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- PDB-4p3g: Structure of the SRP68-RBD from Chaetomium thermophilum -

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Basic information

Entry
Database: PDB / ID: 4p3g
TitleStructure of the SRP68-RBD from Chaetomium thermophilum
ComponentsSignal recognition particle subunit SRP68
KeywordsRNA BINDING PROTEIN / SRP / SRP68 / RNA-binding domain (RBD) / Chaetomium thermophilum / Tetratricopeptide repeat (TPR)
Function / homology
Function and homology information


signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / endoplasmic reticulum signal peptide binding / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding
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
PHOSPHATE ION / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 1.1Apr 23, 2014Group: Data collection
Revision 1.2Jul 9, 2014Group: Structure summary
Revision 1.3Sep 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 / symmetry
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 / _symmetry.Int_Tables_number
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
C: Signal recognition particle subunit SRP68
D: Signal recognition particle subunit SRP68
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8639
Polymers100,3894
Non-polymers4755
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-84 kcal/mol
Surface area38750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.840, 95.050, 223.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Signal recognition particle subunit SRP68 / SRP68


Mass: 25097.150 Da / Num. of mol.: 4 / Fragment: UNP residues 2-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0033730 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5V2
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: NaCl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9919 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9919 Å / Relative weight: 1
ReflectionResolution: 2.7→58.69 Å / Num. obs: 28410 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 63.66 Å2 / Net I/σ(I): 10.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→42.015 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.88 / Phase error: 27.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1436 5.13 %
Rwork0.1995 50052 -
obs0.2022 28260 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 236.39 Å2 / Biso mean: 108.2441 Å2 / Biso min: 41.95 Å2
Refinement stepCycle: final / Resolution: 2.7→42.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6210 0 25 12 6247
Biso mean--130.24 60.11 -
Num. residues----801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096329
X-RAY DIFFRACTIONf_angle_d1.2418532
X-RAY DIFFRACTIONf_chiral_restr0.071980
X-RAY DIFFRACTIONf_plane_restr0.0061066
X-RAY DIFFRACTIONf_dihedral_angle_d12.6172325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.74910.36011180.315326952813100
2.7491-2.8020.34321740.284825782752100
2.802-2.85920.30081370.272126622799100
2.8592-2.92140.33231450.266526372782100
2.9214-2.98930.31551560.263725692725100
2.9893-3.0640.31751530.253126582811100
3.064-3.14680.31371460.244526472793100
3.1468-3.23940.33141590.239425922751100
3.2394-3.34390.24291220.236627282850100
3.3439-3.46340.31631320.224125832715100
3.4634-3.6020.27681570.201326802837100
3.602-3.76580.22351340.185126182752100
3.7658-3.96420.19981270.167626692796100
3.9642-4.21240.20231300.16926622792100
4.2124-4.53730.24491470.162926062753100
4.5373-4.99320.2261480.165426592807100
4.9932-5.71420.27361310.194326472778100
5.7142-7.19340.24031430.212544268797
7.1934-42.02050.20851480.17622618276699
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)
14.28714.4251-0.70838.2378-1.09994.2871-0.16930.74980.7531-1.24860.24810.4652-0.14090.0082-0.02441.01830.3811-0.12710.92090.1070.8342-11.080326.5546-61.9734
24.81822.116-2.5645.56053.95597.61720.25560.1863-0.0629-1.0987-0.428-0.7787-0.22770.40290.1450.71470.1413-0.16190.83250.22690.6609-4.450622.8458-57.8276
31.543-0.6302-0.5457.322-0.74093.64240.27090.12980.05680.1944-0.56250.1668-0.1207-0.18630.24880.3729-0.0722-0.06790.6333-0.0250.4577-9.953114.457-43.2067
