[English] 日本語
Yorodumi
- PDB-4uyj: Crystal structure of a Signal Recognition Particle Alu domain in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4uyj
TitleCrystal structure of a Signal Recognition Particle Alu domain in the elongation arrest conformation
Components
  • SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
  • SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
  • SRP RNASignal recognition particle RNA
KeywordsSIGNALING PROTEIN / SIGNAL RECOGNITION PARTICLE / TRANSLATION / RNA FOLDING
Function / homology
Function and homology information


signal recognition particle receptor complex / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / negative regulation of translational elongation / cotranslational protein targeting to membrane / protein targeting to ER / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane ...signal recognition particle receptor complex / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / negative regulation of translational elongation / cotranslational protein targeting to membrane / protein targeting to ER / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / RNA binding / extracellular region / nucleus / cytosol / cytoplasm
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) / RNA (> 100) / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
PYROCOCCUS HORIKOSHII OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsBousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.
CitationJournal: RNA / Year: 2014
Title: Crystal Structure of a Signal Recognition Particle Alu Domain in the Elongation Arrest Conformation.
Authors: Bousset, L. / Mary, C. / Brooks, M.A. / Scherrer, A. / Strub, K. / Cusack, S.
History
DepositionSep 1, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
R: SRP RNA
S: SRP RNA


Theoretical massNumber of molelcules
Total (without water)116,5596
Polymers116,5596
Non-polymers00
Water0
1
C: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
D: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
S: SRP RNA


Theoretical massNumber of molelcules
Total (without water)58,2793
Polymers58,2793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-47 kcal/mol
Surface area23620 Å2
MethodPISA
2
A: SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN
B: SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN
R: SRP RNA


Theoretical massNumber of molelcules
Total (without water)58,2793
Polymers58,2793
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-46.2 kcal/mol
Surface area23910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.950, 108.600, 128.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein SIGNAL RECOGNITION PARTICLE 9 KDA PROTEIN / SRP9


Mass: 10233.126 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49458
#2: Protein SIGNAL RECOGNITION PARTICLE 14 KDA PROTEIN / SRP14 / 18 KDA ALU RNA-BINDING PROTEIN


Mass: 12386.117 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PEH14DELTAR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37108
#3: RNA chain SRP RNA / Signal recognition particle RNA


Mass: 35660.113 Da / Num. of mol.: 2 / Fragment: ALU DOMAIN, RESIDUES 1-89 AND RESIDUES 289-314 / Source method: obtained synthetically / Source: (synth.) PYROCOCCUS HORIKOSHII OT3 (archaea) / References: GenBank: HG323574
Sequence detailsHUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE ...HUMAN SRP9 RESIDUES 1 TO 85 WERE EXPRESSED IN THIS WORK HUMAN SRP14 RESIDUES 1 TO 107 WERE EXPRESSED IN THIS WORK THE P. HORIKOSHII SRP ALU RNA SEQUENCE HAS THE S-DOMAIN DELETED, AND REPLACED BY A TETRA LOOP. THE CCC (CYCLIC CYTIDINE), PRODUCED DURING IN-VITRO TRANSCRIPTION.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 4.6
Details: 17.5% PEG 3350, 2.5% GLYCEROL, 0.3 M AMMONIUM SULPHATE AND 0.1 M SODIUM ACETATE AT PH 4.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2004 / Details: MIRRORS
RadiationMonochromator: SINGLE SILICON (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 21235 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 4.026 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 9.21
Reflection shellResolution: 3.35→3.47 Å / Redundancy: 3.98 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.85 / % possible all: 89.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SRP914 ALU134 MODEL

Resolution: 3.35→82.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.841 / SU B: 65.401 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23643 1087 5.1 %RANDOM
Rwork0.19229 ---
obs0.19455 20150 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.935 Å2
Baniso -1Baniso -2Baniso -3
1--8.63 Å20 Å20 Å2
2---2.08 Å20 Å2
3---10.7 Å2
Refinement stepCycle: LAST / Resolution: 3.35→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 4722 0 0 7244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0147846
X-RAY DIFFRACTIONr_bond_other_d0.0020.024739
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.49611679
X-RAY DIFFRACTIONr_angle_other_deg1.014311173
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21424110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8371518
X-RAY DIFFRACTIONr_chiral_restr0.0650.21274
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025467
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8877.6291256
X-RAY DIFFRACTIONr_mcbond_other1.8787.6291255
X-RAY DIFFRACTIONr_mcangle_it3.19911.441563
X-RAY DIFFRACTIONr_mcangle_other3.19911.4391564
X-RAY DIFFRACTIONr_scbond_it1.7197.4026590
X-RAY DIFFRACTIONr_scbond_other1.7187.4026591
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.86911.07910117
X-RAY DIFFRACTIONr_long_range_B_refined4.76571.55210002
X-RAY DIFFRACTIONr_long_range_B_other4.76571.55310003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.354→3.441 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 81 -
Rwork0.365 1396 -
obs--95.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.4693.5534-2.19037.86283.201810.77070.16090.35760.09770.48830.0882-1.6158-0.25630.7829-0.24910.3184-0.0056-0.10270.4228-0.03980.951725.341237.1036.2302
21.6607-1.36480.32883.5923-0.04928.47720.0312-0.12660.02950.93490.038-1.0821-0.04750.2254-0.06920.5893-0.0759-0.21640.5288-0.03240.63118.939239.245114.0716
34.2171-4.00282.56926.8184-0.18313.69640.0782-0.3514-0.20780.06240.02940.2072-0.2457-0.8121-0.10770.703-0.09180.01970.67910.00960.34235.286245.949812.4171
48.66781.51721.12624.5882-2.36496.623-0.0350.03390.9420.2365-0.1709-0.1436-0.68270.59960.20590.73660.0473-0.08920.3294-0.08260.237910.671549.76912.0334
50.8859-0.92961.39191.3571-2.15046.1919-0.18950.1844-0.01560.28110.0437-0.1737-0.3640.8210.14580.16710.020.0560.543-0.10840.642440.434987.46172.9164
63.85292.12952.61584.0469-2.739511.45190.02250.3366-0.44050.73540.1422-0.9618-0.53520.9652-0.16470.3060.1423-0.16880.2107-0.07930.77835.539589.449511.597
74.5154-0.94013.89679.4204-2.46029.86-0.1766-0.0367-0.27340.66950.36610.0445-0.5914-0.6436-0.18950.0790.0458-0.01560.11290.04430.081722.547497.113712.6303
86.8904-0.14963.61559.4733-2.19619.88010.15160.16720.60990.8399-0.1644-0.6384-0.73720.85660.01280.25650.0337-0.07820.1728-0.06060.232128.184599.912311.9718
94.0098-3.21933.58473.2527-2.67423.49690.5056-0.334-0.8843-0.1880.24630.61050.2282-0.3616-0.75190.525-0.0539-0.11970.23330.08410.2632-2.282726.28432.2197
104.554-3.22592.12224.2739-2.40871.88850.23730.0375-1.1257-0.1490.27550.60520.3695-0.2676-0.51280.209-0.1037-0.1130.1261-0.00070.314812.05878.941.9853
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 25
2X-RAY DIFFRACTION2A26 - 75
3X-RAY DIFFRACTION3B1 - 39
4X-RAY DIFFRACTION4B51 - 93
5X-RAY DIFFRACTION5C2 - 25
6X-RAY DIFFRACTION6C26 - 75
7X-RAY DIFFRACTION7D1 - 39
8X-RAY DIFFRACTION8D51 - 94
9X-RAY DIFFRACTION9R6 - 115
10X-RAY DIFFRACTION10S6 - 115

+
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