72U263700.09
81H251200.07
82V251200.07
91I256020.07
92W256020.07
101J245080.08
102X245080.08
111K232120.09
112Y232120.09
121L245260.06
122Z245260.06
131M248100.08
132a248100.08
141N234360.08
142b234360.08
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 1683 -
Rwork0.364 32360 -
obs--94.38 %
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)
11.42950.40140.48951.67690.08971.6371-0.02540.11630.0635-0.1497-0.0659-0.3920.09010.57580.09130.29360.13910.08580.26610.06450.182977.1177207.02271.1961
20.75670.01070.02511.5454-0.33621.2968-0.07280.1732-0.1329-0.1958-0.0258-0.31810.38060.3380.09860.61550.17560.06930.1469-0.01870.18665.0325178.06470.1807
31.76180.26860.22822.4554-0.11931.27570.01860.0078-0.5324-0.16430.0417-0.06560.49940.0057-0.06030.7037-0.0888-0.06510.1466-0.00780.26534.0892170.1735-3.8112
40.5912-0.1653-0.96191.2494-0.1051.9277-0.02760.1523-0.1898-0.1897-0.02030.2060.3365-0.44220.04790.5598-0.1569-0.16870.36180.06560.281310.3191188.9789-7.8462
51.873-0.3310.03130.80710.02961.43260.05080.1309-0.2749-0.088-0.02090.22940.1711-0.4926-0.02990.3074-0.0686-0.06790.22760.05010.17049.831219.904-9
61.3317-0.6048-0.03451.7403-0.02481.01940.01530.11440.2032-0.15-0.02820.1399-0.0926-0.12890.01290.21750.0033-0.02360.06260.0510.146732.394240.101-7.584
70.92240.14460.16781.94090.45171.26560.04450.19980.2387-0.2551-0.0748-0.1913-0.16610.31820.03030.22640.00740.05490.15020.09520.172864.017233.587-3.672
80.2242-0.074-0.07631.3402-0.22160.88470.0024-0.0295-0.10250.0423-0.1022-0.12920.05930.41150.09980.2004-0.02320.03940.23630.06330.126771.352213.93239.439
90.35390.25530.51431.1018-0.56521.89640.01320.0465-0.0197-0.1133-0.1611-0.12620.19880.43740.1480.32120.14310.06170.19930.0670.098566.571186.51839.549
100.87410.3865-0.15450.9328-0.3842.6443-0.06280.0787-0.0949-0.19230.02180.14220.5542-0.1090.0410.5122-0.0094-0.0130.015100.132539.129170.26536.27
110.9528-0.1483-0.63971.52650.29622.1656-0.00220.1378-0.1223-0.18240.05230.15410.418-0.4482-0.05010.3772-0.2328-0.12480.26270.11790.20368.034180.78332.228
120.84740.1566-0.4011.20410.24710.8710.0082-0.02870.0253-0.09190.06770.2991-0.0125-0.489-0.07590.2413-0.0664-0.05730.47990.17740.2179-1.575210.26930.853
130.85950.29530.07450.90110.30621.8285-0.03820.02670.11880.06450.10410.1559-0.3423-0.387-0.0660.25810.10580.04380.16330.09140.150316.302237.92133.116
141.603-0.25480.24821.0467-0.10112.03780.02850.05380.0770.0515-0.05980.0098-0.38850.09980.03130.3012-0.06280.02110.02130.01540.076848.774241.43535.653
151.2676-0.06080.43371.5358-0.11991.6837-0.0113-0.11690.27030.13180.00920.4371-0.3503-0.53230.00210.41710.22470.17540.5520.10020.3516-7.241225.984103.023
160.91180.27170.14911.31220.44241.2178-0.0328-0.2020.05990.19120.03430.442-0.0199-0.6539-0.00150.31910.01060.12680.62060.19640.3521-8.293195.55105.0215