49.14570.1151-0.50869.58672.33450.6135-0.68811.3591-1.32990.44610.0897-0.78410.7940.72370.36121.42650.2414-0.01621.2163-0.24540.8103-4.1341-27.5494-33.2328
54.7172.03442.79336.094-0.30284.03580.7821-0.3469-0.53470.9821-0.37750.07792.15721.1988-0.36082.30790.08220.21691.0294-0.23470.9341-13.2458-34.0637-38.3946
66.2483-0.73041.32879.0936-2.08136.842-0.22180.62450.13461.1417-0.13170.87991.1514-1.2030.31731.0575-0.38540.19810.7405-0.2580.952-20.6296-25.0458-39.6844
73.10831.8015-1.75494.8450.85493.05-0.38780.1261-0.24570.6186-0.15920.4912.3903-0.71790.45121.3622-0.32040.33570.6304-0.17370.6894-16.755-16.9877-30.8869
83.49630.544-2.27463.0436-0.01337.0729-0.1654-0.1654-0.1247-0.0393-0.2637-0.00911.61270.1770.50960.874-0.07650.10110.6298-0.10680.5201-11.1025-7.8612-33.5488
96.17536.6616-6.20637.1958-6.69666.2468-0.0135-0.7581-1.63430.5207-0.7805-1.5986-0.161.77980.84390.71170.0847-0.01510.81310.08410.9752-3.583310.1278-31.7745
107.32181.29532.53563.74743.64733.7216-0.65280.33611.26650.26360.0923-0.2194-1.99641.07550.30730.917-0.1256-0.03790.66810.00690.7343-11.529635.561-17.7915
116.1786-3.5261.41548.1934-0.94246.8739-0.11930.0729-0.00161.0201-0.04780.4682-0.5394-0.66680.22390.7188-0.04980.06560.6524-0.14010.6911-21.834930.8297-13.2237
128.2344-2.93993.62616.0088-5.23734.46230.3844-0.6398-0.60850.0816-0.24360.12160.9881-0.8491-0.36490.8348-0.0484-0.0580.5616-0.19550.8574-17.579719.4221-14.5019
132.8298-2.24660.58674.3489-0.38257.9385-0.1657-0.18620.62120.3728-0.1229-1.1457-0.50870.93450.31150.5134-0.1304-0.11370.7069-0.1170.8435-6.410620.6943-23.3038
147.51560.2483.81662.2219-2.11766.0334-0.3056-1.0288-1.53330.6062-0.27491.41252.7048-0.67170.60082.2592-0.27350.76470.8782-0.06641.2801-25.6044-12.6471-1.0569
156.6935-3.4087-0.42528.4561.99115.4997-0.8131-1.3742-0.17352.73160.8407-0.17240.88890.7289-0.02571.80790.06680.06640.9755-0.05950.7165-15.8241-6.01212.6384
162.16290.34541.9422.6052-3.65267.89221.36760.0192.2021-0.9806-0.41870.8993-0.3728-0.7002-1.15830.85810.03830.16421.3579-0.20121.5239-34.861412.2588-4.1061
179.3433-5.16451.00044.0152-3.45197.09880.1991-0.58550.5240.42870.0163-0.47310.35410.4305-0.06691.085-0.19880.04330.7163-0.09840.642-14.7947-0.4512-7.8705
184.2549-0.34461.07747.97041.1634.7716-0.4599-0.0027-0.54521.3803-0.0631.08231.769-0.47380.51561.2559-0.16440.40250.7121-0.17480.6972-21.874-6.2005-16.0404
197.13981.3163.40882.3209-2.04935.8818-1.225-0.4308-2.78291.30360.13641.14651.9523-1.61261.16461.97-0.41960.54761.21150.04011.3349-30.3295-15.6666-12.9371
206.4507-0.8193-1.89822.0938-0.92122.1377-0.09470.7634-0.5533-0.6313-0.49552.08221.2149-2.03710.67931.017-0.22740.17331.3741-0.38051.1535-33.24730.3166-20.1494
212.7331.60990.64725.56845.2495.2689-0.54980.2192-1.0506-2.12830.846-0.7931-0.98030.7556-0.4421.32410.0221-0.16471.2161-0.13281.12-43.894118.172-33.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 47 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 95 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 217 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 19 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 20 through 90 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 91 through 128 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 172 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 173 through 205 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 206 through 217 )B0
10X-RAY DIFFRACTION10chain 'C' and (resid -1 through 19 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 20 through 86 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 87 through 128 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 129 through 199 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 0 through 19 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 20 through 86 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 87 through 95 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 96 through 128 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 129 through 174 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 175 through 186 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 187 through 199 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 200 through 210 )D0

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