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- PDB-5m72: Structure of the human SRP68-72 protein-binding domain complex -

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Basic information

Entry
Database: PDB / ID: 5m72
TitleStructure of the human SRP68-72 protein-binding domain complex
Components(Signal recognition particle subunit ...) x 2
KeywordsPROTEIN TRANSPORT / protein targeting / signal recognition particle / tetratricopeptide repeat / protein-peptide complex
Function / homology
Function and homology information


endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome / response to xenobiotic stimulus ...endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / signal recognition particle / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / TPR domain binding / SRP-dependent cotranslational protein targeting to membrane / ribosome / response to xenobiotic stimulus / protein domain specific binding / focal adhesion / nucleolus / endoplasmic reticulum / RNA binding / cytosol
Similarity search - Function
Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat domain ...Signal recognition particle, SRP72 subunit, RNA-binding / Signal recognition particle, SRP72 subunit / Putative TPR-like repeat / SRP72 RNA-binding domain / Putative TPR-like repeat / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
: / Signal recognition particle subunit SRP72 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsBecker, M.M.M. / Wild, K. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB 638 Germany
German Research FoundationGRK 1188 Germany
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction.
Authors: Becker, M.M. / Lapouge, K. / Segnitz, B. / Wild, K. / Sinning, I.
History
DepositionOct 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Dec 21, 2016Group: Database references
Revision 1.3Jan 18, 2017Group: Database references
Revision 2.0May 8, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Signal recognition particle subunit SRP72
B: Signal recognition particle subunit SRP68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6927
Polymers26,2772
Non-polymers4155
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-48 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.597, 52.269, 62.863
Angle α, β, γ (deg.)90.000, 118.220, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-203-

K

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Components

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Signal recognition particle subunit ... , 2 types, 2 molecules AB

#1: Protein Signal recognition particle subunit SRP72 / SRP72 / Signal recognition particle 72 kDa protein


Mass: 18271.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP72 / Production host: Escherichia coli (E. coli) / References: UniProt: O76094
#2: Protein Signal recognition particle subunit SRP68 / SRP68 / Signal recognition particle 68 kDa protein


Mass: 8005.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UHB9

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Non-polymers , 4 types, 155 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K2SO4 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972422 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972422 Å / Relative weight: 1
ReflectionResolution: 1.6→39 Å / Num. obs: 25085 / % possible obs: 99.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.2
Reflection shellRmerge(I) obs: 0.55

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→39 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.97
RfactorNum. reflection% reflection
Rfree0.1841 1308 5.22 %
Rwork0.1425 --
obs0.1446 25062 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.58 Å2 / Biso mean: 36.1643 Å2 / Biso min: 18.4 Å2
Refinement stepCycle: final / Resolution: 1.6→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1380 0 23 150 1553
Biso mean--65.84 45.52 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051453
X-RAY DIFFRACTIONf_angle_d0.7041969
X-RAY DIFFRACTIONf_chiral_restr0.04222
X-RAY DIFFRACTIONf_plane_restr0.004254
X-RAY DIFFRACTIONf_dihedral_angle_d11.264899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.66410.2481560.19112633278999
1.6641-1.73980.21121440.164326202764100
1.7398-1.83150.22181410.1552618275999
1.8315-1.94630.19571570.13012598275599
1.9463-2.09660.16881330.121226632796100
2.0966-2.30750.20071310.12032633276499
2.3075-2.64140.17081450.13892656280199
2.6414-3.32760.18221510.151426432794100
3.3276-39.04310.1741500.14372690284099

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