[English] 日本語
Yorodumi
- PDB-9ti8: Staphylococcus aureus 50S ribosome in complex with RRF, EF-G and ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ti8
TitleStaphylococcus aureus 50S ribosome in complex with RRF, EF-G and fusidic acid (50S-RRF-EF-G-FA)
Components
  • (50S ribosomal protein ...) x 25
  • (Large ribosomal subunit protein ...) x 3
  • 23S rRNA
  • 5S rRNA
  • Elongation factor G
  • Ribosome-recycling factor
KeywordsRIBOSOME / RRF / EF-G / Recycling
Function / homology
Function and homology information


ribosome disassembly / ribosomal large subunit binding / translation elongation factor activity / translational termination / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit ...ribosome disassembly / ribosomal large subunit binding / translation elongation factor activity / translational termination / large ribosomal subunit / transferase activity / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / tRNA binding / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / RNA binding / cytoplasm
Similarity search - Function
Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L31 type B / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II ...Ribosome recycling factor / Ribosome recycling factor domain / RRF superfamily / Ribosome recycling factor / Ribosomal protein L31 type B / Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / : / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L16 signature 1. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / : / Ribosomal protein L16 signature 2. / Ribosomal protein L16, conserved site / Ribosomal protein L17 signature. / Ribosomal L25p family / Ribosomal protein L25 / 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 L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L28/L24 superfamily / Ribosomal protein L32p, bacterial type / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L28 / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L18, bacterial-type / : / Ribosomal protein L6, bacterial-type / Ribosomal protein L5, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / : / Ribosomal protein L20 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / Ribosomal protein L14P, bacterial-type / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein L35 / Ribosomal protein L33 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L33 / Ribosomal L28 family / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 / Ribosomal protein L30, bacterial-type / L28p-like / Ribosomal protein L16 / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L34
Similarity search - Domain/homology
FUSIDIC ACID / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 ...FUSIDIC ACID / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / 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 bL36 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein bL31B / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL33A / Ribosome-recycling factor / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Elongation factor G / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.18 Å
AuthorsGonzalez-Lopez, A. / Selmer, M.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden
Uppsala Antibiotic Center Sweden
Swedish Research Council2022-04511 Sweden
CitationJournal: To Be Published
Title: Structural mechanism of ribosome recycling inhibited by fusidic acid
Authors: Gonzalez-Lopez, A. / Larsson, D.S.D. / Selmer, M.
History
DepositionDec 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 2 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 3 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Mask / Part number: 4 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: 50S ribosomal protein L28
2: 50S ribosomal protein L29
3: 50S ribosomal protein L30
4: 50S ribosomal protein L31 type B
5: Large ribosomal subunit protein bL32
6: Large ribosomal subunit protein bL33A
7: 50S ribosomal protein L34
8: 50S ribosomal protein L35
9: 50S ribosomal protein L36
A: 23S rRNA
B: 5S rRNA
C: Ribosome-recycling factor
E: Elongation factor G
G: 50S ribosomal protein L2
H: 50S ribosomal protein L3
I: 50S ribosomal protein L4
J: 50S ribosomal protein L5
K: Large ribosomal subunit protein uL6
M: 50S ribosomal protein L13
N: 50S ribosomal protein L14
O: 50S ribosomal protein L15
P: 50S ribosomal protein L16
Q: 50S ribosomal protein L17
R: 50S ribosomal protein L18
S: 50S ribosomal protein L19
T: 50S ribosomal protein L20
U: 50S ribosomal protein L21
V: 50S ribosomal protein L22
W: 50S ribosomal protein L23
X: 50S ribosomal protein L24
Y: 50S ribosomal protein L25
Z: 50S ribosomal protein L27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,458,854151
Polymers1,454,96932
Non-polymers3,886119
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

+
50S ribosomal protein ... , 25 types, 25 molecules 1234789GHIJMNOPQRSTUVWXYZ

#1: Protein 50S ribosomal protein L28


Mass: 6995.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ60
#2: Protein 50S ribosomal protein L29


Mass: 8105.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW14
#3: Protein 50S ribosomal protein L30


Mass: 6565.683 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0G2
#4: Protein 50S ribosomal protein L31 type B


Mass: 9737.912 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FWD8
#7: Protein/peptide 50S ribosomal protein L34


Mass: 5454.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FUQ0
#8: Protein 50S ribosomal protein L35


Mass: 7722.368 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ0
#9: Protein/peptide 50S ribosomal protein L36


