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- PDB-4xco: Signal-sequence induced conformational changes in the signal reco... -

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Basic information

Entry
Database: PDB / ID: 4xco
TitleSignal-sequence induced conformational changes in the signal recognition particle
Components
  • (Signal recognition particle ...) x 2
  • RNA
KeywordsRNA BINDING PROTEIN / SIGNAL RECOGNITION PARTICLE / SIGNAL SEQUENCE / RECOMBINANT FUSION PROTEIN / RNA STRUCTURE
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / molecular adaptor activity / GTPase activity / GTP binding / ATP hydrolysis activity
Similarity search - Function
Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain ...Signal recognition particle, SRP19 subunit, archaeal-type / Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / 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) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / Signal recognition particle 54 kDa protein / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHainzl, T. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Nat Commun / Year: 2015
Title: Signal-sequence induced conformational changes in the signal recognition particle.
Authors: Hainzl, T. / Sauer-Eriksson, A.E.
#1: Journal: Nat. Struct. Mol. Biol. / Year: 2011
Title: Structural basis of signal-sequence recognition by the signal recognition particle.
Authors: Hainzl, T. / Huang, S. / Merilainen, G. / Brannstrom, K. / Sauer-Eriksson, A.E.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: RNA
A: Signal recognition particle 19 kDa protein
E: RNA
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle 54 kDa protein,signal sequence
D: Signal recognition particle 54 kDa protein,signal sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,85521
Polymers121,4926
Non-polymers36315
Water1,26170
1
M: RNA
A: Signal recognition particle 19 kDa protein
D: Signal recognition particle 54 kDa protein,signal sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,96312
Polymers60,7463
Non-polymers2179
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: RNA
B: Signal recognition particle 19 kDa protein
C: Signal recognition particle 54 kDa protein,signal sequence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8929
Polymers60,7463
Non-polymers1466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.227, 112.971, 121.204
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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RNA chain , 1 types, 2 molecules ME

#1: RNA chain RNA


Mass: 31162.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: synthetic construct (others) / References: GenBank: 6626255

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Signal recognition particle ... , 2 types, 4 molecules ABCD

#2: Protein Signal recognition particle 19 kDa protein / SRP19


Mass: 10376.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: srp19, MJ1034 / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): C41 / References: UniProt: Q58440
#3: Protein Signal recognition particle 54 kDa protein,signal sequence / SRP54


Mass: 19206.736 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: srp54, MJ0101, mj0101, srp54 / Plasmid: pNZ8048 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q57565

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Non-polymers , 3 types, 85 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: The complex (3mg/ml) was mixed 1:1 with 35% 2-Methyl-2,4-pentanediol (MPD), 200 mM NaCl, 80 mM MgCl2, 100 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.9→48.025 Å / Num. obs: 28330 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ndb

3ndb


Resolution: 2.9→48.025 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2576 1432 5.06 %
Rwork0.2089 --
obs0.2112 28314 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 4126 15 70 7601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088106
X-RAY DIFFRACTIONf_angle_d0.52111762
X-RAY DIFFRACTIONf_dihedral_angle_d11.0733711
X-RAY DIFFRACTIONf_chiral_restr0.0251469
X-RAY DIFFRACTIONf_plane_restr0.002755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.35741180.31382648X-RAY DIFFRACTION100
3.0036-3.12390.29821270.26232677X-RAY DIFFRACTION100
3.1239-3.2660.28821480.24222633X-RAY DIFFRACTION99
3.266-3.43820.29261420.23642674X-RAY DIFFRACTION100
3.4382-3.65350.24311270.22642670X-RAY DIFFRACTION100
3.6535-3.93550.28551570.21442659X-RAY DIFFRACTION100
3.9355-4.33130.23381630.18942678X-RAY DIFFRACTION100
4.3313-4.95750.23121640.19292665X-RAY DIFFRACTION100
4.9575-6.24370.26021480.20282721X-RAY DIFFRACTION99
6.2437-48.0250.25241380.19772857X-RAY DIFFRACTION99

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