- PDB-1e8o: Core of the Alu domain of the mammalian SRP -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 1e8o
Title
Core of the Alu domain of the mammalian SRP
Components
7SL RNA
SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
Keywords
ALU RIBONUCLEOPROTEIN PARTICLE / PROTEIN RECOGNITION OF AN RNA U-TURN / TRANSLATIONAL CONTROL / ALU RNP ASSEMBLY AND TRANSPORT / ALU RETROPOSITION
Function / homology
Function and homology information
signal recognition particle receptor complex / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / negative regulation of translational elongation / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane ...signal recognition particle receptor complex / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / negative regulation of translational elongation / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / RNA binding / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle alu RNA binding heterodimer, srp9/1 / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology
: / RNA / RNA (> 10) / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein Similarity search - Component
A: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN B: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN C: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN D: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN E: 7SL RNA hetero molecules
THE BIOLOGICALLY RELEVANT TERNARY COMPLEX CONSISTS OF CHAINSC,D AND E. THE SRP9/14 HETERODIMER FORMED BY CHAINS A AND BIS BOUND NON -SPECIFICALLY.
-
Components
#1: Protein
SIGNALRECOGNITIONPARTICLE9KDAPROTEIN / SRP9
Mass: 9996.567 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM, NUCLEUS? / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P49458
#2: Protein
SIGNALRECOGNITIONPARTICLE14KDAPROTEIN / SRP14
Mass: 12114.235 Da / Num. of mol.: 2 / Fragment: TRUNCATED AFTER K107 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: CYTOPLASM, NUCLEUS? / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P37108
#3: RNA chain
7SLRNA
Mass: 16277.622 Da / Num. of mol.: 1 / Fragment: ALU RNA 5' DOMAIN / Mutation: YES / Source method: obtained synthetically Details: THE RNA WAS PRODUCED BY IN VITRO TRANSCRIPTION WITH T7 RNA POLYMERASE USING RIBOZYME TECHNOLOGY. Source: (synth.) HOMO SAPIENS (human) / References: EMBL: X01037
Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Compound details
SIGNAL-RECOGNITION-PARTICLE ASSEMBLY HAS A CRUCIAL ROLE IN TARGETING SECRETORY PROTEINS TO THE ...SIGNAL-RECOGNITION-PARTICLE ASSEMBLY HAS A CRUCIAL ROLE IN TARGETING SECRETORY PROTEINS TO THE ROUGH ENDOPLASMIC RETICULUM MEMBRANE. SRP9 TOGETHER WITH SRP14 AND THE ALU PORTION OF THE SRP RNA, CONSTITUTES THE ELONGATION ARREST DOMAIN OF SRP. THE COMPLEX OF SRP9 AND SRP14 IS REQUIRED FOR SRP RNA BINDING. SIGNAL RECOGNITION PARTICLE CONSISTS OF A 7S RNA MOLECULE OF 300 NUCLEOTIDES AND SIX PROTEIN SUBUNITS: SRP72, SRP68, SRP54, SRP19, SRP14 AND SRP9. CHAIN A CONTAINS ENGINEERED MUTATION U119C
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 2
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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
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