Mass: 4318.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW29
#14: Protein 50S ribosomal protein L2


Mass: 30217.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P60430
#15: Protein 50S ribosomal protein L3


Mass: 23760.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW06
#16: Protein 50S ribosomal protein L4


Mass: 22495.697 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW07
#17: Protein 50S ribosomal protein L5


Mass: 20296.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW18
#19: Protein 50S ribosomal protein L13


Mass: 16359.427 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW38
#20: Protein 50S ribosomal protein L14


Mass: 13157.342 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW16
#21: Protein 50S ribosomal protein L15


Mass: 15628.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: P0A0F8
#22: Protein 50S ribosomal protein L16


Mass: 16274.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW13
#23: Protein 50S ribosomal protein L17


Mass: 13771.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW33
#24: Protein 50S ribosomal protein L18


Mass: 13124.093 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW22
#25: Protein 50S ribosomal protein L19


Mass: 13392.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZ42
#26: Protein 50S ribosomal protein L20


Mass: 13720.295 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXQ1
#27: Protein 50S ribosomal protein L21


Mass: 11354.081 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXS8
#28: Protein 50S ribosomal protein L22


Mass: 12857.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW11
#29: Protein 50S ribosomal protein L23


Mass: 10625.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW08
#30: Protein 50S ribosomal protein L24


Mass: 11561.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW17
#31: Protein 50S ribosomal protein L25 / General stress protein CTC


Mass: 23810.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2G0S0
#32: Protein 50S ribosomal protein L27


Mass: 10334.798 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FXT0

-
Large ribosomal subunit protein ... , 3 types, 3 molecules 56K

#5: Protein Large ribosomal subunit protein bL32 / 50S ribosomal protein L32


Mass: 6500.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FZF1
#6: Protein/peptide Large ribosomal subunit protein bL33A / 50S ribosomal protein L33 1


Mass: 5944.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FYU6
#18: Protein Large ribosomal subunit protein uL6 / 50S ribosomal protein L6


Mass: 19818.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: UniProt: Q2FW21

-
RNA chain , 2 types, 2 molecules AB

#10: RNA chain 23S rRNA


Mass: 946811.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
#11: RNA chain 5S rRNA


Mass: 36974.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
References: GenBank: CP000253.1

-
Protein , 2 types, 2 molecules CE

#12: Protein Ribosome-recycling factor / RRF / Ribosome-releasing factor


Mass: 20576.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: frr, SAOUHSC_01236 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2FZ21
#13: Protein Elongation factor G / EF-G


Mass: 76699.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: fusA, SAOUHSC_00529 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G0N1

-
Non-polymers , 4 types, 119 molecules

#33: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#34: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 115 / Source method: obtained synthetically / Formula: Mg
#35: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#36: Chemical ChemComp-FUA / FUSIDIC ACID


Mass: 516.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H48O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic, Antimicrobial*YM

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: S. aureus 50S ribosome in complex with ribosome recycling factor (RRF) and Elongation factor G (EF-G)
Type: RIBOSOME / Entity ID: #1-#32 / Source: NATURAL
Molecular weightValue: 2.3 MDa / Experimental value: NO
Source (natural)Organism: Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES-KOHC8H18N2O4S-KOH1
295 mMPotassium chlorideKCl1
35 mMAmmonium chlorideNH4Cl1
45 mMMagnesium acetateMg(OAc)21
50.5 mMCalcium chlorideCaCl21
68 mMPutrescine(CH2)4(NH2)21
71 mMSpermidineC7H19N31
85 mMBeta-mercaptoethanolC2H6OS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.45 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 56478
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1-cuda12+250814particle selection
2EPUimage acquisition
4cryoSPARC4.7.1-cuda12+250814CTF correction
7Coot0.9.8.96model fitting
9Coot0.9.8.96model refinement
10Servalcat0.4.105model refinement
11cryoSPARC4.7.1-cuda12+250814initial Euler assignment
12cryoSPARC4.7.1-cuda12+250814final Euler assignment
13cryoSPARC4.7.1-cuda12+250814classification
14cryoSPARC4.7.1-cuda12+2508143D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2556350
3D reconstructionResolution: 2.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77333 / Symmetry type: POINT
Atomic model building

3D fitting-ID: 1

IDPDB-IDAccession codeInitial refinement model-IDSource nameTypeDetails (eV)
19GHG

