[English] 日本語
Yorodumi
- PDB-5vfs: Nucleotide-Driven Triple-State Remodeling of the AAA-ATPase Chann... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5vfs
TitleNucleotide-Driven Triple-State Remodeling of the AAA-ATPase Channel in the Activated 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
  • Sem1
KeywordsHYDROLASE / 26S proteasome / ATP-dependent protease / AAA-ATPase / peptide-unfolding channel / 20S core particle
Function / homology26S proteasome subunit RPN6 C-terminal helix domain / Proteasome regulatory subunit C-terminal / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) ...26S proteasome subunit RPN6 C-terminal helix domain / Proteasome regulatory subunit C-terminal / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Ubiquitin interaction motif / CSN8/PSMD8/EIF3K family / 26S Proteasome non-ATPase regulatory subunit 13 / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / VWFA domain profile. / MPN domain profile. / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / 26S Proteasome non-ATPase regulatory subunit 14 / 26S Proteasome non-ATPase regulatory subunit 12 / Proteasome beta-type subunit profile. / Proteasome subunit beta 6 / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / Proteasome subunit Rpn10 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha 1 / 26S Proteasome non-ATPase regulatory subunit 11 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / Proteasome alpha-type subunit profile. / Activation of NF-kappaB in B cells / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / The role of GTSE1 in G2/M progression after G2 checkpoint / NIK-->noncanonical NF-kB signaling / Defective CFTR causes cystic fibrosis / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / CDT1 association with the CDC6:ORC:origin complex / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RAS by GAPs / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / Neddylation / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Negative regulation of NOTCH4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / AAA+ lid domain / HEAT repeats / RPN1/RPN2 N-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / TNFR2 non-canonical NF-kB pathway / Hedgehog 'on' state / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Separation of Sister Chromatids / ER-Phagosome pathway / Cross-presentation of soluble exogenous antigens (endosomes)
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsZhu, Y. / Wang, W.L. / Yu, D. / Ouyang, Q. / Lu, Y. / Mao, Y.
CitationJournal: Nat Commun / Year: 2018
Title: Structural mechanism for nucleotide-driven remodeling of the AAA-ATPase unfoldase in the activated human 26S proteasome.
Authors: Yanan Zhu / Wei Li Wang / Daqi Yu / Qi Ouyang / Ying Lu / Youdong Mao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 9, 2017 / Release: Jul 18, 2018

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8666
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
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: Sem1
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
B: 26S proteasome regulatory subunit 4
A: 26S proteasome regulatory subunit 7
E: 26S proteasome regulatory subunit 10B
F: 26S proteasome regulatory subunit 6A
C: 26S proteasome regulatory subunit 8
D: 26S proteasome regulatory subunit 6B
f: 26S proteasome non-ATPase regulatory subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,532,63253
Polyers1,529,42746
Non-polymers3,2057
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)205370
ΔGint (kcal/M)-875
Surface area (Å2)545220

-
Components

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

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


Mass: 26727.658 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
#2: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25725.260 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
#3: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 28118.189 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
#4: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27382.178 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
#5: Protein/peptide Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 25569.957 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMA5 / Production host: Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#6: 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: 26728.428 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
#7: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 27287.100 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

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

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


Mass: 20471.129 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
#9: Protein/peptide Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 23745.256 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
#10: 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
#11: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22720.146 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMB2 / Production host: Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#12: 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: 22199.072 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
#13: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 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
#14: 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: 23994.324 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

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

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


Mass: 101263.180 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD1 / Production host: Homo sapiens (human) / References: UniProt: Q99460
#16: Protein/peptide 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 54755.656 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD3 / Production host: Homo sapiens (human) / References: UniProt: O43242
#17: 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
#18: 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: 42868.555 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD11 / Production host: Homo sapiens (human) / References: UniProt: O00231
#19: 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: 44336.906 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD6, KIAA0107, PFAAP4 / Production host: Homo sapiens (human) / References: UniProt: Q15008
#20: 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: 32382.094 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD7, MOV34L / Production host: Homo sapiens (human) / References: UniProt: P51665
#21: 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: 42619.898 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD13 / Production host: Homo sapiens (human) / References: UniProt: Q9UNM6
#22: 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: 20866.023 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD4, MCB1 / Production host: Homo sapiens (human) / References: UniProt: P55036
#23: 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
#24: Protein/peptide 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 30039.699 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD8 / Production host: Homo sapiens (human) / References: UniProt: P48556
#32: 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: 93790.188 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD2, TRAP2 / Production host: Homo sapiens (human) / References: UniProt: Q13200

+
Protein/peptide , 1 types, 1 molecules e

#25: Protein/peptide Sem1


Mass: 8284.611 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

+
26S proteasome regulatory subunit ... , 6 types, 6 molecules BAEFCD

#26: Protein/peptide 26S proteasome regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 41593.488 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC1 / Production host: Homo sapiens (human) / References: UniProt: P62191
#27: 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
#28: Protein/peptide 26S proteasome regulatory subunit 10B / 26S proteasome AAA-ATPase subunit RPT4 / Proteasome 26S subunit ATPase 6 / Proteasome subunit p42


Mass: 45867.027 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC6, SUG2 / Production host: Homo sapiens (human) / References: UniProt: P62333
#29: Protein/peptide 26S proteasome regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / 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
#30: 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: 43719.680 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC5, SUG1 / Production host: Homo sapiens (human) / References: UniProt: P62195
#31: 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

+
Non-polymers , 2 types, 7 molecules

#33: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#34: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 6 / Formula: C10H16N5O12P3S
Comment: ATP-gamma-S (energy-carrying molecule analogue) *YM

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: 26S proteasome bound to ATP-gammaS / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,24,25,32
Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
7Coot0.8.6model fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
19PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 230602 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006103215
ELECTRON MICROSCOPYf_angle_d1.144139617
ELECTRON MICROSCOPYf_dihedral_angle_d9.52162746
ELECTRON MICROSCOPYf_chiral_restr0.06115879
ELECTRON MICROSCOPYf_plane_restr0.00818038

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more