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- PDB-3kl4: Recognition of a signal peptide by the signal recognition particle -

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Basic information

Entry
Database: PDB / ID: 3kl4
TitleRecognition of a signal peptide by the signal recognition particle
Components
  • Signal peptide of yeast dipeptidyl aminopeptidase B
  • Signal recognition 54 kDa protein
KeywordsHYDROLASE / signal recognition particle / SRP / SRP54 / Ffh / signal sequence / signal peptide / GTP-binding / Nucleotide-binding / Ribonucleoprotein / RNA-binding / Signal-anchor / Transmembrane
Function / homology
Function and homology information


Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / aminopeptidase activity / protein processing ...Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / aminopeptidase activity / protein processing / serine-type endopeptidase activity / GTPase activity / GTP binding / ATP hydrolysis activity / proteolysis / plasma membrane
Similarity search - Function
Signal recognition particle, SRP54 subunit, M-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 ...Signal recognition particle, SRP54 subunit, M-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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / 434 Repressor (Amino-terminal Domain) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Alpha/Beta hydrolase fold / 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
Dipeptidyl aminopeptidase B / Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsJanda, C.Y. / Nagai, K. / Li, J. / Oubridge, C.
Citation
Journal: Nature / Year: 2010
Title: Recognition of a signal peptide by the signal recognition particle.
Authors: Janda, C.Y. / Li, J. / Oubridge, C. / Hernandez, H. / Robinson, C.V. / Nagai, K.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the signal sequence binding subunit of the signal recognition particle.
Authors: Keenan, R.J. / Freymann, D.M. / Walter, P. / Stroud, R.M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of the complete core of archaeal signal recognition particle and implications for interdomain communication.
Authors: Rosendal, K.R. / Wild, K. / Montoya, G. / Sinning, I.
#3: Journal: Science / Year: 2000
Title: Crystal structure of the ribonucleoprotein core of the signal recognition particle.
Authors: Batey, R.T. / Rambo, R.P. / Lucast, L. / Rha, B. / Doudna, J.A.
#4: Journal: Structure / Year: 2000
Title: The crystal structure of the conserved GTPase of SRP54 from the archaeon Acidianus ambivalens and its comparison with related structures suggests a model for the SRP-SRP receptor complex.
Authors: Montoya, G. / Kaat, K. / Moll, R. / Schafer, G. / Sinning, I.
#5: Journal: Nature / Year: 2006
Title: Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Authors: Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann /
Abstract: Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal ...Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.
History
DepositionNov 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition 54 kDa protein
B: Signal peptide of yeast dipeptidyl aminopeptidase B


Theoretical massNumber of molelcules
Total (without water)53,0372
Polymers53,0372
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-8 kcal/mol
Surface area24310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.883, 91.883, 133.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsBiological unit is the same as asymmetric unit.

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Components

#1: Protein Signal recognition 54 kDa protein / SRP54


Mass: 48503.363 Da / Num. of mol.: 1 / Fragment: UNP residues 2-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: srp54, SSO0971 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: Q97ZE7, signal-recognition-particle GTPase
#2: Protein/peptide Signal peptide of yeast dipeptidyl aminopeptidase B / DPAP B / YSCV


Mass: 4533.361 Da / Num. of mol.: 1 / Fragment: UNP residues 26-51
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: P18962, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.5
Details: 5-7 % PEG 4000, 100 mM Bis-Tris, 100 mM NaCl, 5-50 mM Mg(OAc)2, 2 % Polypropylene glycol P400. Crystals were obtained by seeding, pH 5.5, VAPOR DIFFUSION, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-110.934
SYNCHROTRONESRF ID14-421.0065, 1.0090, 0.9185
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDDec 16, 2006
ADSC QUANTUM 3152CCDNov 23, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111), Ge (220)SINGLE WAVELENGTHMx-ray1
2Double crystal, Si(111) or Si(311)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
21.00651
31.0091
40.91851
ReflectionResolution: 3.5→58.42 Å / Num. all: 7683 / Num. obs: 7683 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 26.7 % / Biso Wilson estimate: 103.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29.2
Reflection shellResolution: 3.5→3.69 Å / Redundancy: 27.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1098 / % possible all: 100

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Processing

Software
NameClassification
MxCuBEdata collection
SHARPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 3.5→58.42 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.322 392 5.1 %random
Rwork0.301 ---
obs0.301 7640 99.7 %-
all-7660 --
Displacement parametersBiso mean: 151.852 Å2
Baniso -1Baniso -2Baniso -3
1--6.552 Å20 Å20 Å2
2---6.552 Å20 Å2
3---13.104 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.7 Å0.53 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 3.5→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 0 0 3385
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0139
X-RAY DIFFRACTIONc_angle_deg1.619
X-RAY DIFFRACTIONc_dihedral_angle_d22.12
X-RAY DIFFRACTIONc_improper_angle_d1.169
X-RAY DIFFRACTIONc_mcbond_it1.798
X-RAY DIFFRACTIONc_scbond_it2.702
X-RAY DIFFRACTIONc_mcangle_it3.26
X-RAY DIFFRACTIONc_scangle_it4.48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
3.5-3.630.3676400.3282696696736100
3.63-3.770.3793400.3109745100
3.77-3.940.3239360.31875099.9
3.94-4.150.4091390.2992758100
4.15-4.410.4037430.2863740100
4.41-4.750.2731360.2856754100
4.75-5.230.4602450.29876499.9
5.23-5.980.3397370.3276772100
5.98-7.540.3096300.3203780100
7.54-58.420.2532460.288984197.9

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