9ghg

9GHG1PDBexperimental model
2AlphaFoldin silico modelchain C
RefinementResolution: 2.18→403.2 Å / Num. reflection obs: 13250656 / Average fsc work: 0.825
Displacement parametersBiso mean: 47.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.00291018630.011
ELECTRON MICROSCOPYs_angle_nonh_deg0.89041517601.8455
ELECTRON MICROSCOPYs_dihedral_angle_1_deg4.828539455
ELECTRON MICROSCOPYs_dihedral_angle_2_deg2.10134975
ELECTRON MICROSCOPYs_dihedral_angle_3_deg9.0176892610
ELECTRON MICROSCOPYs_dihedral_angle_6_deg9.5322170610
ELECTRON MICROSCOPYs_chiral_restr0.0292193580.1176
ELECTRON MICROSCOPYs_planes0.0037902900.02
ELECTRON MICROSCOPYs_nbd0.18951140300.2
ELECTRON MICROSCOPYs_nbtor0.18781158010.2
ELECTRON MICROSCOPYs_hbond_nbd0.131539010.2
LS refinement shell
Resolution (Å)Refine-IDNum. reflection obsFsc work
2.18-2.197ELECTRON MICROSCOPY3089290.6506
2.197-2.209ELECTRON MICROSCOPY2105910.6698
2.209-2.221ELECTRON MICROSCOPY2076730.6795
2.221-2.234ELECTRON MICROSCOPY2064210.6868
2.234-2.246ELECTRON MICROSCOPY2034610.6928
2.246-2.259ELECTRON MICROSCOPY2011110.6988
2.259-2.272ELECTRON MICROSCOPY1997290.7052
2.272-2.284ELECTRON MICROSCOPY1968490.7114
2.284-2.297ELECTRON MICROSCOPY1947870.7168
2.297-2.311ELECTRON MICROSCOPY1909090.7215
2.311-2.324ELECTRON MICROSCOPY1910850.7253
2.324-2.337ELECTRON MICROSCOPY1879930.7305
2.337-2.351ELECTRON MICROSCOPY1858110.736
2.351-2.365ELECTRON MICROSCOPY1829050.7402
2.365-2.379ELECTRON MICROSCOPY1830610.7439
2.379-2.393ELECTRON MICROSCOPY1792830.7491
2.393-2.407ELECTRON MICROSCOPY1772290.7541
2.407-2.422ELECTRON MICROSCOPY1757490.757
2.422-2.436ELECTRON MICROSCOPY1718590.7602
2.436-2.451ELECTRON MICROSCOPY1720330.7624
2.451-2.466ELECTRON MICROSCOPY1679850.7627
2.466-2.481ELECTRON MICROSCOPY1676410.7671
2.481-2.497ELECTRON MICROSCOPY1639950.7716
2.497-2.512ELECTRON MICROSCOPY1642810.7755
2.512-2.528ELECTRON MICROSCOPY1611090.7775
2.528-2.544ELECTRON MICROSCOPY1580230.7818
2.544-2.56ELECTRON MICROSCOPY1565410.7868
2.56-2.576ELECTRON MICROSCOPY1553970.7927
2.576-2.593ELECTRON MICROSCOPY1529290.796
2.593-2.61ELECTRON MICROSCOPY1499790.7965
2.61-2.627ELECTRON MICROSCOPY1497490.8
2.627-2.644ELECTRON MICROSCOPY1472370.8032
2.644-2.661ELECTRON MICROSCOPY1449430.8081
2.661-2.679ELECTRON MICROSCOPY1425850.8128
2.679-2.697ELECTRON MICROSCOPY1414170.8146
2.697-2.715ELECTRON MICROSCOPY1400950.8168
2.715-2.734ELECTRON MICROSCOPY1377930.8164
2.734-2.752ELECTRON MICROSCOPY1357810.8184
2.752-2.771ELECTRON MICROSCOPY1343610.8251
2.771-2.79ELECTRON MICROSCOPY1324870.8324
2.79-2.81ELECTRON MICROSCOPY1301770.8381
2.81-2.829ELECTRON MICROSCOPY1272090.84
2.829-2.849ELECTRON MICROSCOPY1273510.8421
2.849-2.87ELECTRON MICROSCOPY1249530.8483
2.87-2.89ELECTRON MICROSCOPY1234090.8566
2.89-2.911ELECTRON MICROSCOPY1207090.8648
2.911-2.932ELECTRON MICROSCOPY1191990.8713
2.932-2.954ELECTRON MICROSCOPY1189090.8751
2.954-2.976ELECTRON MICROSCOPY1164810.8784
2.976-2.998ELECTRON MICROSCOPY1136470.8855
