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- PDB-2xxa: The Crystal Structure of the Signal Recognition Particle (SRP) in... -

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Basic information

Entry
Database: PDB / ID: 2xxa
TitleThe Crystal Structure of the Signal Recognition Particle (SRP) in Complex with its Receptor(SR)
Components
  • 4.5S RNA
  • SIGNAL RECOGNITION PARTICLE PROTEIN
  • SRP RECEPTOR FTSY
KeywordsPROTEIN TRANSPORT / RNA/RNA BINDING PROTEIN / HYDROLASE / GTPASE
Function / homology
Function and homology information


signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / ribonucleoprotein complex ...signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-domain / SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / 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 subunit, M-domain / SRP54, nucleotide-binding domain / Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / 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 / 434 Repressor (Amino-terminal Domain) / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesESCHERICHIA COLI K-12 (bacteria)
DEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.94 Å
AuthorsAtaide, S.F. / Schmitz, N. / Shen, K. / Ke, A. / Shan, S. / Doudna, J.A. / Ban, N.
CitationJournal: Science / Year: 2011
Title: The Crystal Structure of the Signal Recognition Particle in Complex with its Receptor.
Authors: Ataide, S.F. / Schmitz, N. / Shen, K. / Ke, A. / Shan, S. / Doudna, J.A. / Ban, N.
History
DepositionNov 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Other / Refinement description ...Other / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Jun 3, 2015Group: Derived calculations
Revision 1.3Dec 20, 2023Group: 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 / pdbx_struct_conn_angle / 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.status_code_sf / _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_atom_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_atom_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.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

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SRP RECEPTOR FTSY
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: SRP RECEPTOR FTSY
F: 4.5S RNA
G: 4.5S RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,07414
Polymers229,8926
Non-polymers2,1828
Water21612
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SRP RECEPTOR FTSY
G: 4.5S RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0377
Polymers114,9463
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-55.1 kcal/mol
Surface area48660 Å2
MethodPISA
2
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: SRP RECEPTOR FTSY
F: 4.5S RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,0377
Polymers114,9463
Non-polymers1,0914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-54.7 kcal/mol
Surface area49170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.100, 131.040, 266.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / / FIFTY-FOUR HOMOLOG / P48


Mass: 47663.531 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-433 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: P0AGD7, signal-recognition-particle GTPase
#2: Protein SRP RECEPTOR FTSY


Mass: 33043.992 Da / Num. of mol.: 2 / Fragment: RESIDUES 196-497
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI K-12 (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P10121

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RNA chain , 1 types, 2 molecules FG

#3: RNA chain 4.5S RNA


Mass: 34238.293 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-106 / Source method: obtained synthetically / Source: (synth.) DEINOCOCCUS RADIODURANS (radioresistant) / References: GenBank: 11612676

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Non-polymers , 3 types, 20 molecules

#4: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 406 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 406 TO SER

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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: 3.13 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 6.9
Details: 12% PEG 2000 MME, 260MM LICL, 50MM MGOAC2, 11% (W/V) GLYCEROL, 50 MM BIS-TRIS PH 6.9

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.94→49.3 Å / Num. obs: 26790 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 168.42 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9
Reflection shellResolution: 3.94→4.17 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 95.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1HQ1 AND 1RJ9

