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- PDB-4c7o: The structural basis of FtsY recruitment and GTPase activation by... -

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Basic information

Entry
Database: PDB / ID: 4c7o
TitleThe structural basis of FtsY recruitment and GTPase activation by SRP RNA
Components
  • (SIGNAL RECOGNITION PARTICLE ...) x 2
  • SRP RNA
KeywordsNUCLEAR PROTEIN/RNA / NUCLEAR PROTEIN-RNA COMPLEX / NUCLEAR PROTEIN / PROTEIN TRANSLOCATION / SIGNAL RECOGNITION PARTICLE / SIGNAL RECOGNITION PARTICLE RECEPTOR / GDP ALF3/4
Function / homology
Function and homology information


signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / ribonucleoprotein complex ...signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / stringent response / protein targeting / cytoplasmic side of plasma membrane / ribonucleoprotein complex / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis activity / plasma membrane / cytosol
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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / : / RNA / RNA (> 10) / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsVoigts-Hoffmann, F. / Schmitz, N. / Shen, K. / Shan, S.O. / Ataide, S.F. / Ban, N.
CitationJournal: Mol.Cell / Year: 2013
Title: The Structural Basis of Ftsy Recruitment and Gtpase Activation by Srp RNA
Authors: Voigts-Hoffmann, F. / Schmitz, N. / Shen, K. / Shan, S.O. / Ataide, S.F. / Ban, N.
History
DepositionSep 23, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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.ptnr3_label_seq_id / _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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
E: SRP RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,56518
Polymers140,8395
Non-polymers2,72513
Water9,026501
1
A: SIGNAL RECOGNITION PARTICLE PROTEIN
B: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
E: SRP RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3129
Polymers78,1713
Non-polymers1,1416
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-35.1 kcal/mol
Surface area29780 Å2
MethodPISA
2
C: SIGNAL RECOGNITION PARTICLE PROTEIN
D: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2529
Polymers62,6682
Non-polymers1,5847
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-27.7 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.720, 166.330, 154.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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SIGNAL RECOGNITION PARTICLE ... , 2 types, 4 molecules ACBD

#1: Protein SIGNAL RECOGNITION PARTICLE PROTEIN / FIFTY-FOUR HOMOLOG / FFH / P48


Mass: 32394.463 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGD7
#2: Protein SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY / SRP RECEPTOR / FTSY


Mass: 30273.680 Da / Num. of mol.: 2 / Fragment: NG DOMAIN, RESIDUES 224-497 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: UniProt: P10121

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RNA chain , 1 types, 1 molecules E

#3: RNA chain SRP RNA


Mass: 15503.189 Da / Num. of mol.: 1
Fragment: TETRALOOP RESIDUES 542524 542543 AND DISTAL SITE RESIDUES 542594-542617
Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: K-12 / References: GenBank: 56384585

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Non-polymers , 4 types, 514 molecules

#4: Chemical
ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.59 Å3/Da / Density % sol: 52.49 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→49.22 Å / Num. obs: 45637 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.28 % / Biso Wilson estimate: 61.96 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.38
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.77 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CNW

