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- PDB-6msd: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Database: PDB / ID: 6msd
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Components
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (26S proteasome regulatory subunit ...) x 6
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit SEM1
  • Ubiquitin
KeywordsHYDROLASE / Proteosome
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Downstream TCR signaling / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / APC-Cdc20 mediated degradation of Nek2A ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Downstream TCR signaling / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / APC-Cdc20 mediated degradation of Nek2A / Assembly Of The HIV Virion / Membrane binding and targetting of GAG proteins / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / p75NTR recruits signalling complexes / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Cyclin B / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TICAM1, RIP1-mediated IKK complex recruitment / NOD1/2 Signaling Pathway / Budding and maturation of HIV virion / Downregulation of ERBB2:ERBB3 signaling / Spry regulation of FGF signaling / Downregulation of ERBB4 signaling / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / ER-Phagosome pathway / Stimuli-sensing channels / ABC-family proteins mediated transport / Myoclonic epilepsy of Lafora / Deactivation of the beta-catenin transactivating complex / Regulation of ornithine decarboxylase (ODC) / Autodegradation of the E3 ubiquitin ligase COP1 / Glycogen synthesis / Regulation of innate immune responses to cytosolic DNA / NOTCH2 Activation and Transmission of Signal to the Nucleus / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD Domain Mutants / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Regulation of activated PAK-2p34 by proteasome mediated degradation / Regulation of PLK1 Activity at G2/M Transition / Oncogene Induced Senescence / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Separation of Sister Chromatids / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of TGF-beta receptor signaling / Activated NOTCH1 Transmits Signal to the Nucleus / NOTCH1 Intracellular Domain Regulates Transcription / Cross-presentation of soluble exogenous antigens (endosomes) / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / 26S Proteasome non-ATPase regulatory subunit 14 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Ubiquitin family / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome subunit beta 5 / Proteasome subunit alpha 3 / MPN domain / von Willebrand factor A-like domain superfamily / Winged helix-like DNA-binding domain superfamily / 26S Proteasome non-ATPase regulatory subunit 13 / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 10B / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 4 / PCI domain / Ubiquitin interaction motif / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Ubiquitin domain profile. / ISG15 antiviral mechanism / Activation of NF-kappaB in B cells / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Ubiquitin-interacting motif (UIM) domain profile. / PCI domain profile. / MPN domain profile. / VWFA domain profile. / Proteasome beta-type subunits signature. / DSS1/SEM1 family / AAA-protein family signature. / Proteasome alpha-type subunits signature. / Ubiquitin domain signature.
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsMao, Y.D.
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 16, 2018 / Release: Dec 5, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 5, 2018Structure modelrepositoryInitial release
1.1Dec 12, 2018Structure modelData collection / Database referencescitation / citation_author_citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Jan 16, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

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Assembly

Deposited unit
U: 26S proteasome non-ATPase regulatory subunit 1
V: 26S proteasome non-ATPase regulatory subunit 3
W: 26S proteasome non-ATPase regulatory subunit 12
X: 26S proteasome non-ATPase regulatory subunit 11
Y: 26S proteasome non-ATPase regulatory subunit 6
Z: 26S proteasome non-ATPase regulatory subunit 7
a: 26S proteasome non-ATPase regulatory subunit 13
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit SEM1
f: 26S proteasome non-ATPase regulatory subunit 2
A: 26S proteasome regulatory subunit 7
B: 26S proteasome regulatory subunit 4
C: 26S proteasome regulatory subunit 8
D: 26S proteasome regulatory subunit 6B
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
u: Ubiquitin
w: Ubiquitin
G: Proteasome subunit alpha type-6
H: Proteasome subunit alpha type-2
I: Proteasome subunit alpha type-4
J: Proteasome subunit alpha type-7
K: Proteasome subunit alpha type-5
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-3
N: Proteasome subunit beta type-6
O: Proteasome subunit beta type-7
P: Proteasome subunit beta type-3
Q: Proteasome subunit beta type-2
R: Proteasome subunit beta type-5
S: Proteasome subunit beta type-1
T: Proteasome subunit beta type-4
g: Proteasome subunit alpha type-6
h: Proteasome subunit alpha type-2
i: Proteasome subunit alpha type-4
j: Proteasome subunit alpha type-7
k: Proteasome subunit alpha type-5
l: Proteasome subunit alpha type-1
m: Proteasome subunit alpha type-3
n: Proteasome subunit beta type-6
o: Proteasome subunit beta type-7
p: Proteasome subunit beta type-3
q: Proteasome subunit beta type-2
r: Proteasome subunit beta type-5
s: Proteasome subunit beta type-1
t: Proteasome subunit beta type-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,681,81560
Polyers1,678,74548
Non-polymers3,07012
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)218040
ΔGint (kcal/M)-1042
Surface area (Å2)559250

