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- PDB-5mmj: Structure of the small subunit of the chloroplast ribosome -

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Basic information

Entry
Database: PDB / ID: 5mmj
TitleStructure of the small subunit of the chloroplast ribosome
Components
  • (30S ribosomal protein ...) x 16
  • (plastid ribosomal protein ...) x 8
  • 16S ribosomal RNA
  • 50S ribosomal protein L31
  • Ribosome-binding factor PSRP1, chloroplastic
KeywordsRIBOSOME / chloroplast / translation / cryo-EM
Function / homology
Function and homology information


plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis ...plastid small ribosomal subunit / plastid translation / negative regulation of translational elongation / primary metabolic process / mitochondrial small ribosomal subunit / plastid / chloroplast stroma / ribosomal small subunit binding / chloroplast / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / cytosolic small ribosomal subunit / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / mitochondrion / RNA binding
Similarity search - Function
Helix Hairpins - #1480 / Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus ...Helix Hairpins - #1480 / Ribosomal protein PSRP-3/Ycf65 / PSRP-3/Ycf65 superfamily / Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) / 30S ribosomal protein S31, plant / Ribosomal protein S31e / Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / Ribosomal protein S4/S9, N-terminal domain / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / S16 Ribosomal Protein; Chain: A; / Ribosomal protein S16 / Ribosomal protein S18 / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein / 30s Ribosomal Protein S18 / 30s ribosomal protein s13; domain 2 / Ribosomal protein S13/S18, C-terminal domain / Ribosomal protein S20 / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / Ribosomal protein S3, C-terminal domain / Ribosomal Protein S8; Chain: A, domain 1 - #30 / RNA-binding S4 domain / Ribosomal Protein S7 / Ribosomal protein S7/S5 / Ribosomal protein S3 C-terminal domain / Helix hairpin bin / Dna Ligase; domain 1 - #10 / Ribosomal protein S11/S14 / Ribosomal protein S10 / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / S15/NS1, RNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Glucose-6-phosphate isomerase like protein; domain 1 / Ribosomal Protein S8; Chain: A, domain 1 / Ribosomal Protein S5; domain 2 - #10 / 30S ribosomal protein / Ribosomal Protein S5; domain 2 / RRM (RNA recognition motif) domain / Ribosomal protein S14, bacterial/plastid / Ribosomal protein S21 superfamily / Ribosomal protein S21 / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein S21 / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Helicase, Ruva Protein; domain 3 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / Ribosomal protein S3, bacterial-type / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / RNA-binding domain superfamily / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein S15, bacterial-type / Ribosomal protein S2 signature 2. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S3, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S10, conserved site / : / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S15/S19, conserved site / Ribosomal protein S19/S15 / Ribosomal protein S19/S15, superfamily / Ribosomal protein S10 / Ribosomal protein S3, C-terminal domain / Few Secondary Structures
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS13c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS17c ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS13c / Small ribosomal subunit protein bS6c alpha / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein uS11c / Small ribosomal subunit protein uS14c / Small ribosomal subunit protein uS19c / Small ribosomal subunit protein uS2c / Small ribosomal subunit protein uS3c / Small ribosomal subunit protein uS8c / Small ribosomal subunit protein uS4c / Ribosome-binding factor PSRP1, chloroplastic / Small ribosomal subunit protein bS16c / Small ribosomal subunit protein bTHXc / Small ribosomal subunit protein uS12cz/uS12cy / Small ribosomal subunit protein bS21c / Small ribosomal subunit protein uS7cz/uS7cy / Small ribosomal subunit protein uS17c / Small ribosomal subunit protein uS10c / Small ribosomal subunit protein uS13c / Large ribosomal subunit protein bL31c / Small ribosomal subunit protein cS22 / Small ribosomal subunit protein uS9c / Small ribosomal subunit protein bS6c alpha / Small ribosomal subunit protein cS23 / Small ribosomal subunit protein uS15c / Small ribosomal subunit protein bS18c / Small ribosomal subunit protein uS5c
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBieri, P. / Leibundgut, M. / Saurer, M. / Boehringer, D. / Ban, N.
CitationJournal: EMBO J / Year: 2017
Title: The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.
Authors: Philipp Bieri / Marc Leibundgut / Martin Saurer / Daniel Boehringer / Nenad Ban /
Abstract: Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, ...Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.
History
DepositionDec 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Derived calculations
Category: em_software / pdbx_struct_conn_angle / struct_conn
Item: _em_software.name
Revision 1.3Oct 17, 2018Group: Data collection / Other / Refinement description / Category: cell / refine / Item: _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Dec 11, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
0: 50S ribosomal protein L31
8: plastid ribosomal protein bS1c
a: 16S ribosomal RNA
b: 30S ribosomal protein S2, chloroplastic
c: 30S ribosomal protein S3, chloroplastic
d: 30S ribosomal protein S4, chloroplastic
e: 30S ribosomal protein S5, chloroplastic
f: plastid ribosomal protein bS6c
g: 30S ribosomal protein S7, chloroplastic
h: 30S ribosomal protein S8, chloroplastic
i: plastid ribosomal protein uS9c
j: plastid ribosomal protein uS10c
k: 30S ribosomal protein S11, chloroplastic
l: 30S ribosomal protein S12, chloroplastic
m: plastid ribosomal protein uS13c
n: 30S ribosomal protein S14, chloroplastic
o: 30S ribosomal protein S15, chloroplastic
p: 30S ribosomal protein S16, chloroplastic
q: plastid ribosomal protein uS17c
r: 30S ribosomal protein S18, chloroplastic
s: 30S ribosomal protein S19 alpha, chloroplastic
t: plastid ribosomal protein bS20c
u: plastid ribosomal protein bS21c
v: 30S ribosomal protein 2, chloroplastic
w: 30S ribosomal protein 3, chloroplastic
x: 30S ribosomal protein S31, chloroplastic
y: Ribosome-binding factor PSRP1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)982,336212
Polymers977,83927
Non-polymers4,496185
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area127160 Å2
ΔGint-2281 kcal/mol
Surface area312860 Å2
MethodPISA

