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- PDB-5l3q: Structure of the GTPase heterodimer of human SRP54 and SRalpha -

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Basic information

Entry
Database: PDB / ID: 5l3q
TitleStructure of the GTPase heterodimer of human SRP54 and SRalpha
Components(Signal recognition particle ...) x 2
KeywordsPROTEIN TRANSPORT / Co-translational protein targeting / Signal Recognition Particle / GTPase
Function / homology
Function and homology information


signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / cotranslational protein targeting to membrane / granulocyte differentiation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation ...signal recognition particle receptor complex / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / cotranslational protein targeting to membrane / granulocyte differentiation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / XBP1(S) activates chaperone genes / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / neutrophil chemotaxis / intracellular protein transport / GDP binding / nuclear speck / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / SRP54, nucleotide-binding domain / 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 receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle, SRP54 subunit, eukaryotic / SRP54, nucleotide-binding domain / 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 / Longin-like domain superfamily / 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
ADENOSINE MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Signal recognition particle receptor subunit alpha / Signal recognition particle subunit SRP54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWild, K. / Segnitz, B. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB638 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
B: Signal recognition particle receptor subunit alpha
C: Signal recognition particle 54 kDa protein
D: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,19127
Polymers238,0774
Non-polymers4,11323
Water2,324129
1
A: Signal recognition particle 54 kDa protein
B: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,14314
Polymers119,0392
Non-polymers2,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-101 kcal/mol
Surface area23590 Å2
MethodPISA
2
C: Signal recognition particle 54 kDa protein
D: Signal recognition particle receptor subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,04713
Polymers119,0392
Non-polymers2,00911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-84 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)241.394, 241.394, 241.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

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Signal recognition particle ... , 2 types, 4 molecules ACBD

#1: Protein Signal recognition particle 54 kDa protein / SRP54


Mass: 49130.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The C-terminal M domain was degraded during crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Production host: Escherichia coli (E. coli) / References: UniProt: P61011
#2: Protein Signal recognition particle receptor subunit alpha / SR-alpha / Docking protein alpha / DP-alpha


Mass: 69908.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal Longin domain (SRX) and the linker to the NG domain are degraded during crystallization
Source: (gene. exp.) Homo sapiens (human) / Gene: SRPRA, SRPR / Production host: Escherichia coli (E. coli) / References: UniProt: P08240

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Non-polymers , 6 types, 152 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 4.67 Å3/Da / Density % sol: 73.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 100 mM Tris pH 8.0, 400 mM lithium sulfate, 10 % (w/v) PEG 8000

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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: Sep 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→76.335 Å / Num. obs: 38582 / % possible obs: 99.9 % / Redundancy: 11.8 % / Rsym value: 0.114 / Net I/σ(I): 11.4
Reflection shellResolution: 3.2→3.32 Å / Rsym value: 0.458