2cnw


Resolution: 2.6→49.222 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 25.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2255 1851 4.1 %
Rwork0.1632 --
obs0.1657 45630 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8681 1028 164 501 10374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110134
X-RAY DIFFRACTIONf_angle_d1.42714012
X-RAY DIFFRACTIONf_dihedral_angle_d14.2773935
X-RAY DIFFRACTIONf_chiral_restr0.0771671
X-RAY DIFFRACTIONf_plane_restr0.0061599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.37491390.27283307X-RAY DIFFRACTION99
2.6703-2.74890.32561410.25563308X-RAY DIFFRACTION100
2.7489-2.83760.2771430.21813378X-RAY DIFFRACTION100
2.8376-2.9390.25931380.19783293X-RAY DIFFRACTION100
2.939-3.05670.28761410.18983317X-RAY DIFFRACTION99
3.0567-3.19580.23321430.1833379X-RAY DIFFRACTION100
3.1958-3.36420.28351400.17833327X-RAY DIFFRACTION99
3.3642-3.5750.26411410.16113345X-RAY DIFFRACTION99
3.575-3.85090.20971430.15093353X-RAY DIFFRACTION99
3.8509-4.23820.18671410.13853358X-RAY DIFFRACTION99
4.2382-4.8510.16781450.12523421X-RAY DIFFRACTION100
4.851-6.110.20831460.15733431X-RAY DIFFRACTION99
6.11-49.23080.21911500.16153562X-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)
10.0718-0.06650.12690.0036-0.06760.18780.3306-0.7977-0.6764-0.3892-0.14490.565-0.820.4292-0.00192.52040.37770.20251.56650.00841.883-9.89122.192-40.3841
20.7343-0.4787-0.6210.28590.40190.5666-0.02850.1094-0.8532-0.12490.08290.14852.22740.6961-0.072.98520.75890.23980.2399-0.28381.3299-15.439210.7225-51.6452
30.34410.02690.25430.0487-0.06450.16560.6206-1.1058-1.53271.4745-0.906-0.62250.23750.7674-0.01061.58980.55640.06821.59120.24711.6275-2.954713.3539-45.3989
42.81540.0212-0.92293.41420.47666.018-0.01730.7463-0.0237-0.64610.2412-0.3666-0.01270.26840.00490.5398-0.07010.08580.6602-0.07090.4056-18.521842.2981-63.779
50.39680.2988-0.01910.4864-0.53221.1667-0.17910.0295-0.40830.49860.2231-0.721.04891.1360.00010.86130.25090.1060.736-0.13780.7335-13.574129.8687-50.3547
60.38920.0576-0.15810.0577-0.08620.1510.3994-0.2436-1.90940.1717-0.66370.44751.3143-0.5329-0.15173.2076-1.0317-0.01480.2567-0.38821.9266-35.60784.231-51.8043
71.51250.45810.74530.10640.07354.591-0.05880.1056-1.1168-0.54060.8410.25372.0827-2.11161.53990.8422-1.28050.34081.8324-0.13761.2745-48.561321.174-47.4926
81.47330.1337-1.99362.69110.50012.95810.13060.6534-0.00560.03510.14850.4632-0.4673-1.55680.00960.49090.15150.05880.98460.16220.495-40.774345.8316-46.853
91.6444-0.658-0.85181.6704-1.61562.6267-0.26820.3642-0.8993-0.11610.35190.65661.3583-1.86380.01020.7746-0.45060.00961.0219-0.00850.823-39.786230.3216-46.1588
100.1777-0.09750.12540.09940.01080.1503-0.41071.2999-0.6163-0.55440.59640.60450.4713-0.5443-0.00441.4161-0.25830.30621.1451-0.37161.6315-28.2943-11.7061-26.8596
110.4026-0.16730.4210.53690.0840.5024-0.22150.1274-1.01870.16820.11180.56310.8493-0.5236-0.00010.7737-0.16880.12650.5346-0.15660.9604-23.7489-6.6276-14.0888
120.52360.09090.06330.4726-0.64170.7214-0.18171.2023-0.2633-0.6751-1.21632.8104-0.1973-1.0599-0.02850.8912-0.0647-0.17031.0922-0.46691.4777-36.3274-2.7542-19.8096
132.650.5637-0.44712.82980.13562.77380.0342-0.54370.33660.4294-0.08930.43330.0481-0.10140.00010.4516-0.0680.14140.5021-0.18630.4857-21.195922.03824.0436
141.1378-0.2656-0.1131.03480.89630.7166-0.06720.3711-0.0401-0.3012-0.01620.75740.047-0.3412-0.00010.4491-0.06370.07270.5607-0.10540.5839-26.185812.2431-11.8123
150.5089-0.2173-0.06650.68730.15720.35660.13410.0059-1.01770.1693-0.26360.76320.6960.4683-00.92020.2170.13160.6280.00870.9614-3.5146-13.601-14.2679
160.1052-0.2331-0.34870.27830.13840.3637-0.02690.199-0.4167-0.25120.0187-0.84630.3440.42050.00010.61620.17370.11480.7474-0.04290.98168.40824.461-16.3561
171.71510.2328-1.39612.4861-0.40882.32460.0636-0.24950.28580.0202-0.1201-0.3357-0.32210.3878-00.3824-0.08140.03670.5142-0.05150.53620.80628.8391-12.1363
181.96130.9315-0.38882.6480.65251.8993-0.068-0.0723-0.2816-0.00490.033-0.5030.41750.33880.00030.38020.06790.06490.5447-0.04910.5335-0.264913.4437-15.4442
190.137-0.0062-0.00770.08170.01890.00740.17230.6114-0.0924-0.19010.2556-0.1527-0.02930.1843-0.00470.4187-0.09560.0620.4477-0.08310.3039-25.379440.5546-54.3228
200.7431-0.70090.85380.6677-0.82141.0016-0.68640.7618-0.45630.29190.22770.2040.3356-0.4698-0.01920.4549-0.15090.07070.68030.08890.3663-33.405939.2887-53.8322
210.0481-0.031-0.00610.09310.03390.05250.2523-0.06540.190.4989-0.40890.4238-0.3975-0.0410.00070.3569-0.12220.06230.3579-0.03370.2946-14.473922.2947-5.7294
221.99370.77320.42280.34330.09520.2262-0.0908-0.3285-0.4533-0.21450.1139-0.34110.05150.0890.07360.17180.22740.58080.2874-0.6237-0.5545-6.42621.0985-6.4595
23-0.0009-0.030.00670.2169-0.04370.0071-0.18930.55390.6264-0.3290.0650.2673-0.2178-0.4044-0.00780.85940.23250.17621.1224-0.04931.1202-15.890431.3088-20.0696
242.49870.94860.9220.33410.09692.9516-0.1507-0.41871.17480.30060.01360.0173-1.3006-0.6055-0.00521.18280.2240.12180.6542-0.03450.9031-28.299356.9026-30.8582
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 2 : 30 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 31 : 60 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 61 : 90 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 91 : 250)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 251 : 297 )
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 30 : 71 )
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 72 : 100 )
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 101 : 200 )
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 201 : 300 )
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 2 : 30 )
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 31 : 60 )
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 61 : 90 )
13X-RAY DIFFRACTION13CHAIN C AND (RESSEQ 91 : 250)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 251 : 297 )
15X-RAY DIFFRACTION15CHAIN D AND (RESSEQ 23 : 71 )
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 72 : 100 )
17X-RAY DIFFRACTION17CHAIN D AND (RESSEQ 101 : 200 )
18X-RAY DIFFRACTION18CHAIN D AND (RESSEQ 201 : 302 )
19X-RAY DIFFRACTION19CHAIN A AND (RESSEQ 1001 : 1007 )
20X-RAY DIFFRACTION20CHAIN B AND (RESSEQ 1001 : 1007 )
21X-RAY DIFFRACTION21CHAIN C AND (RESSEQ 1001 : 1007 )
22X-RAY DIFFRACTION22CHAIN D AND (RESSEQ 1001 : 1007 )
23X-RAY DIFFRACTION23CHAIN D AND (RESSEQ 1306)
24X-RAY DIFFRACTION24CHAIN E (RESSEQ 0 AND 47)

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