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Components

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Protein , 2 types, 2 molecules 0y

#1: Protein 50S ribosomal protein L31 / / plastid ribosomal protein bL31c


Mass: 14748.201 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0R6, UniProt: P82249*PLUS
#27: Protein Ribosome-binding factor PSRP1, chloroplastic / plastid pY / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / ...plastid pY / 30S ribosomal protein 1 / CS-S5 / CS5 / Plastid-specific 30S ribosomal protein 1 / PSrp-1 / Ribosomal protein 1 / S22


Mass: 33799.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P19954

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Plastid ribosomal protein ... , 8 types, 8 molecules 8fijmqtu

#2: Protein plastid ribosomal protein bS1c


Mass: 14826.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach)
#8: Protein plastid ribosomal protein bS6c


Mass: 23510.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R0H2, UniProt: P82403*PLUS
#11: Protein plastid ribosomal protein uS9c


Mass: 22415.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RY17, UniProt: P82278*PLUS
#12: Protein plastid ribosomal protein uS10c


Mass: 21440.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RWE7, UniProt: P82162*PLUS
#15: Protein plastid ribosomal protein uS13c


Mass: 19310.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9R024, UniProt: P82163*PLUS
#19: Protein plastid ribosomal protein uS17c


Mass: 18151.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RRR0, UniProt: P82137*PLUS
#22: Protein plastid ribosomal protein bS20c


Mass: 20147.291 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach)
#23: Protein plastid ribosomal protein bS21c


Mass: 20616.150 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: A0A0K9RHF9, UniProt: P82024*PLUS

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30S ribosomal protein ... , 16 types, 16 molecules bcdeghklnoprsvwx

#4: Protein 30S ribosomal protein S2, chloroplastic / Ribosome / plastid ribosomal protein uS2c


Mass: 26736.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P08242
#5: Protein 30S ribosomal protein S3, chloroplastic / Ribosome / plastid ribosomal protein uS3c


Mass: 24965.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09595
#6: Protein 30S ribosomal protein S4, chloroplastic / Ribosome / plastid ribosomal protein uS4c


Mass: 23454.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P13788
#7: Protein 30S ribosomal protein S5, chloroplastic / Ribosome / plastid ribosomal protein uS5c


Mass: 33626.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Residues 122-150 were built as poly-alanine and deposited as UNK.
Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9ST69
#9: Protein 30S ribosomal protein S7, chloroplastic / Ribosome / plastid ribosomal protein uS7c


Mass: 17378.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82129
#10: Protein 30S ribosomal protein S8, chloroplastic / Ribosome / plastid ribosomal protein uS8c


Mass: 15527.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P09597
#13: Protein 30S ribosomal protein S11, chloroplastic / Ribosome / plastid ribosomal protein uS11c


Mass: 14927.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06506
#14: Protein 30S ribosomal protein S12, chloroplastic / Ribosome / plastid ribosomal protein uS12c


Mass: 13794.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P62128
#16: Protein 30S ribosomal protein S14, chloroplastic / Ribosome / plastid ribosomal protein uS14c


Mass: 11809.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06507
#17: Protein 30S ribosomal protein S15, chloroplastic / Ribosome / plastid ribosomal protein uS15c


Mass: 10778.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3I4
#18: Protein 30S ribosomal protein S16, chloroplastic / Ribosome / plastid ribosomal protein bS16c


Mass: 10454.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P28807
#20: Protein 30S ribosomal protein S18, chloroplastic / Ribosome / plastid ribosomal protein uS18c


Mass: 12079.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: Q9M3K7
#21: Protein 30S ribosomal protein S19 alpha, chloroplastic / Ribosome / plastid ribosomal protein uS19c / CS-S23


Mass: 10632.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P06508
#24: Protein 30S ribosomal protein 2, chloroplastic / Ribosome / plastid ribosomal protein cS22 / Plastid-specific 30S ribosomal protein 2 / PSRP-2