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L3S

5l3s


Resolution: 3.2→76.335 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.67
RfactorNum. reflection% reflection
Rfree0.1905 1910 4.96 %
Rwork0.1452 --
obs0.1475 38508 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→76.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8782 0 247 129 9158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0149175
X-RAY DIFFRACTIONf_angle_d1.26312456
X-RAY DIFFRACTIONf_dihedral_angle_d16.7793384
X-RAY DIFFRACTIONf_chiral_restr0.081438
X-RAY DIFFRACTIONf_plane_restr0.0051550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.28020.30941430.24812608X-RAY DIFFRACTION100
3.2802-3.36890.28721330.2182596X-RAY DIFFRACTION100
3.3689-3.4680.26991320.19982604X-RAY DIFFRACTION100
3.468-3.57990.25581280.18472617X-RAY DIFFRACTION100
3.5799-3.70790.22411310.16952590X-RAY DIFFRACTION100
3.7079-3.85630.20471450.16092589X-RAY DIFFRACTION100
3.8563-4.03180.16621330.13642625X-RAY DIFFRACTION100
4.0318-4.24440.20061150.12472618X-RAY DIFFRACTION100
4.2444-4.51030.16941440.11372607X-RAY DIFFRACTION100
4.5103-4.85850.15271320.1032626X-RAY DIFFRACTION100
4.8585-5.34730.15661450.10752614X-RAY DIFFRACTION100
5.3473-6.12080.16841420.13572618X-RAY DIFFRACTION100
6.1208-7.71040.15551410.14742644X-RAY DIFFRACTION100
7.7104-76.35720.16311460.13462642X-RAY DIFFRACTION97
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)
14.0538-3.6096-3.51734.66452.58023.24050.26441.6301-0.97730.6983-0.5704-0.87810.00310.50830.12080.57920.181-0.05130.9906-0.2160.75278.315261.599818.1463
28.7658-1.6389-6.91766.32831.75198.60250.08330.1759-1.1195-0.5669-0.56630.02031.13370.40040.59540.71540.2153-0.01940.6693-0.08760.548769.159861.100716.6194
37.4759-3.01743.54866.4124-2.20758.44240.50450.51490.3925-0.7891-0.5616-1.3132-0.05980.47710.0730.86150.28960.10860.7174-0.04310.580872.560465.56538.2192
41.930.48392.31522.890.7345.4923-0.0925-0.04420.1452-0.245-0.0659-0.0121-0.6105-0.27030.13270.47230.10650.05210.6055-0.06040.313244.561289.141914.3185
51.9765-1.2521-0.92636.7959-3.34264.52720.1240.3906-0.0308-0.05450.11490.4127-0.226-1.0634-0.18660.43740.0566-0.02720.6649-0.12290.319636.958185.916616.1492
64.6713-2.46636.60226.9579-2.14489.68280.237-0.012-0.24480.4032-0.57990.4105-0.4208-1.06790.30730.396-0.08910.07870.8399-0.0770.478636.332475.917422.5793
76.29110.79891.13023.25590.45925.59010.2020.0004-0.44530.3222-0.059-0.20890.4408-0.0564-0.14230.51860.0341-0.04160.4619-0.06930.329149.49173.710519.4319
83.1280.4012-0.40555.66490.20614.66340.07250.5237-0.0644-0.3251-0.1438-0.4813-0.03110.30070.0480.46360.11410.05010.5862-0.05090.294459.360679.348413.5406
94.0242-4.92653.75538.575-7.25448.10990.11950.0486-0.1176-0.3707-0.1799-0.16620.38650.01640.07770.3860.00570.00070.3461-0.05790.443873.321259.658940.3812
102.2846-0.5448-0.17953.26931.65925.4086-0.0141-0.27240.20790.2037-0.05030.0238-0.4175-0.20030.06930.41510.0051-0.00870.3941-0.0270.294553.241896.892344.1303
112.02740.0158-0.60525.50091.92913.05180.10060.1658-0.012-0.2717-0.0043-0.4694-0.25670.4215-0.06680.40850.0014-0.00530.4498-0.00560.32565.687291.493335.2438
127.2761-0.93160.61273.312-0.39392.94540.1031-0.1673-0.16670.2986-0.0349-0.13230.19140.0141-0.07080.42980.0620.00010.3890.0080.21861.083678.784240.8442
130.1013-0.02480.94284.82810.9998.82060.28930.96231.6123-0.4839-0.38380.3429-0.6048-1.71090.03330.64730.14390.12960.60250.14371.602183.288116.725255.6616
142.6781-1.35573.17254.274-5.02937.03-0.2632-0.89960.32391.72660.18250.4148-1.3667-0.46040.13540.9066-0.04070.25830.4917-0.13751.106491.5988116.596561.9004
158.5734-2.2851-2.47590.74521.50256.02360.27661.09990.2261-0.4479-0.4194-0.3368-0.9848-0.8750.12751.20710.17090.49120.64920.19931.653292.3057123.490652.452
167.51124.612-0.60983.4641-1.68472.80010.0174-0.44680.89920.18540.0517-0.7027-0.29860.0739-0.62370.7042-0.0830.25280.43380.13882.1145121.9002114.884553.3278
173.1102-0.6388-0.68652.3340.37762.00740.2615-0.09680.8431-0.00970.0554-0.8026-0.20.1211-0.24990.4579-0.13830.1370.3898-0.041.1645116.2044100.414352.4229
187.70981.6191-6.68316.6606-0.72347.30340.8984-0.00131.56130.12910.24480.3578-1.6777-0.4842-1.1930.77780.10.20840.55550.02430.685176.8794104.867.177
196.1314-3.9095-6.33054.83073.53717.6354-0.2697-0.09670.20910.05950.04720.02670.1993-0.35130.24790.3493-0.02010.00670.4257-0.05890.378776.016396.214566.5607
203.10890.6997-0.11284.14790.21972.54830.06280.0738-0.238-0.0295-0.0772-0.20370.1199-0.14270.04280.2833-0.05190.00260.30990.04920.4802102.914972.693546.595
211.6556-1.3116-0.89432.84821.24443.28960.14130.18570.3508-0.317-0.07060.0602-0.5225-0.262-0.08510.33160.00950.06260.40850.10310.628495.097486.254342.3607
222.8451-1.0562-0.28941.49-0.22911.98640.1019-0.27480.12520.1845-0.06140.1140.0371-0.1845-0.04690.3678-0.07070.0780.3630.0570.595492.118486.112556.7845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 40 )
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 87 )
4X-RAY DIFFRACTION4chain 'A' and (resid 88 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 198 )
6X-RAY DIFFRACTION6chain 'A' and (resid 199 through 212 )
7X-RAY DIFFRACTION7chain 'A' and (resid 213 through 239 )
8X-RAY DIFFRACTION8chain 'A' and (resid 240 through 296 )
9X-RAY DIFFRACTION9chain 'B' and (resid 332 through 397 )
10X-RAY DIFFRACTION10chain 'B' and (resid 398 through 512 )
11X-RAY DIFFRACTION11chain 'B' and (resid 513 through 572 )
12X-RAY DIFFRACTION12chain 'B' and (resid 573 through 638 )
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 42 )
14X-RAY DIFFRACTION14chain 'C' and (resid 43 through 60 )
15X-RAY DIFFRACTION15chain 'C' and (resid 61 through 87 )
16X-RAY DIFFRACTION16chain 'C' and (resid 88 through 101 )
17X-RAY DIFFRACTION17chain 'C' and (resid 102 through 296 )
18X-RAY DIFFRACTION18chain 'D' and (resid 332 through 351 )
19X-RAY DIFFRACTION19chain 'D' and (resid 352 through 397 )
20X-RAY DIFFRACTION20chain 'D' and (resid 398 through 512 )
21X-RAY DIFFRACTION21chain 'D' and (resid 513 through 572 )
22X-RAY DIFFRACTION22chain 'D' and (resid 573 through 638 )

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