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- PDB-5l3r: Structure of the GTPase heterodimer of chloroplast SRP54 and FtsY... -

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Basic information

Entry
Database: PDB / ID: 5l3r
TitleStructure of the GTPase heterodimer of chloroplast SRP54 and FtsY from Arabidopsis thaliana
Components
  • Cell division protein FtsY homolog, chloroplastic
  • Signal recognition particle 54 kDa protein, chloroplastic
KeywordsPROTEIN TRANSPORT / Co-translational protein targeting / Signal Recognition Particle / GTPase
Function / homology
Function and homology information


protein heterotrimerization / signal recognition particle, endoplasmic reticulum targeting / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / protein domain specific binding / GTPase activity ...protein heterotrimerization / signal recognition particle, endoplasmic reticulum targeting / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / protein domain specific binding / GTPase activity / GTP binding / ATP hydrolysis activity / protein-containing complex / metal ion binding / plasma membrane
Similarity search - Function
Signal-recognition particle receptor FtsY / SRP54, nucleotide-binding domain / Signal recognition particle protein / 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 receptor FtsY / SRP54, nucleotide-binding domain / Signal recognition particle protein / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cell division protein FtsY homolog, chloroplastic / Signal recognition particle subunit SRP54, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBange, G. / Kribelbauer, J. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationGRK1188 Germany
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex.
Authors: Wild, K. / Bange, G. / Motiejunas, D. / Kribelbauer, J. / Hendricks, A. / Segnitz, B. / Wade, R.C. / Sinning, I.
History
DepositionMay 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / 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_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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.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.value / _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: Signal recognition particle 54 kDa protein, chloroplastic
B: Cell division protein FtsY homolog, chloroplastic
C: Signal recognition particle 54 kDa protein, chloroplastic
D: Cell division protein FtsY homolog, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,68314
Polymers128,3174
Non-polymers2,36610
Water2,522140
1
A: Signal recognition particle 54 kDa protein, chloroplastic
B: Cell division protein FtsY homolog, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3427
Polymers64,1582
Non-polymers1,1835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-37 kcal/mol
Surface area22620 Å2
MethodPISA
2
C: Signal recognition particle 54 kDa protein, chloroplastic
D: Cell division protein FtsY homolog, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3427
Polymers64,1582
Non-polymers1,1835
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-39 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.790, 74.750, 107.210
Angle α, β, γ (deg.)90.00, 91.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Signal recognition particle 54 kDa protein, chloroplastic / cpSRP54 / FFC


Mass: 32424.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FFC, CPSRP54, At5g03940, F8F6_150 / Production host: Escherichia coli (E. coli) / References: UniProt: P37107
#2: Protein Cell division protein FtsY homolog, chloroplastic / Chloroplast SRP receptor homolog / alpha subunit CpFtsY / Fused signal recognition particle receptor


Mass: 31733.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CPFTSY, FTSY, At2g45770, F4I18.25 / Production host: Escherichia coli (E. coli) / References: UniProt: O80842

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Non-polymers , 4 types, 150 molecules

#3: Chemical
ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mg
#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.: 140 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.5→35.73 Å / Num. obs: 49064 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rsym value: 0.094 / Net I/σ(I): 9.5
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.54

