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- PDB-3ndb: Crystal structure of a signal sequence bound to the signal recogn... -

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Basic information

Entry
Database: PDB / ID: 3ndb
TitleCrystal structure of a signal sequence bound to the signal recognition particle
Components
  • SRP RNA
  • Signal recognition 54 kDa protein
  • Signal recognition particle 19 kDa protein
KeywordsSIGNALING PROTEIN/RNA / protein-RNA complex / signal recognition particle / signal sequence / ribonucleoprotein / SIGNALING PROTEIN-RNA complex
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane, translocation / molecular adaptor activity / GTPase activity / GTP binding / ATP hydrolysis activity / cytosol
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
PHOSPHATE ION / : / RNA / RNA (> 10) / RNA (> 100) / Signal recognition particle 54 kDa protein / Signal recognition particle 19 kDa protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methanocaldococcus jannaschii DSM 2661 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHainzl, T. / Huang, S. / Sauer-Eriksson, E.
CitationJournal: 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
DepositionJun 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / ndb_struct_conf_na ...atom_site / ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_site
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _ndb_struct_na_base_pair.buckle / _ndb_struct_na_base_pair.hbond_type_12 / _ndb_struct_na_base_pair.hbond_type_28 / _ndb_struct_na_base_pair.i_auth_seq_id / _ndb_struct_na_base_pair.i_label_comp_id / _ndb_struct_na_base_pair.i_label_seq_id / _ndb_struct_na_base_pair.j_auth_seq_id / _ndb_struct_na_base_pair.j_label_comp_id / _ndb_struct_na_base_pair.j_label_seq_id / _ndb_struct_na_base_pair.opening / _ndb_struct_na_base_pair.pair_name / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair.shear / _ndb_struct_na_base_pair.stagger / _ndb_struct_na_base_pair.stretch / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id

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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 54 kDa protein
M: SRP RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6314
Polymers104,5363
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-39 kcal/mol
Surface area46730 Å2
Unit cell
Length a, b, c (Å)108.835, 126.275, 201.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 10376.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ1034, srp19 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q58440
#2: Protein Signal recognition 54 kDa protein / SRP54


Mass: 50014.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0101, srp54 / Plasmid: pNZ8048 / Production host: Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q57565
#3: RNA chain SRP RNA


Mass: 44145.266 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Methanocaldococcus jannaschii DSM 2661 (archaea)
References: GenBank: L77117.1
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 5.6
Details: 30% MPD, 200 mM NH4PO4 (pH 5.6), EVAPORATION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2009
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→63.8 Å / Num. obs: 27778 / % possible obs: 98.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 9.2 / Redundancy: 4.8 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.091

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V3C

2v3c


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 46.48 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.42 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26652 1385 5 %RANDOM
Rwork0.22799 ---
all0.23003 27778 --
obs0.23003 26284 98.37 %-
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: 99.513 Å2
Baniso -1Baniso -2Baniso -3
1--2.78 Å20 Å20 Å2
2--7.16 Å20 Å2
3----4.38 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 2921 5 0 6926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227320
X-RAY DIFFRACTIONr_angle_refined_deg2.0682.49410517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4165504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84925.29155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.24315890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.981524
X-RAY DIFFRACTIONr_chiral_restr0.1040.21309
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024253
X-RAY DIFFRACTIONr_mcbond_it0.6821.52521
X-RAY DIFFRACTIONr_mcangle_it1.32524061
X-RAY DIFFRACTIONr_scbond_it1.46734799
X-RAY DIFFRACTIONr_scangle_it2.3924.56456
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 98 -
Rwork0.359 1835 -
obs--95.74 %
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)
12.1351-0.1091-1.19754.00230.68962.92890.1832-0.67520.6740.0353-0.0146-0.3703-0.60690.4249-0.16860.1955-0.0974-0.06480.2399-0.19930.4302-43.426936.5438-22.8187
21.9443-0.86750.23542.906-2.40365.185-0.0792-0.48190.12620.00680.23860.0198-0.1337-0.1114-0.15930.1712-0.03570.03550.1419-0.060.1846-40.0841-12.4073-25.2984
33.37641.90270.74041.9637-0.11751.3712-0.22470.3059-0.4289-0.17940.0607-0.97590.26040.30080.1640.2810.02750.13290.21040.0330.7768-14.527310.3111-40.9646
48.9857-6.2864-0.06877.51063.46764.3124-1.1596-0.312-1.64732.0024-0.19681.6541.76330.08431.35641.06810.26210.890.61460.76551.7547-38.541520.8479-129.8507
51.9410.96587.746116.5728-18.35463.10460.0184-0.315-0.0328-0.5755-0.7329-0.27531.6135-1.79340.71450.3953-0.37250.30471.391-0.29290.2396-37.901729.0636-111.5272
62.42941.5955-3.53351.1947-1.450412.5721-0.22270.3462-0.3439-0.23460.2935-0.32840.9191-0.5093-0.07080.5982-0.1680.06050.5758-0.10770.2439-32.63427.2343-91.0864
70.36884.3294-0.854251.0125-10.06262.0284-0.1016-0.0633-0.1516-2.6681-0.3775-1.71990.4692-0.18750.47910.8454-0.129-0.0832.2451-0.18250.1256-40.845926.7629-77.2297
81.94840.95021.15271.04212.9912.8783-0.09750.71220.23540.00910.2732-0.0860.28210.3187-0.17570.3518-0.09740.10120.33960.15990.2744-31.364723.8559-64.7906
92.98390.1086-1.45640.21290.43891.93510.08480.83720.16360.0663-0.0745-0.00410.0172-0.7208-0.01030.32450.02850.01760.35-0.01720.2898-52.174129.5736-49.8185
103.549-0.2428-2.20751.21810.20622.1238-0.1901-0.1280.0271-0.07840.087-0.13010.2963-0.07320.10310.2475-0.0560.05330.05490.01770.3207-37.483617.5852-38.245
1153.0293-26.1425-30.015537.500924.291620.6525-1.6566-4.9778-1.76660.32031.3514-0.9540.74832.37580.30520.2160.07640.1160.87810.26610.3699-30.871730.927-128.4771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 87
2X-RAY DIFFRACTION2B2 - 290
3X-RAY DIFFRACTION3B291 - 455
4X-RAY DIFFRACTION4M123 - 129
5X-RAY DIFFRACTION4M252 - 258
6X-RAY DIFFRACTION5M130 - 137
7X-RAY DIFFRACTION5M241 - 248
8X-RAY DIFFRACTION6M138 - 145
9X-RAY DIFFRACTION6M233 - 240
10X-RAY DIFFRACTION7M146 - 147
11X-RAY DIFFRACTION7M232
12X-RAY DIFFRACTION8M187 - 197
13X-RAY DIFFRACTION8M224 - 231
14X-RAY DIFFRACTION9M148 - 186
15X-RAY DIFFRACTION10M198 - 223
16X-RAY DIFFRACTION11M249 - 251

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