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Basic information

Entry
Database: PDB / ID: 6rm3
TitleEvolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome
Components
  • 16S rRNA
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • MDF1
  • MDF2
  • RACK1Receptor for activated C kinase 1
  • eL13
  • eL14
  • eL15List of Subaru engines
  • eL18
  • eL19
  • eL20
  • eL21
  • eL22
  • eL24
  • eL27
  • eL29
  • eL30
  • eL31
  • eL32CD59
  • eL33
  • eL34
  • eL36
  • eL37
  • eL39
  • eL40
  • eL42
  • eL43
  • eL6
  • eL8
  • eS1
  • eS10
  • eS12
  • eS17
  • eS19
  • eS21
  • eS24
  • eS25
  • eS26
  • eS27
  • eS28
  • eS30
  • eS31
  • eS4
  • eS6
  • eS7
  • eS8
  • msL1
  • uL13
  • uL14
  • uL15
  • uL16
  • uL18
  • uL2
  • uL22
  • uL23
  • uL24
  • uL29
  • uL3
  • uL30
  • uL4
  • uL5
  • uL6
  • uS10
  • uS11
  • uS12
  • uS13
  • uS14
  • uS15
  • uS17
  • uS19
  • uS2
  • uS3
  • uS4
  • uS5
  • uS7
  • uS8
  • uS9
KeywordsRIBOSOME / Microsporidia / Intracellular Parasite
Function / homologyRNA / RNA (> 10) / RNA (> 100) / RNA (> 1000)
Function and homology information
Biological speciesVairimorpha necatrix (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBarandun, J. / Hunziker, M. / Vossbrinck, C.R. / Klinge, S.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM123459 United States
Swiss National Science Foundation155515 Switzerland
CitationJournal: Nat Microbiol / Year: 2019
Title: Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome.
Authors: Jonas Barandun / Mirjam Hunziker / Charles R Vossbrinck / Sebastian Klinge /
Abstract: Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are ...Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance, and are significant opportunistic parasites of humans. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle, rudimentary mitochondria and the smallest known eukaryotic genomes. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.
History
DepositionMay 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-4935
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S60: 16S rRNA
L70: 5S rRNA
LA0: uL2
SA0: uS2
LAA: uL15
SAA: eS26
LB0: uL3
SB0: eS1
LBB: eL29
SBB: eS27
LC0: uL4
SC0: uS5
LCC: eL30
SCC: eS28
LD0: uL18
SD0: uS3
LDD: eL31
SDD: uS14
LE0: eL6
SE0: eS4
LEE: eL32
SEE: eS30
LF0: uL30
SF0: uS7
LFF: eL33
SFF: eS31
LG0: eL8
SG0: eS6
LGG: eL34
SGG: RACK1
LH0: uL6
SH0: eS7
LHH: uL29
LI0: uL16
SI0: eS8
LII: eL36
LJ0: uL5
SJ0: uS4
LJJ: eL37
LL0: eL13
SL0: uS17
LLL: eL39
LM0: eL14
LMM: eL40
SM0: eS12
LN0: eL15
SN0: uS15
LNN: MDF2
SNN: MDF1
LO0: uL13
SO0: uS11
LOO: eL42
LP0: uL22
SP0: uS19
LPP: eL43
LQ0: eL18
SQ0: uS9
LR0: eL19
SR0: eS17
LS0: eL20
SS0: uS13
LT0: eL21
ST0: eS19
LU0: eL22
SU0: uS10
LV0: uL14
SV0: eS21
LW0: eL24
SW0: uS8
LX0: uL23
SX0: uS12
LXX: msL1
LY0: uL24
SY0: eS24
LZ0: eL27
SZ0: eS25
SK0: eS10
L50: 23S rRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,572,746261
Polymers2,567,92878
Non-polymers4,818183
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 3 types, 3 molecules S60L70L50

#1: RNA chain 16S rRNA /


Mass: 401303.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#2: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38379.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#78: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 799487.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)

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Protein , 75 types, 75 molecules LA0SA0LAASAALB0SB0LBBSBBLC0SC0LCCSCCLD0SD0LDDSDDLE0SE0LEESEELF0SF0LFFSFFLG0SG0LGGSGGLH0SH0...

