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- PDB-1nrj: Signal Recognition Particle Receptor Beta-Subunit in Complex with... -

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Basic information

Entry
Database: PDB / ID: 1nrj
TitleSignal Recognition Particle Receptor Beta-Subunit in Complex with the SRX Domain from the Alpha-Subunit
Components(Signal recognition particle receptor ...) x 2
KeywordsPROTEIN TRANSPORT / Signal recognition particle / Transmembrane / Receptor / Endoplasmic reticulum / GTP-binding / GTPase-Effector Complex
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle binding / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / protein targeting / GTPase activity / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle binding / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / protein targeting / GTPase activity / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / identical protein binding
Similarity search - Function
Signal recognition particle (SRP) receptor alpha subunit, N-terminal / SRX, signal recognition particle receptor alpha subunit / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Beta-Lactamase - #60 / SRP/SRP receptor, N-terminal / 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 ...Signal recognition particle (SRP) receptor alpha subunit, N-terminal / SRX, signal recognition particle receptor alpha subunit / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Beta-Lactamase - #60 / SRP/SRP receptor, N-terminal / 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 / Longin-like domain superfamily / Beta-Lactamase / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Signal recognition particle receptor subunit alpha homolog / Signal recognition particle receptor subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSchwartz, T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Structural Basis for the Function of the beta Subunit of the Eukaryotic Signal Recognition Particle Receptor
Authors: Schwartz, T. / Blobel, G.
History
DepositionJan 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Signal recognition particle receptor alpha subunit homolog
B: Signal recognition particle receptor beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3896
Polymers42,7552
Non-polymers6344
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-23 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.200, 123.700, 48.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Signal recognition particle receptor ... , 2 types, 2 molecules AB

#1: Protein Signal recognition particle receptor alpha subunit homolog / SR-alpha / Docking protein alpha / DP-alpha


Mass: 18406.727 Da / Num. of mol.: 1 / Fragment: residues 1-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRP101 / Plasmid: pET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32916
#2: Protein Signal recognition particle receptor beta subunit / SR-beta


Mass: 24348.750 Da / Num. of mol.: 1 / Fragment: residues 31-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRP102 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36057

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Non-polymers , 4 types, 439 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 298 K / Method: microbatch under oil / pH: 5.5
Details: 40% (w/v) PEG 3350, 15% (v/v) ethylene glycol, 0.1M ammonium chloride, 0.1M sodium acetate, pH 5.5, Microbatch under oil, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMHEPES1reservoirpH7.5
3150 mM1reservoirNaCl
45 mMdithiothreitol1reservoir
51 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1.3 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.6→29.63 Å / Num. obs: 62208 / Biso Wilson estimate: 36.3 Å2
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Num. obs: 52263 / % possible obs: 98.7 % / Num. measured all: 444199 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.76 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.963 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22886 2623 5 %RANDOM
Rwork0.19435 ---
all0.196 52263 --
obs0.19603 49631 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--0.36 Å20 Å2
3----1.28 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 38 435 3146
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222764
X-RAY DIFFRACTIONr_bond_other_d0.0040.022504
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9783757
X-RAY DIFFRACTIONr_angle_other_deg1.46435885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9385333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1470.2446
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022985
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02527
X-RAY DIFFRACTIONr_nbd_refined0.2240.2496
X-RAY DIFFRACTIONr_nbd_other0.2350.22611
X-RAY DIFFRACTIONr_nbtor_other0.0840.21432
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4351.51687
X-RAY DIFFRACTIONr_mcangle_it2.06622737
X-RAY DIFFRACTIONr_scbond_it2.99831077
X-RAY DIFFRACTIONr_scangle_it4.2514.51006
X-RAY DIFFRACTIONr_rigid_bond_restr3.519234
X-RAY DIFFRACTIONr_sphericity_free5.77921
X-RAY DIFFRACTIONr_sphericity_bonded5.821232
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.284 201
Rwork0.288 3601
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)
12.34420.6862-0.05171.8254-0.22032.4152-0.01520.02370.0092-0.04020.07410.1383-0.0645-0.0939-0.05890.01590.02740.00210.0823-0.03690.092311.884235.715922.1583
27.648-0.1904-3.76212.8790.23573.85050.0881-0.52060.0960.3407-0.04520.18640.0548-0.1565-0.0430.1298-0.0079-0.03450.26860.0090.0859.991131.556639.9376
37.0007-5.53594.26361.92240.280512.6723-0.0851-0.22630.14410.09930.2877-0.5279-0.19330.7131-0.20250.0043-0.024-0.00840.2279-0.06720.152130.447637.17131.5691
414.42458.4673-3.376810.18683.84586.2038-0.24370.4453-0.0068-0.70540.2549-0.5132-0.0790.1619-0.01120.0325-0.0110.010.1865-0.03750.11629.195635.766920.1442
50.40190.18090.05332.86751.71051.4227-0.05230.12920.1497-0.13180.0896-0.0558-0.31270.1821-0.03730.3152-0.0440.01980.19780.0490.244518.911160.469717.8552
60.32630.0510.48655.38844.73043.2005-0.08710.18570.1989-0.25850.0885-0.1732-0.03980.1792-0.00140.4263-0.11320.0220.22520.06080.323522.19172.67615.962
7-0.7404-1.05660.52054.24222.56571.0576-0.00390.43-0.0932-0.2352-0.1299-0.0336-0.5462-0.21550.13380.465-0.0427-0.03820.31260.06980.269216.368556.64141.9633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BB36 - 15410 - 128
2X-RAY DIFFRACTION1BB212 - 225186 - 199
3X-RAY DIFFRACTION1BB234 - 244208 - 218
4X-RAY DIFFRACTION2BB162 - 187136 - 161
5X-RAY DIFFRACTION3BB155 - 161129 - 135
6X-RAY DIFFRACTION4BB226 - 233200 - 207
7X-RAY DIFFRACTION5AA2 - 942 - 94
8X-RAY DIFFRACTION5AA128 - 152128 - 152
9X-RAY DIFFRACTION6AA95 - 11695 - 116
10X-RAY DIFFRACTION7AA117 - 127117 - 127
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.026
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.95

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