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- PDB-2v3c: Crystal structure of the SRP54-SRP19-7S.S SRP RNA complex of M. j... -

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Basic information

Entry
Database: PDB / ID: 2v3c
TitleCrystal structure of the SRP54-SRP19-7S.S SRP RNA complex of M. jannaschii
Components
  • 7S RNA
  • SIGNAL RECOGNITION 54 KDA PROTEIN
  • SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
KeywordsSIGNALING PROTEIN / NUCLEOTIDE-BINDING / SIGNAL RECOGNITION PARTICLE / RNA / GTP-BINDING / RNA-BINDING / RIBONUCLEOPROTEIN
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 / SRP54, nucleotide-binding domain / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit ...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 / SRP54, nucleotide-binding domain / 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) / 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 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / 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: 2.5 Å
AuthorsHainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Interaction of Signal-Recognition Particle 54 Gtpase Domain and Signal-Recognition Particle RNA in the Free Signal-Recognition Particle.
Authors: Hainzl, T. / Huang, S. / Sauer-Eriksson, A.E.
History
DepositionJun 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 4, 2022Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
B: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
C: SIGNAL RECOGNITION 54 KDA PROTEIN
D: SIGNAL RECOGNITION 54 KDA PROTEIN
M: 7S RNA
N: 7S RNA


Theoretical massNumber of molelcules
Total (without water)179,4636
Polymers179,4636
Non-polymers00
Water8,539474
1
A: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
C: SIGNAL RECOGNITION 54 KDA PROTEIN
M: 7S RNA


Theoretical massNumber of molelcules
Total (without water)89,7313
Polymers89,7313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-1.9 kcal/mol
Surface area46010 Å2
MethodPQS
2
B: SIGNAL RECOGNITION PARTICLE 19 KDA PROTEIN
D: SIGNAL RECOGNITION 54 KDA PROTEIN
N: 7S RNA


Theoretical massNumber of molelcules
Total (without water)89,7313
Polymers89,7313
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-1 kcal/mol
Surface area47660 Å2
MethodPQS
Unit cell
Length a, b, c (Å)70.286, 129.402, 163.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: 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)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q58440
#2: Protein SIGNAL RECOGNITION 54 KDA PROTEIN / SRP54


Mass: 48192.355 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCALDOCOCCUS JANNASCHII (archaea)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q57565
#3: RNA chain 7S RNA


Mass: 31162.604 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) METHANOCALDOCOCCUS JANNASCHII (archaea)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.15 Å3/Da / Density % sol: 40.1 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 49835 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.3
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.6 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LNG

1lng


Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.902 / SU B: 15.979 / SU ML: 0.348 / Cross valid method: THROUGHOUT / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 2620 5.1 %RANDOM
Rwork0.244 ---
obs0.247 48767 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.42 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å20 Å20 Å2
2---3.41 Å20 Å2
3---6.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 4126 0 474 12336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.02212452
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9532.41117672
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7743974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.895151760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1360.21974
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027524
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3550.37532
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2910.51207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3670.3228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6871.54866
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24327848
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.95637586
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2574.59824
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.478 178
Rwork0.334 2959

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