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- PDB-5o60: Structure of the 50S large ribosomal subunit from Mycobacterium s... -

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Basic information

Entry
Database: PDB / ID: 5o60
TitleStructure of the 50S large ribosomal subunit from Mycobacterium smegmatis
Components
  • (50S ribosomal protein ...) x 32
  • 23S rRNA23S ribosomal RNA
  • 5S rRNA5S ribosomal RNA
  • tRNA CCA-end acetylated (Phe)
KeywordsRIBOSOME / translation
Function / homology
Function and homology information


large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation ...large ribosomal subunit rRNA binding / large ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / metal ion binding / cytoplasm
Similarity search - Function
Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain ...Ribosomal protein L10, N-terminal RNA-binding domain / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12, N-terminal domain / Ribosomal protein L33 / Helix Hairpins - #3980 / Ribosomal protein L17 / 50s Ribosomal Protein L17; Chain: A, / Ribosomal protein L2; domain 3 / Ribosomal protein L2, domain 3 / Ribosomal protein L11/L12, C-terminal domain / Ribosomal protein L30/L7 / Nucleotidyltransferase; domain 5 - #100 / Ribosomal protein L16/L10 / Ribosomal protein L22/L17 / Ribosomal Protein L14 / Ribosomal protein L14/L23 / Ribosomal Protein L22; Chain A / Ribosomal Protein L30; Chain: A, / Aldehyde Oxidoreductase; domain 3 / Rubrerythrin, domain 2 / Ribosomal protein L10, eubacterial, conserved site / Ribosomal protein L10 signature. / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Ribosomal protein L10 / : / RRM (RNA recognition motif) domain / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Single Sheet / Ribosomal protein L11, conserved site / Ribosomal protein L10-like domain superfamily / Nucleic acid-binding proteins / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L16, conserved site / Ribosomal protein L16 signature 2. / Ribosomal protein L11, N-terminal / Ribosomal protein L17 signature. / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11/L12 / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11, RNA binding domain / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein L28/L24 superfamily / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein L20 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35
Similarity search - Domain/homology
PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 ...PHENYLALANINE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein bL33A / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein uL10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Uncharacterized protein / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL25 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein bL34
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsHentschel, J. / Burnside, C. / Mignot, I. / Leibundgut, M. / Boehringer, D. / Ban, N.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation310030B_163478 Switzerland
NCCR RNA and disease program, SNSF51NF40_141735 Switzerland
CitationJournal: Cell Rep / Year: 2017
Title: The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Authors: Jendrik Hentschel / Chloe Burnside / Ingrid Mignot / Marc Leibundgut / Daniel Boehringer / Nenad Ban /
Abstract: The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death ...The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.3Dec 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
3: 50S ribosomal protein bL37
A: 23S rRNA
B: 5S rRNA
C: 50S ribosomal protein L2
D: 50S ribosomal protein L3
E: 50S ribosomal protein L4
F: 50S ribosomal protein L5
G: 50S ribosomal protein L6
H: 50S ribosomal protein L9
I: 50S ribosomal protein L10
J: 50S ribosomal protein L11
K: 50S ribosomal protein L13
L: 50S ribosomal protein L14
M: 50S ribosomal protein L15
N: 50S ribosomal protein L16
O: 50S ribosomal protein L17
P: 50S ribosomal protein L18
Q: 50S ribosomal protein L19
R: 50S ribosomal protein L20
S: 50S ribosomal protein L21
T: 50S ribosomal protein L22
U: 50S ribosomal protein L23
V: 50S ribosomal protein L24
W: 50S ribosomal protein L25
X: 50S ribosomal protein L27
Y: 50S ribosomal protein L28
Z: 50S ribosomal protein L29
a: 50S ribosomal protein L30
b: 50S ribosomal protein L32
c: 50S ribosomal protein L33 1
d: 50S ribosomal protein L34
e: 50S ribosomal protein L35
f: 50S ribosomal protein L36
g: 50S ribosomal protein L31
2: tRNA CCA-end acetylated (Phe)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,496,822448
Polymers1,486,47835
Non-polymers10,343413
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area213070 Å2
ΔGint-4898 kcal/mol
Surface area534060 Å2
MethodPISA

