[English] 日本語
Yorodumi
- PDB-2j28: MODEL OF E. COLI SRP BOUND TO 70S RNCS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j28
TitleMODEL OF E. COLI SRP BOUND TO 70S RNCS
Components
  • (50S RIBOSOMAL PROTEIN ...) x 29
  • 23S RIBOSOMAL RNA
  • 4.5S SIGNAL RECOGNITION PARTICLE RNA
  • 5S RIBOSOMAL RNA
  • SIGNAL RECOGNITION PARTICLE 54
  • SIGNAL SEQUENCE
KeywordsRIBOSOME / PROTEIN-RNA COMPLEX / SIGNAL RECOGNITION PARTICLE
Function / homology
Function and homology information


absorption of visible light / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane ...absorption of visible light / G protein-coupled photoreceptor activity / signal recognition particle / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / negative regulation of cytoplasmic translational initiation / photoreceptor outer segment membrane / stringent response / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / translation repressor activity / translational initiation / negative regulation of DNA-templated DNA replication initiation / visual perception / ribosome assembly / mRNA regulatory element binding translation repressor activity / response to reactive oxygen species / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / : / regulation of cell growth / DNA-templated transcription termination / response to radiation / mRNA 5'-UTR binding / photoreceptor disc membrane / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / transferase activity / tRNA binding / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / mRNA binding / GTPase activity / negative regulation of DNA-templated transcription / GTP binding / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily ...Signal recognition particle protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / Ribosomal protein L25, short-form / Ribosomal protein L11, bacterial-type / Ribosomal protein L31 type A / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal protein L11, conserved site / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11 signature. / Ribosomal protein L16 signature 1. / : / Serpentine type 7TM GPCR chemoreceptor Srsx / 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 L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / 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 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 / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / L28p-like / Ribosomal protein L20 / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rhodopsin / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 ...RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Rhodopsin / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein uL11 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL31 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein bL34 / Large ribosomal subunit protein bL35 / 50S ribosomal protein L35 / Large ribosomal subunit protein bL36A / Large ribosomal subunit protein bL9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL17 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL6 / Signal recognition particle protein / Large ribosomal subunit protein uL18 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein bL25
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsHalic, M. / Blau, M. / Becker, T. / Mielke, T. / Pool, M.R. / Wild, K. / Sinning, I. / Beckmann, R.
CitationJournal: Nature / Year: 2006
Title: Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Authors: Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann /
Abstract: Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal ...Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 19, 2017Group: Other
Revision 1.4Aug 30, 2017Group: Data collection / Source and taxonomy / Category: em_image_scans / entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Oct 3, 2018Group: Data collection / Derived calculations
Category: em_software / ndb_struct_conf_na ...em_software / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn
Item: _em_software.image_processing_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-1261
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1262
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-1263
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: 50S RIBOSOMAL PROTEIN L32
1: 50S RIBOSOMAL PROTEIN L33
2: 50S RIBOSOMAL PROTEIN L34
3: 50S RIBOSOMAL PROTEIN L35
4: 50S RIBOSOMAL PROTEIN L36
7: SIGNAL SEQUENCE
8: 4.5S SIGNAL RECOGNITION PARTICLE RNA
9: SIGNAL RECOGNITION PARTICLE 54
A: 5S RIBOSOMAL RNA
B: 23S RIBOSOMAL RNA
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
V: 50S RIBOSOMAL PROTEIN L25
W: 50S RIBOSOMAL PROTEIN L27
X: 50S RIBOSOMAL PROTEIN L29
Y: 50S RIBOSOMAL PROTEIN L30
Z: 50S RIBOSOMAL PROTEIN L31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,428,776145
Polymers1,426,07834
Non-polymers2,698111
Water9,224512
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

-
Components

+
50S RIBOSOMAL PROTEIN ... , 29 types, 29 molecules 01234CDEFGHIJKLMNOPQRSTUVWXYZ

#1: Protein 50S RIBOSOMAL PROTEIN L32 /


Mass: 6332.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7N4
#2: Protein 50S RIBOSOMAL PROTEIN L33 /


Mass: 6257.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7N9
#3: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 5397.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7P5
#4: Protein 50S RIBOSOMAL PROTEIN L35 /


Mass: 7181.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7Q2, UniProt: P0A7Q1*PLUS
#5: Protein/peptide 50S RIBOSOMAL PROTEIN L36 /


Mass: 4377.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7Q6
#11: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 29248.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P60422
#12: Protein 50S RIBOSOMAL PROTEIN L3 /


Mass: 22277.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P60438
#13: Protein 50S RIBOSOMAL PROTEIN L4 /


Mass: 22121.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P60723
#14: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 20202.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P62399
#15: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 18801.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG55
#16: Protein 50S RIBOSOMAL PROTEIN L9 /


Mass: 15789.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7R1
#17: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 14763.165 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7J7
#18: Protein 50S RIBOSOMAL PROTEIN L13 /


Mass: 15822.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AA10
#19: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 13320.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ADY3
#20: Protein 50S RIBOSOMAL PROTEIN L15 /


Mass: 15008.471 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P02413
#21: Protein 50S RIBOSOMAL PROTEIN L16 /


Mass: 15312.269 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ADY7
#22: Protein 50S RIBOSOMAL PROTEIN L17 /


Mass: 14393.657 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG44
#23: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12794.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C018
#24: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 13028.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7K6
#25: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13396.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7L3
#26: Protein 50S RIBOSOMAL PROTEIN L21 /


Mass: 11586.374 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG48
#27: Protein 50S RIBOSOMAL PROTEIN L22 /


Mass: 12253.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P61175
#28: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 11093.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0ADZ0
#29: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 11078.874 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P60624
#30: Protein 50S RIBOSOMAL PROTEIN L25 /


Mass: 10713.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P68919
#31: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9015.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7L8
#32: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 7286.464 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7M6
#33: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6423.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AG51
#34: Protein 50S RIBOSOMAL PROTEIN L31 /


Mass: 7887.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A7M9

-
RNA chain , 3 types, 3 molecules 8AB

#7: RNA chain 4.5S SIGNAL RECOGNITION PARTICLE RNA


Mass: 23968.311 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli)
#9: RNA chain 5S RIBOSOMAL RNA /


Mass: 37848.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli)
#10: RNA chain 23S RIBOSOMAL RNA /


Mass: 941612.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli)

-
Protein/peptide / Protein , 2 types, 2 molecules 79

#6: Protein/peptide SIGNAL SEQUENCE /


Mass: 2121.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O62798*PLUS
#8: Protein SIGNAL RECOGNITION PARTICLE 54 /


Mass: 47362.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: MRE600 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0AGD7

-
Non-polymers , 2 types, 623 molecules

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


Mass: 24.305 Da / Num. of mol.: 111 / Source method: obtained synthetically / Formula: Mg
#36: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: SRP BOUND TO 70S RNCS / Type: RIBOSOME
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: CARBON
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: KODAK SO-163 FILM
Radiation wavelengthRelative weight: 1

-
Processing

EM softwareName: SPIDER / Category: 3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Symmetry type: POINT
RefinementHighest resolution: 8 Å
Refinement stepCycle: LAST / Highest resolution: 8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29643 65092 111 512 95358

+
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