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- PDB-4csu: Cryo-EM structures of the 50S ribosome subunit bound with ObgE -

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Basic information

Entry
Database: PDB / ID: 4csu
TitleCryo-EM structures of the 50S ribosome subunit bound with ObgE
Components
  • (50S RIBOSOMAL PROTEIN ...) x 30
  • 23S RRNA23S ribosomal RNA
  • 5S RRNA5S ribosomal RNA
  • GTPASE OBGE/CGTA
KeywordsRIBOSOME / (P)PPGPP / OBG / RIBOSOME ASSEMBLY / STRINGENT RESPONSE / GTPASE
Function / homology
Function and homology information


guanyl ribonucleotide binding / negative regulation of ribosome biogenesis / dormancy process / Hydrolases, Acting on acid anhydrides, Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit binding / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity ...guanyl ribonucleotide binding / negative regulation of ribosome biogenesis / dormancy process / Hydrolases, Acting on acid anhydrides, Acting on GTP to facilitate cellular and subcellular movement / ribosomal large subunit binding / stringent response / positive regulation of ribosome biogenesis / endoribonuclease inhibitor activity / negative regulation of endoribonuclease activity / translation repressor activity / maturation of LSU-rRNA / mature ribosome assembly / negative regulation of translational initiation / ribosome assembly / polysomal ribosome / translational termination / assembly of large subunit precursor of preribosome / DNA-templated transcription, termination / translation repressor activity, mRNA regulatory element binding / DNA-binding transcription repressor activity / regulation of cell growth / response to reactive oxygen species / chromosome segregation / cytoplasmic translation / large ribosomal subunit rRNA binding / GDP binding / cytosolic large ribosomal subunit / large ribosomal subunit / ribosomal large subunit assembly / ribosome binding / 5S rRNA binding / protein-DNA complex / response to radiation / transferase activity / tRNA binding / negative regulation of translation / ribosome / rRNA binding / structural constituent of ribosome / translation / GTPase activity / mRNA binding / response to antibiotic / GTP binding / negative regulation of transcription, DNA-templated / magnesium ion binding / RNA binding / DNA binding / zinc ion binding / cytosol
Ribosomal protein L2, C-terminal / Ribosomal protein L35 / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site ...Ribosomal protein L2, C-terminal / Ribosomal protein L35 / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L11, C-terminal / Ribosomal protein L11, N-terminal / Ribosomal protein L11, conserved site / Ribosomal protein L16, conserved site / Ribosomal protein L5, conserved site / Ribosomal protein L5, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L18e/L15P / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L9, C-terminal / Ribosomal prokaryotic L21 protein / Ribosomal protein L2, conserved site / Ribosomal protein L5 domain superfamily / Ribosomal protein L13, conserved site / Ribosomal protein L4 domain superfamily / Ribosomal protein L1, conserved site / Ribosomal protein L1-like / Ribosomal protein L28/L24 / P-loop containing nucleoside triphosphate hydrolase / Ribosomal protein L9, N-terminal / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L21-like / Ribosomal protein L29, conserved site / 50S ribosomal protein uL4 / Ribosomal protein L25/L23 / GTP-binding protein Obg/CgtA / Ribosomal protein L2, domain 2 / Ribosomal protein L2, domain 3 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L10e/L16 / Ribosomal protein L30, conserved site / Ribosomal protein L19, conserved site / Ribosomal protein L25, short-form / Ribosomal protein L21, conserved site / Ribosomal protein L22/L17, conserved site / Ribosomal protein L27, conserved site / Ribosomal protein L33, conserved site / Ribosomal protein L35, conserved site / Ribosomal protein L6, bacterial-type / Ribosomal protein L3, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L14P, conserved site / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L25 / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L19 superfamily / Ribosomal Protein L26/L24, KOW domain / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L22p/L17e / Ribosomal protein L14p/L23e / Ribosomal protein L16p/L10e / Ribosomal protein L23 / Ribosomal protein L5 / Ribosomal protein L3 / Ribosomal protein L30p/L7e / Ribosomal protein L35 superfamily / Ribosomal protein L6 / Ribosomal protein L36 / Ribosomal protein L20 / KOW motif / Ribosomal protein L34 / Ribosomal protein L33 / Ribosomal protein L13 / Ribosomal protein L4/L1 family / ribosomal L5P family C-terminus / Ribosomal protein L33 superfamily / Ribosomal protein L28/L24 superfamily / Ribosomal protein L15 / Ribosomal L18e/L15P superfamily / OBG-type guanine nucleotide-binding (G) domain / Ribosomal protein L5, C-terminal / Ribosomal protein L5, N-terminal / L28p-like / GTP-binding protein, Obg-type / Ribosomal protein L20, C-terminal / Ribosomal protein L36 superfamily / Ribosomal protein L29/L35 superfamily / L21-like superfamily / Ribosomal protein L17 superfamily / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L22/L17 superfamily / GTP1/OBG domain superfamily / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein L9, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L14 superfamily / Ribosomal protein L13 superfamily / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L23/L15e core domain superfamily / Nucleic acid-binding, OB-fold / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / 50S ribosome-binding GTPase
GTPase ObgE/CgtA / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L3 / 50S ribosomal protein L2 / 50S ribosomal protein L16 / 50S ribosomal protein L24 ...GTPase ObgE/CgtA / 50S ribosomal protein L17 / 50S ribosomal protein L21 / 50S ribosomal protein L30 / 50S ribosomal protein L6 / 50S ribosomal protein L18 / 50S ribosomal protein L3 / 50S ribosomal protein L2 / 50S ribosomal protein L16 / 50S ribosomal protein L24 / 50S ribosomal protein L4 / 50S ribosomal protein L22 / 50S ribosomal protein L5 / 50S ribosomal protein L23 / 50S ribosomal protein L27 / 50S ribosomal protein L14 / 50S ribosomal protein L13 / 50S ribosomal protein L9 / 50S ribosomal protein L36 / 50S ribosomal protein L35 / 50S ribosomal protein L34 / 50S ribosomal protein L33 / 50S ribosomal protein L32 / 50S ribosomal protein L29 / 50S ribosomal protein L28 / 50S ribosomal protein L20 / 50S ribosomal protein L1 / 50S ribosomal protein L19 / 50S ribosomal protein L11 / 50S ribosomal protein L15 / 50S ribosomal protein L25
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsFeng, B. / Mandava, C.S. / Guo, Q. / Wang, J. / Cao, W. / Li, N. / Zhang, Y. / Zhang, Y. / Wang, Z. / Wu, J. / Sanyal, S. / Lei, J. / Gao, N.
CitationJournal: PLoS Biol. / Year: 2014
Title: Structural and functional insights into the mode of action of a universally conserved Obg GTPase.
Authors: Boya Feng / Chandra Sekhar Mandava / Qiang Guo / Jie Wang / Wei Cao / Ningning Li / Yixiao Zhang / Yanqing Zhang / Zhixin Wang / Jiawei Wu / Suparna Sanyal / Jianlin Lei / Ning Gao /
Abstract: Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed ...Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed molecular roles in two global processes, ribosome assembly and stringent response. Here, using pre-steady state fast kinetics we demonstrate that ObgE is an anti-association factor, which prevents ribosomal subunit association and downstream steps in translation by binding to the 50S subunit. ObgE is a ribosome dependent GTPase; however, upon binding to guanosine tetraphosphate (ppGpp), the global regulator of stringent response, ObgE exhibits an enhanced interaction with the 50S subunit, resulting in increased equilibrium dissociation of the 70S ribosome into subunits. Furthermore, our cryo-electron microscopy (cryo-EM) structure of the 50S·ObgE·GMPPNP complex indicates that the evolutionarily conserved N-terminal domain (NTD) of ObgE is a tRNA structural mimic, with specific interactions with peptidyl-transferase center, displaying a marked resemblance to Class I release factors. These structural data might define ObgE as a specialized translation factor related to stress responses, and provide a framework towards future elucidation of functional interplay between ObgE and ribosome-associated (p)ppGpp regulators. Together with published data, our results suggest that ObgE might act as a checkpoint in final stages of the 50S subunit assembly under normal growth conditions. And more importantly, ObgE, as a (p)ppGpp effector, might also have a regulatory role in the production of the 50S subunit and its participation in translation under certain stressed conditions. Thus, our findings might have uncovered an under-recognized mechanism of translation control by environmental cues.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 2.0Aug 2, 2017Group: Atomic model / Data collection / Derived calculations
Category: atom_site / em_software / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "KA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "WA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

