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- PDB-1mfq: Crystal Structure Analysis of a Ternary S-Domain Complex of Human... -

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Basic information

Entry
Database: PDB / ID: 1mfq
TitleCrystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle
Components
  • (signal recognition particle ...) x 2
  • 7S RNA of human SRP
KeywordsSIGNALING PROTEIN/RNA / RNA-protein complex / A-minor motif / 3-helix junction / 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 targeting / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding ...SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / neutrophil chemotaxis / GDP binding / nuclear body / nuclear speck / GTPase activity / nucleolus / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Signal recognition particle, SRP19-like subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, eukaryotic / 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-like subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, eukaryotic / 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) / RNA (> 100) / Signal recognition particle 19 kDa protein / Signal recognition particle subunit SRP54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsKuglstatter, A. / Oubridge, C. / Nagai, K.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Induced structural changes of 7SL RNA during the assembly of human signal recognition particle
Authors: Kuglstatter, A. / Oubridge, C. / Nagai, K.
History
DepositionAug 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_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: 7S RNA of human SRP
B: signal recognition particle 19kDa protein
C: signal recognition particle 54kDa protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,05410
Polymers68,8613
Non-polymers1927
Water34219
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.180, 131.180, 204.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain 7S RNA of human SRP


Mass: 41566.715 Da / Num. of mol.: 1 / Fragment: S-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: in vitro transcription with T7 RNA polymerase / Plasmid: pUC18

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Signal recognition particle ... , 2 types, 2 molecules BC

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


Mass: 12561.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP19 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: P09132
#3: Protein signal recognition particle 54kDa protein / SRP54


Mass: 14733.043 Da / Num. of mol.: 1 / Fragment: M-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Plasmid: pRK172 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61011

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Non-polymers , 3 types, 26 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 300.5 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14% (w/v) PEG8000, 100mM Na-cacodylate, 400mM lithium sulfate, 80mM magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG800011
2Na-cacodylate11
3LiSO411
4MgCl11
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1300 mMammonium acetate1drop
210 mMTris-HCl1droppH7.4
35 mM1dropMgCl2
410 %(v/v)glycerol1drop
55 mg/mlprotein1drop
614 %(w/v)PEG80001reservoir
7100 mMsodium citrate1reservoirpH6.5
8400 mM1reservoirLi2SO4
980 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 19354 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 16.6 % / Rsym value: 0.117 / Net I/σ(I): 24.3
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 15.9 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 1886 / Rsym value: 0.602 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.117
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.602

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS
Starting model: PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)

1l9a

1jid

1qb2


Resolution: 3.1→49.63 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 992 5.1 %RANDOM
Rwork0.229 ---
obs-19309 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.551 Å2 / ksol: 0.264604 e/Å3
Displacement parametersBiso mean: 97.6 Å2
Baniso -1Baniso -2Baniso -3
1--12.72 Å24.68 Å20 Å2
2---12.72 Å20 Å2
3---25.45 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.45 Å
Refinement stepCycle: LAST / Resolution: 3.1→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 2751 7 19 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.5
X-RAY DIFFRACTIONc_improper_angle_d1.26
X-RAY DIFFRACTIONc_mcbond_it3.681.5
X-RAY DIFFRACTIONc_mcangle_it6.522
X-RAY DIFFRACTIONc_scbond_it4.682
X-RAY DIFFRACTIONc_scangle_it8.282.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.383 162 5.3 %
Rwork0.298 2875 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP_AK.PARAMDNA-RNA_AK.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor Rfree: 0.383 / Rfactor Rwork: 0.298

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