2.998-3.02ELECTRON MICROSCOPY1131570.8921
3.02-3.043ELECTRON MICROSCOPY1107610.8977
3.043-3.066ELECTRON MICROSCOPY1104970.9012
3.066-3.089ELECTRON MICROSCOPY1069590.9052
3.09-3.113ELECTRON MICROSCOPY1062130.9104
3.114-3.138ELECTRON MICROSCOPY1053330.915
3.138-3.162ELECTRON MICROSCOPY1027510.9186
3.162-3.187ELECTRON MICROSCOPY1010250.9214
3.187-3.213ELECTRON MICROSCOPY990370.922
3.213-3.238ELECTRON MICROSCOPY991270.923
3.239-3.265ELECTRON MICROSCOPY962850.924
3.265-3.291ELECTRON MICROSCOPY951250.9251
3.291-3.318ELECTRON MICROSCOPY936210.9256
3.319-3.346ELECTRON MICROSCOPY922150.9248
3.346-3.374ELECTRON MICROSCOPY909010.9243
3.374-3.402ELECTRON MICROSCOPY883890.9247
3.403-3.431ELECTRON MICROSCOPY869470.9252
3.432-3.461ELECTRON MICROSCOPY864930.925
3.461-3.491ELECTRON MICROSCOPY849250.923
3.491-3.521ELECTRON MICROSCOPY824970.9227
3.521-3.552ELECTRON MICROSCOPY820510.9222
3.552-3.584ELECTRON MICROSCOPY803290.9209
3.584-3.616ELECTRON MICROSCOPY789330.9207
3.616-3.649ELECTRON MICROSCOPY766990.9228
3.649-3.682ELECTRON MICROSCOPY759570.9248
3.682-3.716ELECTRON MICROSCOPY753250.9258
3.716-3.751ELECTRON MICROSCOPY731550.9245
3.751-3.786ELECTRON MICROSCOPY717970.922
3.786-3.822ELECTRON MICROSCOPY702970.9207
3.822-3.858ELECTRON MICROSCOPY702690.9212
3.858-3.896ELECTRON MICROSCOPY669430.9225
3.896-3.934ELECTRON MICROSCOPY668610.9231
3.934-3.972ELECTRON MICROSCOPY654970.9219
3.972-4.012ELECTRON MICROSCOPY640950.9202
4.012-4.052ELECTRON MICROSCOPY629050.9199
4.052-4.093ELECTRON MICROSCOPY610450.9197
4.093-4.135ELECTRON MICROSCOPY611490.92
4.135-4.178ELECTRON MICROSCOPY593830.9191
4.178-4.222ELECTRON MICROSCOPY579450.9183
4.222-4.266ELECTRON MICROSCOPY561610.917
4.267-4.312ELECTRON MICROSCOPY553630.9157
4.312-4.359ELECTRON MICROSCOPY542730.9154
4.359-4.406ELECTRON MICROSCOPY531730.9151
4.407-4.455ELECTRON MICROSCOPY518850.9136
4.455-4.505ELECTRON MICROSCOPY512950.913
4.505-4.556ELECTRON MICROSCOPY498450.9131
4.556-4.608ELECTRON MICROSCOPY486370.9124
4.608-4.661ELECTRON MICROSCOPY472390.9109
4.661-4.715ELECTRON MICROSCOPY465690.9097
4.716-4.771ELECTRON MICROSCOPY457690.9097
4.772-4.828ELECTRON MICROSCOPY440670.9089
4.829-4.887ELECTRON MICROSCOPY432730.9088
4.887-4.947ELECTRON MICROSCOPY423330.9101
4.947-5.008ELECTRON MICROSCOPY415930.9093
5.009-5.071ELECTRON MICROSCOPY400150.9086
5.072-5.136ELECTRON MICROSCOPY391890.9115
5.136-5.202ELECTRON MICROSCOPY378610.913
5.203-5.27ELECTRON MICROSCOPY374550.9132
5.271-5.34ELECTRON MICROSCOPY363730.9126
5.341-5.411ELECTRON MICROSCOPY350130.913
5.412-5.485ELECTRON MICROSCOPY348490.9126
5.486-5.561ELECTRON MICROSCOPY333430.9134
5.562-5.639ELECTRON MICROSCOPY328650.9124
5.639-5.719ELECTRON MICROSCOPY312850.9119
5.719-5.8ELECTRON MICROSCOPY306030.9121
5.802-5.886ELECTRON MICROSCOPY303130.9119
5.886-5.973ELECTRON MICROSCOPY287410.9088
5.973-6.062ELECTRON MICROSCOPY284550.907
6.063-6.155ELECTRON MICROSCOPY271570.9065
6.156-6.251ELECTRON MICROSCOPY270450.9055