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Assembly

Deposited unit
0: 50S RIBOSOMAL PROTEIN L28
1: 50S RIBOSOMAL PROTEIN L29
2: 50S RIBOSOMAL PROTEIN L30
3: 50S RIBOSOMAL PROTEIN L32
4: 50S RIBOSOMAL PROTEIN L33
5: 50S RIBOSOMAL PROTEIN L1
6: 50S RIBOSOMAL PROTEIN L34
7: 50S RIBOSOMAL PROTEIN L35
8: 50S RIBOSOMAL PROTEIN L36
9: GTPASE OBGE/CGTA
A: 5S RRNA
B: 23S 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 L11
J: 50S RIBOSOMAL PROTEIN L13
K: 50S RIBOSOMAL PROTEIN L14
L: 50S RIBOSOMAL PROTEIN L15
M: 50S RIBOSOMAL PROTEIN L16
N: 50S RIBOSOMAL PROTEIN L17
O: 50S RIBOSOMAL PROTEIN L18
P: 50S RIBOSOMAL PROTEIN L19
Q: 50S RIBOSOMAL PROTEIN L20
R: 50S RIBOSOMAL PROTEIN L21
S: 50S RIBOSOMAL PROTEIN L22
T: 50S RIBOSOMAL PROTEIN L23
U: 50S RIBOSOMAL PROTEIN L24
W: 50S RIBOSOMAL PROTEIN L25
Y: 50S RIBOSOMAL PROTEIN L27


