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- PDB-1914: SIGNAL RECOGNITION PARTICLE ALU RNA BINDING HETERODIMER, SRP9/14 -

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Basic information

Entry
Database: PDB / ID: 1914
TitleSIGNAL RECOGNITION PARTICLE ALU RNA BINDING HETERODIMER, SRP9/14
ComponentsSIGNAL RECOGNITION PARTICLE 9/14 FUSION PROTEIN
KeywordsALU DOMAIN / RNA BINDING / SIGNAL RECOGNITION PARTICLE (SRP) / TRANSLATION REGULATION
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / protein targeting to ER / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / Neutrophil degranulation / nucleus
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 / 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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / Signal recognition particle 14 kDa protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.53 Å
AuthorsBirse, D. / Kapp, U. / Strub, K. / Cusack, S. / Aberg, A.
Citation
Journal: EMBO J. / Year: 1997
Title: The crystal structure of the signal recognition particle Alu RNA binding heterodimer, SRP9/14.
Authors: Birse, D.E. / Kapp, U. / Strub, K. / Cusack, S. / Aberg, A.
#1: Journal: FEBS Lett. / Year: 1996
Title: Crystallization and Preliminary Crystallographic Analysis of the Signal Recognition Particle Srpphi14-9 Fusion Protein
Authors: Birse, D.E. / Doublie, S. / Kapp, U. / Strub, K. / Cusack, S. / Aberg, A.
History
DepositionNov 13, 1997Processing site: BNL
Revision 1.0Dec 30, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE 9/14 FUSION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5633
Polymers26,3901
Non-polymers1732
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.020, 69.020, 90.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-9000-

HOH

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Components

#1: Protein SIGNAL RECOGNITION PARTICLE 9/14 FUSION PROTEIN / SRP9/14 / ALU BM / RBD


Mass: 26389.631 Da / Num. of mol.: 1 / Fragment: ALU RNA BINDING HETERODIMER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 PLYSS / Cellular location: CYTOPLASM / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / References: UniProt: P16254
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 34 %
Description: DATA WERE COLLECTED ON SELENIUM, MERCURY AND PLATINUM DERIVATIVES TO SOLVE MIR STRUCTURE
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7.7
Details: THE SRPPHI14-9 PROTEIN WAS CRYSTALLIZED (BIRSE ET AL., FEBS LETTERS, 1996) BY THE HANGING DROP METHOD IN 2.0 M NAH2/K2H PO4, PH 7.7, 2% MPD, 1.0 MM NAN3 AT 4 DEGREES C WITH A FINAL PROTEIN ...Details: THE SRPPHI14-9 PROTEIN WAS CRYSTALLIZED (BIRSE ET AL., FEBS LETTERS, 1996) BY THE HANGING DROP METHOD IN 2.0 M NAH2/K2H PO4, PH 7.7, 2% MPD, 1.0 MM NAN3 AT 4 DEGREES C WITH A FINAL PROTEIN CONCENTRATION OF 5-8 MG ML-1. CRYSTALS FORMED OVER 2-3 WEEKS AND WERE TYPICALLY 150 X 150 X 300 MM3 IN SPACE, hanging drop, temperature 277K
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.0 M1reservoirNaH2/K2HPO4
22 %MPD1reservoir
31.0 mM1reservoirNaN3
45-8 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.9 / Wavelength: 0.900, 1.100
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: TOROIDAL MIRRORS
RadiationMonochromator: CU FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.11
ReflectionResolution: 2.53→30 Å / Num. obs: 36596 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 5.8
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.0218 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.0218 / % possible all: 97.2
Reflection
*PLUS
Num. obs: 7634 / Num. measured all: 36956
Reflection shell
*PLUS
Lowest resolution: 2.64 Å / % possible obs: 97.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.53→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE MODEL INCLUDES 77 RESIDUES OF SRP9 (4-81) AND 84 RESIDUES OF SRP14 (1-34) AND (47-97). THE SRP14 LOOP ELECTRON DENSITY CONNECTING 14B1-14B2 (34-47) IS WEAK SUGGESTING THAT THE LOOP IS ...Details: THE MODEL INCLUDES 77 RESIDUES OF SRP9 (4-81) AND 84 RESIDUES OF SRP14 (1-34) AND (47-97). THE SRP14 LOOP ELECTRON DENSITY CONNECTING 14B1-14B2 (34-47) IS WEAK SUGGESTING THAT THE LOOP IS FLEXIBLE. 5 C-TERMINAL AND 3 N-TERMINAL RESIDUES OF SRP9 AND 13 C-TERMINAL RESIDUES OF SRP14 HAVE POORLY DEFINED DENSITY. IN ADDITION, THE MODEL DOES NOT INCLUDE THE SRPF14-9 N-TERMINAL F EXTENSION (18 RESIDUES) NOR THE ENTIRE LINKER REGION OF WHICH ONLY 8 OF 17 RESIDUES ARE ORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 -8 %RANDOM
Rwork0.248 ---
obs0.248 7634 98.7 %-
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.53→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1383 0 2 39 1424
LS refinement shellResolution: 2.53→2.64 Å / % reflection obs: 97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO

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