172.40290.36640.13242.17760.471.91290.0462-0.0667-0.57780.16930.03280.31840.4915-0.416-0.0790.4268-0.06830.01720.32660.12160.35715.399175.1908109.833
180.58960.0758-0.32320.91880.11222.1394-0.0755-0.1564-0.18980.02750.06760.12880.25150.05810.0080.32010.00810.03140.21590.05890.176645.6665181.8931113.1424
191.5396-0.351-0.03041.1241-0.17511.6619-0.0792-0.2541-0.10080.2477-0.0013-0.1615-0.06680.50250.08040.384-0.0963-0.01220.2930.01790.120558.9111210.3988114.2055
202.02540.6599-0.50541.5216-0.03861.3110.142-0.3220.13720.1961-0.0644-0.206-0.50920.2759-0.07760.6581-0.08550.04650.159-0.04590.146147.318238.2877111.8982
211.31630.15850.01471.4497-0.31030.9919-0.0243-0.21820.41370.22480.0220.0908-0.489-0.14960.00230.68370.21430.12680.2807-0.02730.265716.6547245.5235107.5566
220.82930.43470.1431.2232-0.01350.80490.0167-0.0413-0.02340.08540.0980.1943-0.1656-0.4977-0.11470.33370.18880.12660.37450.12060.21281.5994231.05565.2345
230.49260.07850.46420.9740.53921.7180.0013-0.00870.04180.01040.10540.1904-0.1086-0.6546-0.10660.2128-0.01120.04920.52450.21450.264-6.1314203.726665.3626
240.7601-0.0774-0.12181.03940.17331.9008-0.0542-0.0692-0.08750.00530.13070.02950.3711-0.2252-0.07650.3028-0.1668-0.02890.20040.11530.211711.4985177.209268.7888
251.31670.3787-0.64871.25210.00332.2117-0.0371-0.2189-0.09090.0348-0.04340.00940.44560.1470.08050.32450.0379-0.00670.06180.05120.093644.0185173.39873.0344
260.8664-0.1198-0.52991.1958-0.03351.42050.026-0.0694-0.00340.0449-0.1234-0.16430.07450.45880.09730.1990.00230.00880.21630.05930.103165.7458196.136974.1563
270.7185-0.0344-0.06081.1631-0.56621.9123-0.0019-0.0660.06110.1471-0.0767-0.1004-0.35310.35250.07860.3089-0.12370.00050.1246-0.00390.087260.9145228.914271.1449
281.59070.00130.01971.0419-0.19391.8937-0.0071-0.07560.09950.17030.01260.0549-0.4857-0.0398-0.00550.48790.0640.06640.0257-0.02140.133.0828246.025868.0247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 232
2X-RAY DIFFRACTION2B2 - 249
3X-RAY DIFFRACTION3C2 - 238
4X-RAY DIFFRACTION4D9 - 241
5X-RAY DIFFRACTION5E4 - 237
6X-RAY DIFFRACTION6F6 - 244
7X-RAY DIFFRACTION7G2 - 245
8X-RAY DIFFRACTION8H1 - 220
9X-RAY DIFFRACTION9I1 - 204
10X-RAY DIFFRACTION10J1 - 196
11X-RAY DIFFRACTION11K1 - 200
12X-RAY DIFFRACTION12L1 - 213
13X-RAY DIFFRACTION13M1 - 216
14X-RAY DIFFRACTION14N1 - 202
15X-RAY DIFFRACTION15O3 - 232
16X-RAY DIFFRACTION16P2 - 248
17X-RAY DIFFRACTION17Q2 - 240
18X-RAY DIFFRACTION18R9 - 241
19X-RAY DIFFRACTION19S4 - 239
20X-RAY DIFFRACTION20T5 - 244
21X-RAY DIFFRACTION21U2 - 245
22X-RAY DIFFRACTION22V1 - 220
23X-RAY DIFFRACTION23W1 - 204
24X-RAY DIFFRACTION24X1 - 196
25X-RAY DIFFRACTION25Y1 - 199
26X-RAY DIFFRACTION26Z1 - 213
27X-RAY DIFFRACTION27a1 - 216
28X-RAY DIFFRACTION28b1 - 203

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