#3: Protein uL2


Mass: 26019.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#4: Protein uS2


Mass: 29692.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#5: Protein uL15


Mass: 17300.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#6: Protein eS26


Mass: 12113.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#7: Protein uL3


Mass: 43234.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#8: Protein eS1


Mass: 26982.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#9: Protein eL29


Mass: 6374.493 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#10: Protein eS27


Mass: 10610.259 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#11: Protein uL4


Mass: 37979.027 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#12: Protein uS5


Mass: 25904.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#13: Protein eL30


Mass: 11874.985 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#14: Protein eS28


Mass: 7639.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#15: Protein uL18


Mass: 34483.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#16: Protein uS3


Mass: 23717.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#17: Protein eL31


Mass: 12757.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#18: Protein uS14


Mass: 7877.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#19: Protein eL6


Mass: 20199.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#20: Protein eS4


Mass: 29931.486 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#21: Protein eL32 / CD59


Mass: 16177.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#22: Protein eS30


Mass: 6917.247 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#23: Protein uL30


Mass: 27664.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#24: Protein uS7


Mass: 20970.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#25: Protein eL33


Mass: 11214.232 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#26: Protein eS31


Mass: 17086.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#27: Protein eL8


Mass: 23081.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#28: Protein eS6


Mass: 24946.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#29: Protein eL34 /


Mass: 12299.665 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#30: Protein RACK1 / Receptor for activated C kinase 1


Mass: 36890.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#31: Protein uL6


Mass: 21038.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#32: Protein eS7


Mass: 18695.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#33: Protein uL29


Mass: 14798.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#34: Protein uL16


Mass: 24989.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#35: Protein eS8


Mass: 18885.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#36: Protein eL36


Mass: 11134.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#37: Protein uL5


Mass: 19628.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#38: Protein uS4


Mass: 21724.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#39: Protein eL37


Mass: 10699.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#40: Protein eL13


Mass: 18980.395 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#41: Protein uS17


Mass: 18230.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#42: Protein eL39


Mass: 6462.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#43: Protein eL14


Mass: 11991.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#44: Protein eL40


Mass: 14239.560 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#45: Protein eS12


Mass: 14731.950 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#46: Protein eL15 / List of Subaru engines


Mass: 24032.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#47: Protein uS15


Mass: 17069.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#48: Protein MDF2


Mass: 19306.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#49: Protein MDF1


Mass: 19264.152 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#50: Protein uL13


Mass: 22335.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#51: Protein uS11


Mass: 14468.902 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#52: Protein eL42


Mass: 12015.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#53: Protein uL22


Mass: 19434.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#54: Protein uS19


Mass: 16041.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#55: Protein eL43


Mass: 9826.513 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#56: Protein eL18


Mass: 21878.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#57: Protein uS9


Mass: 17545.838 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#58: Protein eL19


Mass: 20385.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#59: Protein eS17


Mass: 13964.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#60: Protein eL20


Mass: 20986.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#61: Protein uS13


Mass: 18051.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#62: Protein eL21 /


Mass: 18675.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#63: Protein eS19


Mass: 15276.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#64: Protein eL22


Mass: 12327.101 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#65: Protein uS10


Mass: 11507.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#66: Protein uL14


Mass: 16046.837 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#67: Protein eS21


Mass: 7575.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#68: Protein eL24


Mass: 10363.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#69: Protein uS8


Mass: 14515.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#70: Protein uL23


Mass: 11569.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#71: Protein uS12


Mass: 15494.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#72: Protein msL1


Mass: 8746.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#73: Protein uL24


Mass: 16133.752 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#74: Protein eS24


Mass: 15526.099 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#75: Protein eL27


Mass: 14489.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#76: Protein eS25


Mass: 13935.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)
#77: Protein eS10


Mass: 11795.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vairimorpha necatrix (fungus)

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Non-polymers , 2 types, 183 molecules

#79: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 174 / Source method: obtained synthetically / Formula: Mg
#80: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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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: Microsporidian Ribosome / Type: COMPLEX / Entity ID: #1-#78 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Vairimorpha necatrix (fungus)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
130 mMTris-HCLTris1
25 mMMgOAc1
325 mMKCl1
41 mMDTT1
51 mMEDTAEthylenediaminetetraacetic acid1
SpecimenConc.: 11 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 50 mA / Grid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 500 nm / Calibrated defocus min: 4000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 5.55 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 3284
Image scansMovie frames/image: 32

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4RELION3CTF correction
7Coot0.8.9model fitting
9RELIONinitial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.14model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 471121
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 185445 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingPDB-ID: 4V88

4v88

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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

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