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Components

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50S ribosomal protein ... , 32 types, 32 molecules 3CDEFGHIJKLMNOPQRSTUVWXYZabcdefg

#1: Protein/peptide 50S ribosomal protein bL37 / / bl37


Mass: 2841.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QTP4
#4: Protein 50S ribosomal protein L2 / / uL2


Mass: 30425.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD4
#5: Protein 50S ribosomal protein L3 / / uL3


Mass: 23011.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD1
#6: Protein 50S ribosomal protein L4 / / uL4


Mass: 22920.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD2
#7: Protein 50S ribosomal protein L5 / / uL5


Mass: 21152.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG1
#8: Protein 50S ribosomal protein L6 / / uL6


Mass: 19483.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG4
#9: Protein 50S ribosomal protein L9 / / bL9


Mass: 15949.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 44 to 73 modeled as poly-alanine
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7F6
#10: Protein 50S ribosomal protein L10 / / uL10


Mass: 18035.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS62
#11: Protein 50S ribosomal protein L11 / / uL11


Mass: 15023.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS45
#12: Protein 50S ribosomal protein L13 / / uL13


Mass: 16146.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSP8
#13: Protein 50S ribosomal protein L14 / / uL14


Mass: 13400.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSF9
#14: Protein 50S ribosomal protein L15 / / uL15


Mass: 15602.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG8
#15: Protein 50S ribosomal protein L16 / / uL16


Mass: 15774.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD8
#16: Protein 50S ribosomal protein L17 / / bL17


Mass: 21892.246 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL9
#17: Protein 50S ribosomal protein L18 / / uL18


Mass: 13711.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG5
#18: Protein 50S ribosomal protein L19 / / bL19


Mass: 12892.806 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QV42
#19: Protein 50S ribosomal protein L20 / / bL20


Mass: 14494.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QYU6
#20: Protein 50S ribosomal protein L21 / / bL21


Mass: 11055.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R151
#21: Protein 50S ribosomal protein L22 / / uL22


Mass: 16353.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD6
#22: Protein 50S ribosomal protein L23 / / uL23


Mass: 11047.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD3
#23: Protein 50S ribosomal protein L24 / / uL24


Mass: 11228.946 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: residues 48 to 55 not modeled
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG0
#24: Protein 50S ribosomal protein L25 / / bL25 / General stress protein CTC


Mass: 22571.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R3D2
#25: Protein 50S ribosomal protein L27 / / bL27


Mass: 9249.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R150
#26: Protein 50S ribosomal protein L28 / / bL28


Mass: 6891.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QV03
#27: Protein 50S ribosomal protein L29 / / uL29


Mass: 8790.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSD9
#28: Protein 50S ribosomal protein L30 / / uL30


Mass: 7022.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSG7
#29: Protein 50S ribosomal protein L32 / / bL32


Mass: 6467.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R3I9
#30: Protein 50S ribosomal protein L33 1 / Ribosome / bL33


Mass: 6468.501 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QS39
#31: Protein/peptide 50S ribosomal protein L34 / / bL34


Mass: 5522.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R7K0
#32: Protein 50S ribosomal protein L35 / / bL35


Mass: 7298.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QYU7
#33: Protein/peptide 50S ribosomal protein L36 / / bL36


Mass: 4341.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0QSL4
#34: Protein 50S ribosomal protein L31 / / bL31


Mass: 8312.485 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: UniProt: A0R215

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RNA chain , 3 types, 3 molecules AB2

#2: RNA chain 23S rRNA / 23S ribosomal RNA


Mass: 1012140.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#3: RNA chain 5S rRNA / 5S ribosomal RNA


Mass: 38061.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)
References: GenBank: 118168627
#35: RNA chain tRNA CCA-end acetylated (Phe)


Mass: 894.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: tRNA CCA polyribonucleotid, acetylated (Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

