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- PDB-4p3f: Structure of the human SRP68-RBD -

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Basic information

Entry
Database: PDB / ID: 4p3f
TitleStructure of the human SRP68-RBD
ComponentsSignal recognition particle subunit SRP68
KeywordsRNA BINDING PROTEIN / SRPSRP68RNA-binding domain (RBD) / Tetratricopeptide repeat (TPR)
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 / SRP-dependent cotranslational protein targeting to membrane / ribosome / response to xenobiotic stimulus / protein domain specific binding ...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 / 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, SRP68 subunit, RNA-binding domain / Hyaluronidase domain-like / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.699 Å
AuthorsGrotwinkel, J.T. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB638 Germany
CitationJournal: Science / Year: 2014
Title: SRP RNA remodeling by SRP68 explains its role in protein translocation.
Authors: Grotwinkel, J.T. / Wild, K. / Segnitz, B. / Sinning, I.
History
DepositionMar 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7759
Polymers51,2082
Non-polymers5677
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint27 kcal/mol
Surface area21160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.810, 93.310, 60.100
Angle α, β, γ (deg.)90.000, 109.340, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Signal recognition particle subunit SRP68 / / SRP68 / Signal recognition particle 68 kDa protein


Mass: 25604.229 Da / Num. of mol.: 2 / Fragment: UNP residues 47-254 / Mutation: E108D
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
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.13 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: K/Na tartrate, PEG5000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.699→48.86 Å / Num. obs: 42912 / % possible obs: 99.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.78 Å2 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.746 / Rsym value: 0.02

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P3G

4p3g


Resolution: 1.699→35.676 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 2145 5 %
Rwork0.176 40756 -
obs0.1781 42901 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.02 Å2 / Biso mean: 26.0577 Å2 / Biso min: 7.31 Å2
Refinement stepCycle: final / Resolution: 1.699→35.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 37 367 3665
Biso mean--39.78 35.97 -
Num. residues----391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013421
X-RAY DIFFRACTIONf_angle_d1.2264577
X-RAY DIFFRACTIONf_chiral_restr0.09478
X-RAY DIFFRACTIONf_plane_restr0.005589
X-RAY DIFFRACTIONf_dihedral_angle_d15.5161352
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6991-1.73860.27881330.24582526265993
1.7386-1.78210.291430.221327222865100
1.7821-1.83030.25891440.215327362880100
1.8303-1.88410.26451460.201527722918100
1.8841-1.94490.24211410.197426692810100
1.9449-2.01450.26371440.19922741288599
2.0145-2.09510.27161420.18692710285299
2.0951-2.19040.22731440.175527232867100
2.1904-2.30590.251440.1827422886100
2.3059-2.45030.23711430.172127172860100
2.4503-2.63950.21961420.17792691283398
2.6395-2.9050.2121450.174427532898100
2.905-3.32510.21121440.170527342878100
3.3251-4.18820.16821440.15112747289199
4.1882-35.68420.20281460.16842773291999
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)
12.70340.50293.23870.3680.95116.33480.1567-0.0417-0.3711-0.08120.0161-0.02190.25970.2349-0.14410.07940.03540.0050.13880.01490.14026.4429-23.5238-18.0485
20.7659-1.37721.40764.6944-4.17946.1083-0.0839-0.0185-0.03170.2091-0.082-0.11320.08640.05080.140.1052-0.0059-0.00060.0994-0.01130.1378-3.6398-28.9921-8.766
33.1319-0.98371.47386.4053-2.76424.6422-0.04240.01150.09420.10950.00870.1581-0.1815-0.02960.02490.05120.00360.00650.128-0.03220.0899-1.5647-17.5057-12.7885
46.3963-4.99292.70588.0048-3.27624.1708-0.2219-0.27270.12770.60830.1043-0.0246-0.3754-0.03050.10130.1322-0.05010.00880.1163-0.04640.09592.0048-11.3324-8.007
52.2969-0.9206-0.35352.7698-0.51461.34820.0920.0307-0.0116-0.0329-0.0812-0.1619-0.09830.1539-0.01250.0704-0.0353-0.02150.1251-0.00720.101913.5029-8.5316-17.6704
66.47550.3022-0.76163.9566-0.25884.01090.1422-0.36530.05670.54540.02940.0908-0.2075-0.0149-0.11810.21360.0110.00970.0945-0.0250.10741.1057-42.8848-8.6757
73.90873.9165-3.29177.1392-4.18024.9131-0.1458-0.01490.073-0.27830.1021-0.1809-0.22230.00270.03950.22830.05920.02270.1663-0.02870.15360.9058-33.9543-24.8963
86.60494.3902-2.18946.7725-1.80083.8366-0.0181-0.01720.1212-0.02680.01740.23180.1141-0.25620.01660.10920.04730.00660.1064-0.02340.098-0.8447-47.6694-18.8171
97.9887.06490.0518.148-0.05752.548-0.1416-0.0735-0.1436-0.17020.0278-0.09990.3585-0.02990.10280.17220.04050.01860.0997-0.00490.08793.6889-53.9998-21.3154
103.23631.55720.49193.9653-0.6662.2319-0.0038-0.2572-0.10740.1675-0.1247-0.26050.43050.22250.11880.23650.08240.02810.17570.0130.102810.1667-57.113-9.9699
113.45081.9942-0.46398.1822-2.03391.51130.3168-0.40380.15090.5712-0.44470.29260.3814-0.00840.12320.2878-0.03980.0120.25210.01980.08546.9283-57.6962-1.0596
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 106 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 142 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 143 through 171 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 244 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 71 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 72 through 105 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 106 through 140 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 141 through 171 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 172 through 218 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 219 through 244 )B0

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