6.251-6.349ELECTRON MICROSCOPY257770.9041
6.351-6.451ELECTRON MICROSCOPY244350.9014
6.451-6.555ELECTRON MICROSCOPY242770.9022
6.556-6.664ELECTRON MICROSCOPY233170.9039
6.665-6.776ELECTRON MICROSCOPY228510.9053
6.777-6.891ELECTRON MICROSCOPY217450.9071
6.893-7.011ELECTRON MICROSCOPY210330.909
7.012-7.135ELECTRON MICROSCOPY207130.9116
7.137-7.264ELECTRON MICROSCOPY196470.9157
7.265-7.397ELECTRON MICROSCOPY188410.9174
7.398-7.534ELECTRON MICROSCOPY182170.917
7.537-7.679ELECTRON MICROSCOPY177270.9179
7.68-7.828ELECTRON MICROSCOPY171250.9194
7.831-7.981ELECTRON MICROSCOPY161250.9195
7.985-8.144ELECTRON MICROSCOPY158710.9166
8.146-8.312ELECTRON MICROSCOPY152250.9146
8.314-8.487ELECTRON MICROSCOPY145330.9199
8.489-8.669ELECTRON MICROSCOPY137530.9251
8.671-8.858ELECTRON MICROSCOPY130590.9271
8.862-9.059ELECTRON MICROSCOPY129730.9253
9.064-9.267ELECTRON MICROSCOPY120210.9259
9.27-9.482ELECTRON MICROSCOPY117310.9327
9.488-9.714ELECTRON MICROSCOPY109810.9388
9.716-9.953ELECTRON MICROSCOPY107250.9425
9.956-10.205ELECTRON MICROSCOPY101170.9446
10.208-10.47ELECTRON MICROSCOPY93750.9473
10.474-10.745ELECTRON MICROSCOPY91330.9509
10.753-11.043ELECTRON MICROSCOPY85770.955
11.048-11.354ELECTRON MICROSCOPY82270.9573
11.359-11.678ELECTRON MICROSCOPY75970.959
11.688-12.032ELECTRON MICROSCOPY73770.9608
12.037-12.402ELECTRON MICROSCOPY69010.9604
12.408-12.795ELECTRON MICROSCOPY63030.961
12.802-13.214ELECTRON MICROSCOPY60730.9639
13.221-13.654ELECTRON MICROSCOPY56130.9639
13.67-14.141ELECTRON MICROSCOPY52750.9601
14.15-14.655ELECTRON MICROSCOPY49810.9594
14.664-15.196ELECTRON MICROSCOPY45330.9628
15.218-15.803ELECTRON MICROSCOPY43030.9669
15.815-16.447ELECTRON MICROSCOPY40170.9675
16.461-17.146ELECTRON MICROSCOPY35650.9649
17.161-17.907ELECTRON MICROSCOPY33010.9661
17.924-18.718ELECTRON MICROSCOPY29910.9686
18.759-19.651ELECTRON MICROSCOPY28570.9699
19.674-20.657ELECTRON MICROSCOPY25170.968
20.711-21.739ELECTRON MICROSCOPY21790.9686
21.803-23.012ELECTRON MICROSCOPY20850.9727
23.049-24.403ELECTRON MICROSCOPY18610.9697
24.448-25.972ELECTRON MICROSCOPY16690.9664
26.136-27.757ELECTRON MICROSCOPY13110.9691
27.823-29.724ELECTRON MICROSCOPY12490.9648
29.887-32.179ELECTRON MICROSCOPY10890.9519
32.386-34.962ELECTRON MICROSCOPY9070.9478
35.094-37.93ELECTRON MICROSCOPY7290.949
38.444-42.267ELECTRON MICROSCOPY6250.9483
42.501-47.191ELECTRON MICROSCOPY5710.9582
47.518-53.405ELECTRON MICROSCOPY3810.9568
53.88-61.487ELECTRON MICROSCOPY3010.9519
62.215-71.276ELECTRON MICROSCOPY2250.9706
73.614-87.985ELECTRON MICROSCOPY1750.9794
90.158-111.828ELECTRON MICROSCOPY1050.9775
116.394-142.553ELECTRON MICROSCOPY490.9688
164.606-403.2ELECTRON MICROSCOPY400.9063

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

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

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

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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more