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- PDB-9pf4: Saccharomyces cerevisiae SRP54 NG domain -

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Basic information

Entry
Database: PDB / ID: 9pf4
TitleSaccharomyces cerevisiae SRP54 NG domain
ComponentsSignal recognition particle subunit SRP54
KeywordsPROTEIN TRANSPORT / Signal recognition particle / GTPase / RNA binding
Function / homology
Function and homology information


endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / GTPase activator activity / GTPase activity ...endoplasmic reticulum signal sequence receptor activity / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / GTPase activator activity / GTPase activity / GTP binding / endoplasmic reticulum / cytosol
Similarity search - Function
Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP54 subunit / SRP/SRP receptor, N-terminal / 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 ...Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP54 subunit / SRP/SRP receptor, N-terminal / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / Signal recognition particle subunit SRP54
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBruner, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentFDOH23L04 United States
CitationJournal: To Be Published
Title: Structure of the NG domain of yeast SRP54
Authors: Bruner, S.D.
History
DepositionJul 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition particle subunit SRP54
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5072
Polymers34,4481
Non-polymers591
Water52229
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.064, 158.954, 35.811
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 34448.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SRP54, SRH1, YPR088C, P9513.14 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P20424, signal-recognition-particle GTPase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.24 % / Description: prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% v/v Tacsimate 7.0, 0.1 M HEPES 7.5, 10 % PEG 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 7, 2025
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 2.55→39.74 Å / Num. obs: 11989 / % possible obs: 100 % / Redundancy: 8.13 % / Biso Wilson estimate: 35.56 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.152 / Net I/σ(I): 9.98
Reflection shellResolution: 2.55→2.65 Å / Rmerge(I) obs: 0.696 / Num. unique obs: 1271 / CC1/2: 0.913

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5156refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→39.74 Å / SU ML: 0.351 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2714 1199 10 %
Rwork0.2136 10790 -
obs0.2194 11989 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.98 Å2
Refinement stepCycle: LAST / Resolution: 2.55→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 4 29 2278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792277
X-RAY DIFFRACTIONf_angle_d0.87733058
X-RAY DIFFRACTIONf_chiral_restr0.0502358
X-RAY DIFFRACTIONf_plane_restr0.0073391
X-RAY DIFFRACTIONf_dihedral_angle_d15.2012851
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.650.28341270.22231144X-RAY DIFFRACTION100
2.65-2.770.30191320.25011184X-RAY DIFFRACTION100
2.77-2.920.32231290.24871163X-RAY DIFFRACTION100
2.92-3.10.36561310.25311183X-RAY DIFFRACTION100
3.1-3.340.35151330.24211187X-RAY DIFFRACTION100
3.34-3.680.29071310.22151179X-RAY DIFFRACTION100
3.68-4.210.24441340.19461212X-RAY DIFFRACTION100
4.21-5.30.21171360.16921231X-RAY DIFFRACTION100
5.3-39.740.23631460.21231307X-RAY DIFFRACTION100

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