Mass: 28327.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82277
#25: Protein 30S ribosomal protein 3, chloroplastic / Ribosome / plastid ribosomal protein cS23 / Plastid-specific 30S ribosomal protein 3 / PSRP-3


Mass: 20312.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P82412
#26: Protein 30S ribosomal protein S31, chloroplastic / Ribosome / plastid ribosomal protein bTHXc / Plastid-specific 30S ribosomal protein 4 / PSRP-4


Mass: 10602.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: UniProt: P47910

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RNA chain / Non-polymers , 2 types, 186 molecules a

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


Mass: 24.305 Da / Num. of mol.: 185 / Source method: obtained synthetically / Formula: Mg
#3: RNA chain 16S ribosomal RNA / / plastid 16S rRNA


Mass: 483466.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Spinacia oleracea (spinach) / References: GenBank: 7636084

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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: Chloroplast 70S ribosome / Type: RIBOSOME / Entity ID: #1-#27 / Source: NATURAL
Molecular weightValue: 2.4 MDa / Experimental value: NO
Source (natural)Organism: Spinacia oleracea (spinach) / Organelle: chloroplast / Tissue: leaf
Buffer solutionpH: 7.6
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris hydrochlorideTris-HClTris1
225 mMPotassium chlorideKCl1
325 mMMagnesium acetateMg(CH3COO)21
42 mMDithiothreitolDTT1
50.05 mMSpermine1
62 mMSpermidine1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 278 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 FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 2796
Image scansMovie frames/image: 8 / Used frames/image: 2-8

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN1.9particle selectionBatchboxer
2EPUimage acquisition
4CTFFIND3CTF correctionCTF estimation
5RELION1.4CTF correctionAmplitude correction
8UCSF Chimera1.11.2model fitting
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 326094
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127031 / Symmetry type: POINT
Atomic model buildingB value: 111.6 / Protocol: OTHER / Space: RECIPROCAL
RefinementResolution: 3.646→300.24 Å / SU ML: 0.55 / σ(F): 1.01 / Phase error: 29.71 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2492 29364 2.51 %
Rwork0.2354 --
obs0.2357 1168752 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00859305
ELECTRON MICROSCOPYf_angle_d1.08487437
ELECTRON MICROSCOPYf_dihedral_angle_d16.64626903
ELECTRON MICROSCOPYf_chiral_restr0.04410992
ELECTRON MICROSCOPYf_plane_restr0.0055572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.646-3.68750.51389900.491237843ELECTRON MICROSCOPY100
3.6875-3.73090.420510200.409137921ELECTRON MICROSCOPY100
3.7309-3.77640.41089430.39437862ELECTRON MICROSCOPY100
3.7764-3.82420.39739800.386938564ELECTRON MICROSCOPY100
3.8242-3.87450.38769700.381138020ELECTRON MICROSCOPY100
3.8745-3.92760.3949770.367837784ELECTRON MICROSCOPY100
3.9276-3.98370.37879640.352637946ELECTRON MICROSCOPY100
3.9837-4.04320.3589870.344238004ELECTRON MICROSCOPY100
4.0432-4.10630.34819950.334938223ELECTRON MICROSCOPY100
4.1063-4.17370.35459670.324137663ELECTRON MICROSCOPY100
4.1737-4.24560.323210070.312238382ELECTRON MICROSCOPY100
4.2456-4.32290.33129480.300937989ELECTRON MICROSCOPY100
4.3229-4.4060.29779830.288138005ELECTRON MICROSCOPY100
4.406-4.4960.29499440.282837615ELECTRON MICROSCOPY100
4.496-4.59370.300310330.272238169ELECTRON MICROSCOPY100
4.5937-4.70060.268110110.26438085ELECTRON MICROSCOPY100
4.7006-4.81820.27089980.250837811ELECTRON MICROSCOPY100
4.8182-4.94840.241410160.240137918ELECTRON MICROSCOPY100
4.9484-5.09410.24819580.233638250ELECTRON MICROSCOPY100
5.0941-5.25850.25479500.226637875ELECTRON MICROSCOPY100
5.2585-5.44650.221910160.221238114ELECTRON MICROSCOPY100
5.4465-5.66450.20759550.206938061ELECTRON MICROSCOPY100
5.6645-5.92240.22659410.205737771ELECTRON MICROSCOPY100
5.9224-6.23460.203710160.193338109ELECTRON MICROSCOPY100
6.2346-6.62530.20899630.194838134ELECTRON MICROSCOPY100
6.6253-7.13690.192510060.178837837ELECTRON MICROSCOPY100
7.1369-7.85510.1749750.167738057ELECTRON MICROSCOPY100
7.8551-8.99180.18479780.172237953ELECTRON MICROSCOPY100
8.9918-11.32890.16769500.156937728ELECTRON MICROSCOPY99
11.3289-301.2630.15789230.14937695ELECTRON MICROSCOPY99

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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