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- PDB-5a0q: Cryo-EM reveals the conformation of a substrate analogue in the h... -

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Entry
Database: PDB / ID: 5a0q
TitleCryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core
Components
  • (PROTEASOME SUBUNIT ALPHA TYPE- ...) x 7
  • (PROTEASOME SUBUNIT BETA TYPE- ...) x 7
KeywordsHYDROLASE / PROTEASOME / 20S / ADAAHX3L3VS / LIGAND / INHIBITOR / DRUG DESIGN
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex ...purine ribonucleoside triphosphate binding / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / response to organonitrogen compound / proteolysis involved in protein catabolic process / proteasome complex / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / proteasomal protein catabolic process / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / lipopolysaccharide binding / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / response to virus / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / nuclear matrix / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / UCH proteinases / The role of GTSE1 in G2/M progression after G2 checkpoint / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of NF-kappaB transcription factor activity / peptidase activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / nuclear body / Ub-specific processing proteases / ribosome / cadherin binding / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / mitochondrion / proteolysis
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 alpha6 / Proteasome subunit alpha5 ...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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADA-(AHX)3-(LEU)3-VINYL SULFONE / 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 ...ADA-(AHX)3-(LEU)3-VINYL SULFONE / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsdaFonseca, P.C.A. / Morris, E.P.
CitationJournal: Nat Commun / Year: 2015
Title: Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core.
Authors: Paula C A da Fonseca / Edward P Morris /
Abstract: The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, ...The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.
History
DepositionApr 22, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
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  • EMDB-2981
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)723,18534
Polymers717,48928
Non-polymers5,6966
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source
Details: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS)
Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
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 natural source
Details: SUBUNIT PARTIALLY BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS)
Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein 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 method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
References: UniProt: P49720, proteasome endopeptidase complex
#11: Protein 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 method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
References: UniProt: P49721, proteasome endopeptidase complex
#12: Protein PROTEASOME SUBUNIT BETA TYPE-5 / PSMB5 / 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
Details: SUBUNIT BOUND TO THE INHIBITOR ADAMANTANE-ACETYL-(6-AMINOHEXANOYL)3-(LEUCINYL)3-VINYL-(METHYL)-SULFONE (ADAAHX3L3VS)
Source: (natural) HOMO SAPIENS (human) / Cell: ERYTHROCYTES
References: UniProt: P28074, proteasome endopeptidase complex
#13: Protein PROTEASOME SUBUNIT BETA TYPE-1 / PSMB1 / 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: ERYTHROCYTES
References: UniProt: P20618, proteasome endopeptidase complex
#14: Protein PROTEASOME SUBUNIT BETA TYPE-4 / PSMB4 / 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: ERYTHROCYTES
References: UniProt: P28070, proteasome endopeptidase complex

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Non-polymers , 1 types, 6 molecules

#15: Chemical
ChemComp-KNM / ADA-(AHX)3-(LEU)3-VINYL SULFONE


Mass: 949.377 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H92N6O8S

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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

ComponentName: HUMAN 20S PROTEASOME CORE / Type: COMPLEX
Details: THE POWER SPECTRA OF THE IMAGES SELECTED FOR ANALYSIS HAD ISOTROPIC THON RINGS DIRECTLY OBSERVED TO 4 ANGSTROMS OR BETTER
Buffer solutionName: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL / pH: 7.5 / Details: 50 MM TRIS-HCL, 5 MM MGCL2 AND 1MM DITHIOTREITOL
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 95, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III, METHOD- BLOT 2. 5 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 4, 2014
Details: EACH EXPOSURE WAS RECORDED AS 17 INDIVIDUAL FRAMES CAPTURED AT A RATE OF 0.056 SECONDS PER FRAME, WITH AN ELECTRON DOSE OF 2.8 ELECTRONS PER SQUARE ANGSTROM. DATA-SET RECORDED USING EPU SOFTWARE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 134461 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1700 nm / Cs: 2.7 mm
Specimen holderTemperature: 85 K
Image recordingElectron dose: 4.8 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 960

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2PHENIXmodel fitting
3IMAGIC3D reconstruction
4SPIDER3D reconstruction
5TIGRIS3D reconstruction
CTF correctionDetails: FULL RECORDED IMAGE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 3.5 Å / Num. of particles: 76500 / Actual pixel size: 1.04 Å
Details: DISORDERED REGIONS, NOT RECOVERED IN THE EM MAP, WHERE NOT MODELED. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2981. (DEPOSITION ID: 13310).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: METHOD--FLEXIBLE
Atomic model buildingPDB-ID: 3UNE

3une

RefinementHighest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43264 0 184 0 43448

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