Theoretical massNumber of molelcules
Total (without water)1,422,77733
Polymers1,422,77733
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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50S RIBOSOMAL PROTEIN ... , 30 types, 30 molecules 012345678CDEFGHIJKLMNOPQRSTUWY

#1: Protein/peptide 50S RIBOSOMAL PROTEIN L28 /


Mass: 8896.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7M2
#2: Protein/peptide 50S RIBOSOMAL PROTEIN L29 /


Mass: 7286.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7M6
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L30 /


Mass: 6423.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0AG51
#4: Protein/peptide 50S RIBOSOMAL PROTEIN L32 /


Mass: 6332.249 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7N4
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L33 /


Mass: 6257.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7N9
#6: Protein/peptide 50S RIBOSOMAL PROTEIN L1 /


Mass: 24765.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7L0
#7: Protein/peptide 50S RIBOSOMAL PROTEIN L34 / / RIBOSOMAL PROTEIN A


Mass: 5397.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7P5
#8: Protein/peptide 50S RIBOSOMAL PROTEIN L35 /


Mass: 7181.835 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7Q1
#9: Protein/peptide 50S RIBOSOMAL PROTEIN L36 / / RIBOSOMAL PROTEIN B


Mass: 4377.390 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7Q6
#13: Protein/peptide 50S RIBOSOMAL PROTEIN L2 /


Mass: 29792.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P60422
#14: Protein/peptide 50S RIBOSOMAL PROTEIN L3 /


Mass: 22277.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P60438
#15: Protein/peptide 50S RIBOSOMAL PROTEIN L4 /


Mass: 22121.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P60723
#16: Protein/peptide 50S RIBOSOMAL PROTEIN L5 /


Mass: 20202.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P62399
#17: Protein/peptide 50S RIBOSOMAL PROTEIN L6 /


Mass: 18801.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0AG55
#18: Protein/peptide 50S RIBOSOMAL PROTEIN L9 /


Mass: 15789.020 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7R1
#19: Protein/peptide 50S RIBOSOMAL PROTEIN L11 /


Mass: 14763.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7J7
#20: Protein/peptide 50S RIBOSOMAL PROTEIN L13 /


Mass: 16050.606 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0AA10
#21: Protein/peptide 50S RIBOSOMAL PROTEIN L14 /


Mass: 13565.067 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0ADY3
#22: Protein/peptide 50S RIBOSOMAL PROTEIN L15 /


Mass: 14877.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P02413
#23: Protein/peptide 50S RIBOSOMAL PROTEIN L16 /


Mass: 15312.269 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0ADY7
#24: Protein/peptide 50S RIBOSOMAL PROTEIN L17 /


Mass: 14393.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0AG44
#25: Protein/peptide 50S RIBOSOMAL PROTEIN L18 /


Mass: 12663.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0C018
#26: Protein/peptide 50S RIBOSOMAL PROTEIN L19 /


Mass: 13028.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7K6
#27: Protein/peptide 50S RIBOSOMAL PROTEIN L20 /


Mass: 13396.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7L3
#28: Protein/peptide 50S RIBOSOMAL PROTEIN L21 /


Mass: 11586.374 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0AG48
#29: Protein/peptide 50S RIBOSOMAL PROTEIN L22 /


Mass: 12253.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P61175
#30: Protein/peptide 50S RIBOSOMAL PROTEIN L23 /


Mass: 11222.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0ADZ0
#31: Protein/peptide 50S RIBOSOMAL PROTEIN L24 /


Mass: 11208.054 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P60624
#32: Protein/peptide 50S RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P68919
#33: Protein/peptide 50S RIBOSOMAL PROTEIN L27 /


Mass: 9015.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P0A7L8

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Protein/peptide , 1 types, 1 molecules 9

#10: Protein/peptide GTPASE OBGE/CGTA / GTP-BINDING PROTEIN OBG / OBGE


Mass: 43340.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P42641

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RNA chain , 2 types, 2 molecules AB

#11: RNA chain 5S RRNA / 5S ribosomal RNA


Mass: 38177.762 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12
#12: RNA chain 23S RRNA / 23S ribosomal RNA


Mass: 941306.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12

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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 RIBOSOME BOUND WITH OBGE / Type: RIBOSOME
Buffer solutionName: 20MM TRIS-HCL, 100MM NH4CL,10MM MGCL2 / pH: 7.5 / Details: 20MM TRIS-HCL, 100MM NH4CL,10MM MGCL2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jul 27, 2011
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: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI EAGLE (4k x 4k)
Image scansNum. digital images: 2000

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Processing

EM software
IDNameCategory
1MDFFmodel fitting
2RELION3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: REFERENCE PROJECTIONS / Resolution: 5.5 Å / Num. of particles: 102814 / Nominal pixel size: 1.5 Å / Actual pixel size: 1.5 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2605. (DEPOSITION ID: 12315)
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 3OFC

3ofc
PDB Unreleased entry

RefinementHighest resolution: 5.5 Å
Refinement stepCycle: LAST / Highest resolution: 5.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29853 64772 0 0 94625

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