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- PDB-5ck3: Signal recognition particle receptor SRb-GTP/SRX complex from Cha... -

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Basic information

Entry
Database: PDB / ID: 5ck3
TitleSignal recognition particle receptor SRb-GTP/SRX complex from Chaetomium thermophilum
Components
  • Putative signal recognition particle protein
  • SRX domain
KeywordsSIGNALING PROTEIN / GTPase / Longin domain / regulator complex / protein translocation
Function / homology
Function and homology information


histone H4S1 kinase activity / : / histone H3S57 kinase activity / histone H2BS14 kinase activity / signal recognition particle receptor complex / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity ...histone H4S1 kinase activity / : / histone H3S57 kinase activity / histone H2BS14 kinase activity / signal recognition particle receptor complex / histone H3S28 kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / ribosomal protein S6 kinase activity / histone H2AT120 kinase activity / histone H2BS36 kinase activity / Rho-dependent protein serine/threonine kinase activity / AMP-activated protein kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / histone H3T3 kinase activity / 3-phosphoinositide-dependent protein kinase activity / histone H3T45 kinase activity / signal recognition particle binding / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / histone H3T11 kinase activity / SRP-dependent cotranslational protein targeting to membrane / histone H3S10 kinase activity / telomere maintenance / DNA damage checkpoint signaling / intracellular protein transport / chromosome / non-specific serine/threonine protein kinase / DNA repair / GTPase activity / endoplasmic reticulum membrane / GTP binding / ATP hydrolysis activity / metal ion binding / nucleus
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Beta-Lactamase - #60 / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / SRP/SRP receptor, N-terminal / Signal recognition particle SRP54, helical bundle ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Beta-Lactamase - #60 / UME domain / UME (NUC010) domain / Domain in UVSB PI-3 kinase, MEI-41 and ESR-1 / SRP/SRP receptor, N-terminal / 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 / Longin-like domain superfamily / : / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Beta-Lactamase / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / non-specific serine/threonine protein kinase / Signal recognition particle receptor subunit beta
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJadhav, B.R. / Wild, K. / Sinning, I.
CitationJournal: Structure / Year: 2015
Title: Structure and Switch Cycle of SR beta as Ancestral Eukaryotic GTPase Associated with Secretory Membranes.
Authors: Jadhav, B. / Wild, K. / Pool, M.R. / Sinning, I.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: SRX domain
B: Putative signal recognition particle protein
C: SRX domain
D: Putative signal recognition particle protein
E: SRX domain
F: Putative signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,29014
Polymers161,4596
Non-polymers1,8318
Water00
1
A: SRX domain
B: Putative signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5556
Polymers53,8202
Non-polymers7364
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-43 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: SRX domain
D: Putative signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3674
Polymers53,8202
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-23 kcal/mol
Surface area17150 Å2
MethodPISA
3
E: SRX domain
F: Putative signal recognition particle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3674
Polymers53,8202
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-24 kcal/mol
Surface area14550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.277, 83.609, 90.213
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 6 molecules ACEBDF

#1: Protein SRX domain


Mass: 20568.152 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0014570 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S1R8
#2: Protein Putative signal recognition particle protein


Mass: 33251.621 Da / Num. of mol.: 3 / Fragment: residues 42-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0022040 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S401

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Non-polymers , 4 types, 8 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20% (w/v) PEG3350 and 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.2→45.5 Å / Num. obs: 21109 / % possible obs: 99.9 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2fh5

2fh5


Resolution: 3.2→45.467 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2996 1077 5.14 %
Rwork0.2762 --
obs0.2775 20939 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→45.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7790 0 110 0 7900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078062
X-RAY DIFFRACTIONf_angle_d1.21410950
X-RAY DIFFRACTIONf_dihedral_angle_d22.0062933
X-RAY DIFFRACTIONf_chiral_restr0.0451264
X-RAY DIFFRACTIONf_plane_restr0.0061352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.34560.38061370.33272406X-RAY DIFFRACTION98
3.3456-3.5220.3871270.3312492X-RAY DIFFRACTION99
3.522-3.74250.30941190.29772489X-RAY DIFFRACTION100
3.7425-4.03130.32111340.28222470X-RAY DIFFRACTION99
4.0313-4.43670.30371240.2552499X-RAY DIFFRACTION100
4.4367-5.0780.2641400.24422484X-RAY DIFFRACTION100
5.078-6.39490.29351340.28842513X-RAY DIFFRACTION99
6.3949-45.47130.27081620.25782509X-RAY DIFFRACTION99

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