1hq1

1rj9


Resolution: 3.94→49.3 Å / Cor.coef. Fo:Fc: 0.9495 / Cor.coef. Fo:Fc free: 0.9299 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2669 1281 5.08 %RANDOM
Rwork0.2317 ---
obs0.2334 25213 --
Displacement parametersBiso mean: 230.68 Å2
Baniso -1Baniso -2Baniso -3
1--20.3453 Å20 Å20 Å2
2---7.7334 Å20 Å2
3---28.0786 Å2
Refine analyzeLuzzati coordinate error obs: 1.421 Å
Refinement stepCycle: LAST / Resolution: 3.94→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10570 4376 132 12 15090
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815712HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0822214HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7670SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes322HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1840HARMONIC5
X-RAY DIFFRACTIONt_it15712HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.86
X-RAY DIFFRACTIONt_other_torsion3.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2266SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance208HARMONIC1
X-RAY DIFFRACTIONt_utility_angle44HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16328SEMIHARMONIC4
LS refinement shellResolution: 3.94→4.1 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2785 145 5.11 %
Rwork0.28 2695 -
all0.2799 2840 -
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)
10.4222-0.55240.31290.4831-0.73780.13140-0.0030.00390.0196-0.0026-0.0064-0.01440.00290.0027-0.03440.0228-0.0553-0.01080.0307-0.02020.7134-18.694627.3062
26.65022.359-1.25850-1.27395.83690.028-0.16520.03720.3446-0.0694-0.3487-0.06910.20040.0414-0.304-0.1497-0.14850.13840.15080.1304-17.4995-3.989729.6325
36.06681.4632-0.4138.1368-0.29867.2282-0.1783-0.5370.54420.2603-0.133-0.117-0.5442-0.25470.3112-0.14660.1391-0.1134-0.0121-0.152-0.0133-49.25460.442923.4149
43.2267-0.6324-2.34832.52630.93281.26180.00540.0110.0165-0.01420.0024-0.0140.0168-0.0108-0.00780.15490.02540.03130.08210.09710.1211-14.8467-17.613741.0911
58.08582.82232.01048.3155-2.90747.29570.0005-0.13730.2056-0.01690.0176-0.1679-0.26810.1481-0.01810.12160.0514-0.08790.29990.1520.2976-2.0109-31.808875.9188
60.0394-0.00470.05680.19160.19960.02670.0010.00140.006-0.0169-0.00210.0033-0.01510.00050.0011-0.0070.0222-0.04050.0214-0.03610.0181-77.5654-23.152781.701
75.8134-1.5444-2.91047.679-0.30886.22510.0090.05730.065-0.0803-0.03080.0639-0.1009-0.08660.02180.22090.1368-0.10310.250.0830.2429-60.0487-9.755384.4062
81.60491.77812.71078.2834-2.71251.0155-0.001-0.03370.34380.1226-0.01810.0293-0.25780.01570.01910.2186-0.1075-0.152-0.29660.14550.3023-28.4032-6.316291.7019
91.4304-2.1372-0.15323.78560.2920.5819-0.0080.0164-0.0269-0.0160.007-0.01190.0104-0.00150.0010.1490.12260.01080.11040.02390.1275-62.6477-20.506570.4693
108.1989-2.8888-1.95387.5116-2.29198.1379-0.00650.07580.4047-0.0197-0.00490.3296-0.4922-0.17120.0114-0.11130.062-0.15150.25590.15060.0962-74.8275-27.126733.3867
114.83712.9028-1.30658.3155-2.54138.2682-0.01140.03370.1501-0.0594-0.06550.004-0.2247-0.06630.07690.0552-0.07890.15180.22560.15140.304-17.3972.2259-0.226
128.16650.66021.48016.8572-0.11558.2894-0.07740.54420.303-0.5432-0.2519-0.23190.54420.23370.32930.18410.0190.152-0.2938-0.0138-0.2806-44.8442-15.36740.6667
138.3155-2.7327-2.71288.31550.21097.4027-0.01270.04420.1150.0298-0.0433-0.0428-0.09750.12510.0560.30340.04080.10440.248-0.07140.304-60.4847-9.9294114.881
148.31550.24931.79885.65091.23872.68760.0166-0.530.15920.3130.02020.0148-0.4494-0.3905-0.03680.304-0.1098-0.152-0.3040.1463-0.0891-32.8042-26.638110.598
150.00492.86461.59970.59192.4384.294-0.0803-0.2645-0.1315-0.4861-0.05590.46960.0691-0.2160.1362-0.1212-0.1346-0.1511-0.3040.0093-0.304-62.6447-32.608510.9485
164.9518-0.7677-0.22150-2.91046.4752-0.0007-0.0226-0.02970.01270.0449-0.14530.01160.0824-0.04410.16480.12050.01290.3040.1520.1922-31.462-37.740939.6877
177.96342.6017-2.91045.07420.11738.2782-0.00760.0162-0.19460.03560.0106-0.16060.15110.0885-0.0030.28630.135-0.11990.28260.150.0923-2.8736-49.482363.1324
187.6661-1.15681.01625.4026-2.90681.0776-0.0258-0.2739-0.0090.28420.0251-0.54420.11740.42930.0007-0.1069-0.1379-0.1515-0.00840.15160.0072-14.8992-40.918997.868
191.8191-0.6649-0.15460.90291.26898.31550.00340.00650.02150.0325-0.0070.1280.0203-0.04520.00360.29820.0136-0.02670.3008-0.0960.0204-45.8063-40.642668.0484
203.4197-0.5462-2.91043.054-2.77471.78390.02920.0323-0.4129-0.1642-0.08080.43820.4073-0.25680.0517-0.04-0.12080.152-0.16550.1472-0.1837-75.0028-46.823343.0058
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A4 - A17)
2X-RAY DIFFRACTION2(A18 - A88, A282 - A294)
3X-RAY DIFFRACTION3(A89 - A281)
4X-RAY DIFFRACTION4(A295 - A319)
5X-RAY DIFFRACTION5(A320 - A431)
6X-RAY DIFFRACTION6(C7 - C17)
7X-RAY DIFFRACTION7(C18 - C88, C282 - C294)
8X-RAY DIFFRACTION8(C89 - C281)
9X-RAY DIFFRACTION9(C295 - C319)
10X-RAY DIFFRACTION10(C320 - C431)
11X-RAY DIFFRACTION11(B20 - B88, B289 - B302)
12X-RAY DIFFRACTION12(B89 - B288)
13X-RAY DIFFRACTION13(D20 - D88, D289 - D302)
14X-RAY DIFFRACTION14(D89 - D288)
15X-RAY DIFFRACTION15(G1 - G20, G79 - G102)
16X-RAY DIFFRACTION16(G21 - G31, G66 - G78)
17X-RAY DIFFRACTION17(G32 - G65)
18X-RAY DIFFRACTION18(F1 - F20, F79 - F102)
19X-RAY DIFFRACTION19(F21 - F31, F66 - F78)
20X-RAY DIFFRACTION20(F32 - F65)

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