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Non-polymers , 3 types, 413 molecules

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


Mass: 24.305 Da / Num. of mol.: 408 / Source method: obtained synthetically / Formula: Mg
#37: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#38: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H11NO2 / Details: tRNA CCA polyribonucleotid, acetylated (Phe)
Source: (natural) Mycobacterium smegmatis str. MC2 155 (bacteria)

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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: 50S large ribosomal subunit / Type: RIBOSOME / Entity ID: #1-#35 / Source: NATURAL
Source (natural)Organism: Mycobacterium smegmatis str. MC2 155 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding 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: 96 %

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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 / Calibrated magnification: 100719 X
Specimen holderCryogen: NITROGEN / Specimen 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) / Details: FEI EPU data collection
Image scansMovie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: 1.9_1692 / Classification: refinement
EM software
IDNameVersionCategory
1EMAN Boxer1.9particle selection
4CTFFIND3CTF correction
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionDetails: CTF correction in Relion / Type: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 224584 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementResolution: 3.203→49.359 Å / SU ML: 0.42 / σ(F): 1.04 / Phase error: 24.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2369 43228 2.51 %
Rwork0.2196 --
obs0.22 1725191 99.97 %
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_d0.008106493
ELECTRON MICROSCOPYf_angle_d1.074160029
ELECTRON MICROSCOPYf_dihedral_angle_d17.42749852
ELECTRON MICROSCOPYf_chiral_restr0.04520563
ELECTRON MICROSCOPYf_plane_restr0.0068269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2026-3.2390.517914870.508456880ELECTRON MICROSCOPY100
3.239-3.27710.400914320.373255268ELECTRON MICROSCOPY100
3.2771-3.3170.366714570.349656290ELECTRON MICROSCOPY100
3.317-3.3590.349714470.330956010ELECTRON MICROSCOPY100
3.359-3.40320.322714660.31556627ELECTRON MICROSCOPY100
3.4032-3.44980.350713810.304455639ELECTRON MICROSCOPY100
3.4498-3.49910.326814710.29556033ELECTRON MICROSCOPY100
3.4991-3.55130.299813690.286555944ELECTRON MICROSCOPY100
3.5513-3.60670.307115150.281556214ELECTRON MICROSCOPY100
3.6067-3.66590.289514360.268356156ELECTRON MICROSCOPY100
3.6659-3.72910.270514670.25456037ELECTRON MICROSCOPY100
3.7291-3.79680.271214400.247656376ELECTRON MICROSCOPY100
3.7968-3.86980.255914610.237555639ELECTRON MICROSCOPY100
3.8698-3.94880.227213820.22255955ELECTRON MICROSCOPY100
3.9488-4.03460.236414700.217956290ELECTRON MICROSCOPY100
4.0346-4.12840.221614460.208956398ELECTRON MICROSCOPY100
4.1284-4.23160.213914260.197655482ELECTRON MICROSCOPY100
4.2316-4.3460.211414210.191156305ELECTRON MICROSCOPY100
4.346-4.47380.200514050.184356427ELECTRON MICROSCOPY100
4.4738-4.61810.186915160.174355878ELECTRON MICROSCOPY100
4.6181-4.7830.189114820.171255981ELECTRON MICROSCOPY100
4.783-4.97430.184514320.167755906ELECTRON MICROSCOPY100
4.9743-5.20050.171614370.162955984ELECTRON MICROSCOPY100
5.2005-5.47430.167814040.156856333ELECTRON MICROSCOPY100
5.4743-5.81680.168914290.157456140ELECTRON MICROSCOPY100
5.8168-6.26510.160814300.151856064ELECTRON MICROSCOPY100
6.2651-6.89410.176514450.156555941ELECTRON MICROSCOPY100
6.8941-7.88820.163314500.148556288ELECTRON MICROSCOPY100
7.8882-9.9250.170313940.152555844ELECTRON MICROSCOPY100
9.925-49.3650.159314300.146655634ELECTRON MICROSCOPY99

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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.
  • 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

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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.
  • 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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