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- PDB-6y31: NG domain of human SRP54 T117 deletion mutant -

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Basic information

Entry
Database: PDB / ID: 6y31
TitleNG domain of human SRP54 T117 deletion 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 / protein targeting to ER / granulocyte differentiation / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / exocrine pancreas development ...SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / protein targeting to ER / granulocyte differentiation / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 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 / GDP binding / nuclear speck / GTPase activity / GTP binding / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / cytoplasm / cytosol
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: 4.001 Å
AuthorsJuaire, K.D. / Lapouge, K. / Becker, M.M.M. / Kotova, I. / Haas, M. / Carapito, R. / Wild, K. / Bahram, S. / 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 54 kDa protein
B: Signal recognition particle 54 kDa protein
C: Signal recognition particle 54 kDa protein
D: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)133,6424
Polymers133,6424
Non-polymers00
Water00
1
A: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,4111
Polymers33,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,4111
Polymers33,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,4111
Polymers33,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Signal recognition particle 54 kDa protein


Theoretical massNumber of molelcules
Total (without water)33,4111
Polymers33,4111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.356, 50.607, 181.629
Angle α, β, γ (deg.)90.000, 99.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid 1 through 141 or resid 147 through 296))
31(chain C and (resid 1 through 141 or resid 147 through 296))
41(chain D and (resid 1 through 141 or resid 147 through 296))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYchain AAA1 - 2969 - 303
21METMETARGARG(chain B and (resid 1 through 141 or resid 147 through 296))BB1 - 1419 - 148
22GLNGLNGLYGLY(chain B and (resid 1 through 141 or resid 147 through 296))BB147 - 296154 - 303
31METMETARGARG(chain C and (resid 1 through 141 or resid 147 through 296))CC1 - 1419 - 148
32GLNGLNGLYGLY(chain C and (resid 1 through 141 or resid 147 through 296))CC147 - 296154 - 303
41METMETARGARG(chain D and (resid 1 through 141 or resid 147 through 296))DD1 - 1419 - 148
42GLNGLNGLYGLY(chain D and (resid 1 through 141 or resid 147 through 296))DD147 - 296154 - 303

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Components

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


Mass: 33410.605 Da / Num. of mol.: 4
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

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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: 58.5 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.8 M Na2HPO4 , 0.8 M K2HPO4 HEPES 0.1 M (pH 7.5)

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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: 4→45.724 Å / Num. obs: 13630 / % possible obs: 94.58 % / Redundancy: 6.6 % / Rpim(I) all: 0.213 / Net I/σ(I): 2.27
Reflection shellResolution: 4→4.14 Å / Num. unique obs: 1343 / Rpim(I) all: 1.25

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6y2z

6y2z


Resolution: 4.001→45.724 Å / SU ML: 0.86 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 38.33
RfactorNum. reflection% reflection
Rfree0.3312 624 4.8 %
Rwork0.3114 --
obs0.3124 12990 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 264.85 Å2 / Biso mean: 140.99 Å2 / Biso min: 67.64 Å2
Refinement stepCycle: final / Resolution: 4.001→45.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9043 0 0 0 9043
Num. residues----1175
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5619X-RAY DIFFRACTION13.719TORSIONAL
12B5619X-RAY DIFFRACTION13.719TORSIONAL
13C5619X-RAY DIFFRACTION13.719TORSIONAL
14D5619X-RAY DIFFRACTION13.719TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
4.001-4.40280.37751470.3721262482
4.4028-5.03920.39091500.3524320699
5.0392-6.34620.38671510.3573323199
6.3462-45.7240.26731760.2502330599

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