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- PDB-5l3v: Structure of the crenarchaeal SRP54 GTPase bound to GDP -

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Basic information

Entry
Database: PDB / ID: 5l3v
TitleStructure of the crenarchaeal SRP54 GTPase bound to GDP
ComponentsSignal recognition particle 54 kDa protein
KeywordsPROTEIN TRANSPORT / co-translational protein targeting / Signal Recognition Particle / GTPase / Signaling protein
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
SRP54, nucleotide-binding domain / 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 / 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 ...SRP54, nucleotide-binding domain / 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 / 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 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBange, G. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK1188 Germany
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.
Authors: Wild, K. / Bange, G. / Motiejunas, D. / Kribelbauer, J. / Hendricks, A. / Segnitz, B. / Wade, R.C. / Sinning, I.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal recognition particle 54 kDa protein
B: Signal recognition particle 54 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5157
Polymers66,3412
Non-polymers1,1755
Water3,207178
1
A: Signal recognition particle 54 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8064
Polymers33,1701
Non-polymers6353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle 54 kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7103
Polymers33,1701
Non-polymers5392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.168, 92.168, 148.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-416-

HOH

21A-433-

HOH

31B-416-

HOH

41B-436-

HOH

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Components

#1: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 33170.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: srp54, SSO0971 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97ZE7
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M CHES pH 6.0, 15 % (w/v) PEG 8000, 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.3→39.14 Å / Num. obs: 33058 / % possible obs: 99.8 % / Redundancy: 19.4 % / Rsym value: 0.059 / Net I/σ(I): 22.3
Reflection shellResolution: 2.3→2.38 Å / Rsym value: 0.465

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3S

5l3s


Resolution: 2.3→39.136 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.29
RfactorNum. reflection% reflection
Rfree0.2222 1648 4.99 %
Rwork0.1759 --
obs0.1782 33055 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 71 178 4777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094674
X-RAY DIFFRACTIONf_angle_d1.1636315
X-RAY DIFFRACTIONf_dihedral_angle_d13.8741767
X-RAY DIFFRACTIONf_chiral_restr0.071718
X-RAY DIFFRACTIONf_plane_restr0.005793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2978-2.36540.31031380.21472552X-RAY DIFFRACTION99
2.3654-2.44170.20271350.1792564X-RAY DIFFRACTION100
2.4417-2.52890.24771370.17262578X-RAY DIFFRACTION100
2.5289-2.63020.20061340.17082612X-RAY DIFFRACTION100
2.6302-2.74990.25641290.18432575X-RAY DIFFRACTION100
2.7499-2.89480.26691340.19032599X-RAY DIFFRACTION100
2.8948-3.07610.25511180.20182642X-RAY DIFFRACTION100
3.0761-3.31350.22471340.20412605X-RAY DIFFRACTION100
3.3135-3.64670.23881650.17762600X-RAY DIFFRACTION100
3.6467-4.17390.21641440.17022631X-RAY DIFFRACTION100
4.1739-5.25660.18251340.1482675X-RAY DIFFRACTION100
5.2566-39.14190.21371460.17542774X-RAY DIFFRACTION99
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)
13.2921-0.0456-1.11683.10792.38592.31260.02980.041-0.5685-0.31090.09730.51080.3853-0.2059-0.26630.73150.209-0.29440.72740.16960.744512.909587.100330.1301
20.5414-0.23380.25151.479-0.58980.39780.07670.15720.1437-0.14670.1250.418-0.0191-0.11260.23570.64040.439-0.02180.72180.23390.549112.552993.201442.8433
30.1081-0.03310.21531.8312-1.24792.1328-0.00790.18960.2789-0.2508-0.0003-0.0092-0.34040.00220.29510.77270.3726-0.08860.58160.12380.428721.719898.117434.7778
42.1484-0.89060.30630.60260.05950.2044-0.00450.17070.2153-0.1704-0.01270.1906-0.256-0.22110.01650.50430.2165-0.00640.34140.01380.276136.539572.214252.0743
50.93730.1859-0.06951.3867-0.13632.0287-0.0109-0.1373-0.21620.0185-0.00470.21790.3521-0.23750.01650.460.17480.07860.33210.02750.27337.780460.106159.7943
64.4914-0.7535-0.92271.3754-0.42622.1683-0.0158-0.239-0.1310.12480.03530.2389-0.2009-0.4234-0.00910.4360.16960.01440.4691-0.00220.233633.449871.58368.8862
70.9093-0.0863-0.07430.7335-0.02760.16270.09260.2710.1701-0.14320.02470.3256-0.2838-0.33350.15590.57860.3978-0.08520.46430.01880.306626.062677.460451.3324
83.70620.91621.32350.4148-0.00752.11180.1559-0.4561-0.1470.51240.00060.1479-0.00080.23030.07060.85390.2618-0.0460.48160.11380.473829.525396.175173.9539
90.6591-0.19310.18170.0669-0.01720.11460.11520.05210.2088-0.0871-0.1298-0.24570.13020.28650.06830.6110.3144-0.0080.47660.07080.445232.7872105.89762.6105
100.8008-0.5032-0.08461.8487-0.27570.8888-0.0299-0.1217-0.35350.24290.05870.21460.1986-0.0529-0.04390.55310.1970.05580.30780.04530.40796.3964116.239258.6887
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 122 )
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 193 )
6X-RAY DIFFRACTION6chain 'A' and (resid 194 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 293 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 96 )
10X-RAY DIFFRACTION10chain 'B' and (resid 97 through 293 )

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