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Components

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules UVWXYZabcdf

#1: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105958.234 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Production host: Homo sapiens (human) / References: UniProt: Q99460
#2: Protein/peptide 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 61066.500 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD3 / Production host: Homo sapiens (human) / References: UniProt: O43242
#3: Protein/peptide 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD12 / Production host: Homo sapiens (human) / References: UniProt: O00232
#4: Protein/peptide 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 47526.688 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD11 / Production host: Homo sapiens (human) / References: UniProt: O00231
#5: Protein/peptide 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 45592.285 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD6, KIAA0107, PFAAP4 / Production host: Homo sapiens (human) / References: UniProt: Q15008
#6: Protein/peptide 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 37086.441 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD7, MOV34L / Production host: Homo sapiens (human) / References: UniProt: P51665
#7: Protein/peptide 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42995.359 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD13 / Production host: Homo sapiens (human) / References: UniProt: Q9UNM6
#8: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Homo sapiens (human) / References: UniProt: P55036
#9: Protein/peptide 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34488.824 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD14, POH1 / Production host: Homo sapiens (human)
References: UniProt: O00487, Hydrolases, Acting on peptide bonds (peptidases), Omega peptidases
#10: Protein/peptide 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39536.676 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD8 / Production host: Homo sapiens (human) / References: UniProt: P48556
#12: Protein/peptide 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 100313.625 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Production host: Homo sapiens (human) / References: UniProt: Q13200

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Protein/peptide , 2 types, 3 molecules euw

#11: Protein/peptide 26S proteasome complex subunit SEM1 / 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SEM1, C7orf76, DSS1, SHFDG1, SHFM1 / Production host: Homo sapiens (human) / References: UniProt: P60896
#19: Protein/peptide Ubiquitin /


Mass: 8604.845 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: P0CG47

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26S proteasome regulatory subunit ... , 6 types, 6 molecules ABCDEF

#13: Protein/peptide 26S proteasome regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48700.805 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC2, MSS1 / Production host: Homo sapiens (human) / References: UniProt: P35998
#14: Protein/peptide 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC1 / Production host: Homo sapiens (human) / References: UniProt: P62191
#15: Protein/peptide 26S proteasome regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 44852.121 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Production host: Homo sapiens (human) / References: UniProt: P62195
#16: Protein/peptide 26S proteasome regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 47426.141 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC4, MIP224, TBP7 / Production host: Homo sapiens (human) / References: UniProt: P43686
#17: Protein/peptide 26S proteasome regulatory subunit 10B


Mass: 45867.027 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6 / Production host: Homo sapiens (human) / References: UniProt: A0A087X2I1
#18: Protein/peptide 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 49266.457 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC3, TBP1 / Production host: Homo sapiens (human) / References: UniProt: P17980

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

#20: Protein/peptide Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27301.262 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA6, PROS27 / Production host: Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#21: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25796.338 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA2, HC3, PSC3 / Production host: Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#22: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29394.648 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA4, HC9, PSC9 / Production host: Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#23: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27798.695 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA7, HSPC / Production host: Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#24: Protein/peptide Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26304.779 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#25: Protein/peptide Proteasome subunit alpha type-1 / / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 30150.277 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA1, HC2, NU, PROS30, PSC2 / Production host: Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#26: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28338.057 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA3, HC8, PSC8 / Production host: Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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

#27: Protein/peptide Proteasome subunit beta type-6 / / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 25246.455 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB6, LMPY, Y / Production host: Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#28: Protein/peptide Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 29869.223 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB7, Z / Production host: Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#29: Protein/peptide Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22841.701 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB3 / Production host: Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#30: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#31: Protein/peptide Proteasome subunit beta type-5 / PSMB5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 28379.053 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB5, LMPX, MB1, X / Production host: Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#32: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26391.201 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB1, PSC5 / Production host: Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#33: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29099.986 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB4, PROS26 / Production host: Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

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Non-polymers , 4 types, 12 molecules

#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#35: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#36: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Formula: Mg / Magnesium
#37: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Human 26S proteasome / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33
Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 44 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 79691 / Symmetry type: POINT

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