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- PDB-6rey: Human 20S-PA200 Proteasome Complex -

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Basic information

Entry
Database: PDB / ID: 6rey
TitleHuman 20S-PA200 Proteasome Complex
Components
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • Proteasome activator complex subunit 4
KeywordsHYDROLASE / proteasome / PA200 / activator
Function / homology
Function and homology information


spermatoproteasome complex / sperm DNA condensation / peptidase activator activity / purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / proteasomal ubiquitin-independent protein catabolic process ...spermatoproteasome complex / sperm DNA condensation / peptidase activator activity / purine ribonucleoside triphosphate binding / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / proteasomal ubiquitin-independent protein catabolic process / proteasome binding / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / : / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / : / Degradation of beta-catenin by the destruction complex / response to virus / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / positive regulation of NF-kappaB transcription factor activity / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / endopeptidase activity / response to oxidative stress / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Ub-specific processing proteases / nuclear speck / nuclear body / ciliary basal body / cilium / ribosome / cadherin binding / DNA repair
Similarity search - Function
Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / Proteasome subunit alpha 1 / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / 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 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 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 / Armadillo-like helical / Armadillo-type fold / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / Chem-K0W / 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 ...INOSITOL HEXAKISPHOSPHATE / Chem-K0W / 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 activator complex subunit 4 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsToste Rego, A. / da Fonseca, P.C.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/5 United Kingdom
CitationJournal: Mol Cell / Year: 2019
Title: Characterization of Fully Recombinant Human 20S and 20S-PA200 Proteasome Complexes.
Authors: Ana Toste Rêgo / Paula C A da Fonseca /
Abstract: Proteasomes are essential in all eukaryotic cells. However, their function and regulation remain considerably elusive, particularly those of less abundant variants. We demonstrate the human 20S ...Proteasomes are essential in all eukaryotic cells. However, their function and regulation remain considerably elusive, particularly those of less abundant variants. We demonstrate the human 20S proteasome recombinant assembly and confirmed the recombinant complex integrity biochemically and with a 2.6 Å resolution cryo-EM map. To assess its competence to form higher-order assemblies, we prepared and analyzed recombinant human 20S-PA200, a poorly characterized nuclear complex. Its 3.0 Å resolution cryo-EM structure reveals the PA200 unique architecture; the details of its intricate interactions with the proteasome, resulting in unparalleled proteasome α ring rearrangements; and the molecular basis for PA200 allosteric modulation of the proteasome active sites. Non-protein cryo-EM densities could be assigned to PA200-bound inositol phosphates, and we speculate regarding their functional role. Here we open extensive opportunities to study the fundamental properties of the diverse and distinct eukaryotic proteasome variants and to improve proteasome targeting under different therapeutic conditions.
History
DepositionApr 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 16, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Oct 7, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / pdbx_validate_close_contact / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1May 22, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,143,89834
Polymers1,140,93830
Non-polymers2,9604
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area114120 Å2
ΔGint-456 kcal/mol
Surface area331320 Å2
MethodPISA

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Components

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

#1: 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: 27432.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P60900, proteasome endopeptidase complex
#2: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P25787, proteasome endopeptidase complex
#3: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P25789, proteasome endopeptidase complex
#4: Protein Proteasome subunit alpha type-7 / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27929.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O14818, proteasome endopeptidase complex
#5: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28066, proteasome endopeptidase complex
#6: 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: 29595.627 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P25786, proteasome endopeptidase complex
#7: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P25788, proteasome endopeptidase complex

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

#8: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB6, LMPY, Y / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28072, proteasome endopeptidase complex
#9: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB7, Z / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q99436, proteasome endopeptidase complex
#10: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB3 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49720, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P49721, proteasome endopeptidase complex
#12: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB5, LMPX, MB1, X / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28074, proteasome endopeptidase complex
#13: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB1, PSC5 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P20618, proteasome endopeptidase complex
#14: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB4, PROS26 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P28070, proteasome endopeptidase complex

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Protein , 1 types, 2 molecules cd

#15: Protein Proteasome activator complex subunit 4 / Proteasome activator PA200


Mass: 211593.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: I6P and K0W molecules bound to PA200 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSME4, KIAA0077 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14997

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Non-polymers , 2 types, 4 molecules

#16: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#17: Chemical ChemComp-K0W / [(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy-cyclohexyl] phosphono hydrogen phosphate


Mass: 819.995 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H20O30P8

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Human 20S-PA200 Proteasome complexCOMPLEXHuman 20S Proteasome in complex with activator PA200#1-#140RECOMBINANT
220S ProteasomeCOMPLEX#1-#141RECOMBINANT
3PA200 activatorORGANELLE OR CELLULAR COMPONENT#151RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
111.138 MDaNO
210.716 MDaNO
310.211 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
32Spodoptera frugiperda (fall armyworm)7108
43Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTrizma bufferTris-HCl1
2100 mMSodium ChlorideNaCl1
31 mMEthylenediaminetetraacetic acidEDTA1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was homogeneous
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 95000 X
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 45.7 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 717

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Processing

EM software
IDNameVersionCategoryFitting-ID
3EPUimage acquisition
5cisTEM1.0.0CTF correction
8Cootmodel fitting1
12PHENIXmodel refinement1
13Cootmodel refinement1
16cisTEM1.0.0.initial Euler assignment
18cisTEM1.0.0.final Euler assignment
21cisTEM1.0.0.3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 29434
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20351 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceDetails
1FLEXIBLE FITREALThe model of the human recombinant 20S proteasome was built based on PDB: 5LE5 using real-space refinement in Coot and Phenix
2AB INITIO MODELthe model for the human PA200 derived from Phyre2 and I-Tasser. These PA200 models were used as initial guides for the assignment of secondary structure using real-space refinement in Coot and Phenix, followed by correction of the sequence register using the amino acid side chain densities clearly resolved in our cryo-EM map. Connecting loops and all other regions were built ab initio from the cryo-EM density.
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15LE5

5le5

15LE51PDBexperimental model
22

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