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- PDB-6y30: NG domain of human SRP54 T115A mutant -

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Basic information

Entry
Database: PDB / ID: 6y30
TitleNG domain of human SRP54 T115A mutant
ComponentsSignal recognition particle 54 kDa protein
KeywordsRNA BINDING PROTEIN / SRP54 NG domain / Protein translocation / Severe congenital neutropenia / Disease mutant
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane ...SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / granulocyte differentiation / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / neutrophil chemotaxis / GDP binding / nuclear speck / GTPase activity / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle, SRP54 subunit, eukaryotic / 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 ...Signal recognition particle, SRP54 subunit, eukaryotic / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle subunit SRP54
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsJuaire, K.D. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
CitationJournal: Structure / Year: 2021
Title: Structural and Functional Impact of SRP54 Mutations Causing Severe Congenital Neutropenia.
Authors: Juaire, K.D. / Lapouge, K. / Becker, M.M.M. / Kotova, I. / Michelhans, M. / Carapito, R. / Wild, K. / Bahram, S. / Sinning, I.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Signal recognition particle 54 kDa protein
B: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)66,6872
Polymers66,6872
Non-polymers00
Water45025
1
A: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,3441
Polymers33,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,3441
Polymers33,3441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.795, 53.903, 91.366
Angle α, β, γ (deg.)90.000, 105.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 33343.539 Da / Num. of mol.: 2 / Mutation: T115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SRP54 / Production host: Escherichia coli (E. coli) / References: UniProt: P61011
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.05 Å3/Da / Density % sol: 59.62 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1M Potassium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.65→53.26 Å / Num. obs: 22749 / % possible obs: 95.9 % / Redundancy: 7 % / Rpim(I) all: 0.12 / Net I/σ(I): 7.51
Reflection shellResolution: 2.65→2.75 Å / Num. unique obs: 2164 / Rpim(I) all: 0.59

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y2Z

6y2z


Resolution: 2.65→53.257 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 37.56
RfactorNum. reflection% reflection
Rfree0.3086 1118 4.92 %
Rwork0.2764 --
obs0.278 22734 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.51 Å2 / Biso mean: 65.6995 Å2 / Biso min: 20.96 Å2
Refinement stepCycle: final / Resolution: 2.65→53.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4486 0 0 25 4511
Biso mean---53.91 -
Num. residues----582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024556
X-RAY DIFFRACTIONf_angle_d0.4596138
X-RAY DIFFRACTIONf_chiral_restr0.041714
X-RAY DIFFRACTIONf_plane_restr0.003780
X-RAY DIFFRACTIONf_dihedral_angle_d17.2942784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.65-2.77060.37311300.3536262193
2.7706-2.91670.36451300.3516270197
2.9167-3.09940.39081610.3525270698
3.0994-3.33870.42031530.3474270497
3.3387-3.67460.3381380.3359261994
3.6746-4.20610.33471340.2669277498
4.2061-5.29850.25191170.2204270095
5.2985-53.2570.23331550.2244279196

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