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3S

5l3s


Resolution: 2.5→44.886 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2415 5.06 %0
Rwork0.1727 ---
obs0.1751 47771 96.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8388 0 144 140 8672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088623
X-RAY DIFFRACTIONf_angle_d0.98211649
X-RAY DIFFRACTIONf_dihedral_angle_d13.6665247
X-RAY DIFFRACTIONf_chiral_restr0.0531387
X-RAY DIFFRACTIONf_plane_restr0.0051470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55110.29511120.23952471X-RAY DIFFRACTION90
2.5511-2.60650.2671410.22792513X-RAY DIFFRACTION92
2.6065-2.66720.3161340.22022595X-RAY DIFFRACTION93
2.6672-2.73390.2781290.21212539X-RAY DIFFRACTION94
2.7339-2.80780.24991360.21012628X-RAY DIFFRACTION95
2.8078-2.89040.28111410.20552649X-RAY DIFFRACTION96
2.8904-2.98360.26641300.20172654X-RAY DIFFRACTION96
2.9836-3.09030.26181220.21672664X-RAY DIFFRACTION97
3.0903-3.2140.25151650.20262668X-RAY DIFFRACTION98
3.214-3.36020.25511490.18782703X-RAY DIFFRACTION98
3.3602-3.53730.20661490.17212736X-RAY DIFFRACTION99
3.5373-3.75880.22361550.16492716X-RAY DIFFRACTION99
3.7588-4.04880.18741450.14542762X-RAY DIFFRACTION99
4.0488-4.4560.18751450.13462734X-RAY DIFFRACTION99
4.456-5.10.18121540.12432760X-RAY DIFFRACTION99
5.1-6.42240.21131660.17812753X-RAY DIFFRACTION99
6.4224-44.89330.1611420.15722811X-RAY DIFFRACTION98
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)
11.19960.14551.10530.01740.12631.0338-0.6921-1.02980.95221.23620.3605-0.3691-0.84830.03250.40091.11530.1652-0.2360.5525-0.18760.54793.732612.458643.5484
24.1343.96214.84314.03174.95436.083-0.6221-0.64911.16090.8416-0.3669-0.261-1.02080.21430.6790.93180.0415-0.37080.4568-0.08350.638813.21197.561348.1684
32.2931-0.2404-0.04553.70040.03431.73160.0294-0.1034-0.23030.3773-0.06560.0570.2272-0.01810.01010.2411-0.02710.00170.16310.01190.1724-0.4986-17.951329.5206
42.281.57472.5645.2290.20393.80130.0823-0.0525-0.04090.36170.1756-0.99940.18070.6069-0.22750.20680.0261-0.08010.31690.03020.347513.6794-7.077731.4226
52.0378-1.9289-0.47182.2941.38242.22910.0745-0.01750.37160.00870.0196-0.0641-0.19380.0818-0.07630.3185-0.06180.03730.11690.02690.3607-12.871820.365128.8152
61.5865-0.26870.06052.27040.50572.45920.07320.18570.0198-0.1237-0.1129-0.0988-0.05040.19640.04360.1228-0.0011-0.00570.20630.04290.19460.5521-0.97546.0233
71.1794-1.22091.24892.5635-1.5264.5124-0.23780.50180.8564-0.0122-0.2742-0.3355-0.7261-0.38270.42590.4775-0.0904-0.15060.87340.34820.662734.381120.565214.463
80.4040.0018-0.60231.41960.90021.55280.04831.0085-0.1371-0.5541-0.04590.2270.38660.0459-0.03730.6409-0.1217-0.00640.9676-0.12140.358536.8537-14.36519.6871
91.41971.8241-1.11332.4383-1.17391.6877-0.14430.1589-0.74710.2382-0.1030.03090.9293-0.20390.11490.784-0.15810.04080.6429-0.30610.399340.3235-26.166416.4485
101.81650.38550.09751.51040.0261.9261-0.24291.0737-0.1039-0.53730.1956-0.00470.295-0.07820.01770.4916-0.12390.02880.9294-0.0180.278241.0074-7.876512.4416
112.58292.542-1.22985.6463-1.18110.83790.21730.13740.40120.25680.09150.2904-0.3355-0.2073-0.20350.2230.06680.03150.21410.0120.256651.518414.358837.3239
121.91380.7404-0.30822.8307-0.86171.9935-0.07620.2007-0.2157-0.14460.0493-0.11530.2069-0.10240.01950.1717-0.00360.02030.1701-0.0440.204639.9104-12.08339.4909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 100 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 161 )
3X-RAY DIFFRACTION3chain 'A' and (resid 162 through 349 )
4X-RAY DIFFRACTION4chain 'A' and (resid 350 through 371 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 148 )
6X-RAY DIFFRACTION6chain 'B' and (resid 149 through 366 )
7X-RAY DIFFRACTION7chain 'C' and (resid 97 through 161 )
8X-RAY DIFFRACTION8chain 'C' and (resid 162 through 218 )
9X-RAY DIFFRACTION9chain 'C' and (resid 219 through 242 )
10X-RAY DIFFRACTION10chain 'C' and (resid 243 through 370 )
11X-RAY DIFFRACTION11chain 'D' and (resid 78 through 164 )
12X-RAY DIFFRACTION12chain 'D' and (resid 165 through 366 )

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