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- PDB-6o2u: Crystal structure of the SARAF luminal domain -

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Basic information

Entry
Database: PDB / ID: 6o2u
TitleCrystal structure of the SARAF luminal domain
ComponentsStore-operated calcium entry-associated regulatory factor
KeywordsSIGNALING PROTEIN / SOCE / Store Operated Calcium Entry / SARAF / ER / Endoplasmic reticulum / Calcium signaling / Domain swap
Function / homologyStore-operated calcium entry-associated regulatory factor / SOCE-associated regulatory factor of calcium homoeostasis / endoplasmic reticulum-plasma membrane contact site / regulation of store-operated calcium entry / calcium ion transport / endoplasmic reticulum membrane / endoplasmic reticulum / Store-operated calcium entry-associated regulatory factor
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.8 Å
AuthorsKimberlin, C.R. / Minor, D.L.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL080050 United States
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R01-DC007664 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32HL007731 United States
American Heart Association14POST18740062 United States
CitationJournal: J.Mol.Biol. / Year: 2019
Title: SARAF Luminal Domain Structure Reveals a Novel Domain-Swapped beta-Sandwich Fold Important for SOCE Modulation.
Authors: Kimberlin, C.R. / Meshcheriakova, A. / Palty, R. / Raveh, A. / Karbat, I. / Reuveny, E. / Minor Jr., D.L.
History
DepositionFeb 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Store-operated calcium entry-associated regulatory factor
B: Store-operated calcium entry-associated regulatory factor


Theoretical massNumber of molelcules
Total (without water)31,0352
Polymers31,0352
Non-polymers00
Water2,684149
1
A: Store-operated calcium entry-associated regulatory factor

A: Store-operated calcium entry-associated regulatory factor


Theoretical massNumber of molelcules
Total (without water)31,0352
Polymers31,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4480 Å2
ΔGint-15 kcal/mol
Surface area14470 Å2
MethodPISA
2
B: Store-operated calcium entry-associated regulatory factor

B: Store-operated calcium entry-associated regulatory factor


Theoretical massNumber of molelcules
Total (without water)31,0352
Polymers31,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area3170 Å2
ΔGint-15 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.980, 63.930, 79.920
Angle α, β, γ (deg.)90.000, 100.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Store-operated calcium entry-associated regulatory factor / SOCE-associated regulatory factor / HBV X-transactivated gene 3 protein / HBV XAg-transactivated ...SOCE-associated regulatory factor / HBV X-transactivated gene 3 protein / HBV XAg-transactivated protein 3 / Protein FOAP-7 / Transmembrane protein 66


Mass: 15517.307 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: SARAF, TMEM66, XTP3, HSPC035, NPD003, PSEC0019, UNQ1967/PRO4499
Production host: Escherichia coli (E. coli) / References: UniProt: Q96BY9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BisTris, pH 6.5, 18-20% PEG 5000 MME / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.8→39.432 Å / Num. obs: 23024 / % possible obs: 98.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.028 / Rrim(I) all: 0.075 / Net I/σ(I): 12.1
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.819 / Num. unique obs: 1167 / CC1/2: 0.349 / Rpim(I) all: 0.846 / Rrim(I) all: 2.013 / % possible all: 83.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.8→39.432 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.99
RfactorNum. reflection% reflection
Rfree0.2275 1095 4.76 %
Rwork0.1933 --
obs0.1951 23014 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.42 Å2 / Biso mean: 46.5437 Å2 / Biso min: 22.36 Å2
Refinement stepCycle: final / Resolution: 1.8→39.432 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 0 152 2090
Biso mean---44.83 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071985
X-RAY DIFFRACTIONf_angle_d0.9342697
X-RAY DIFFRACTIONf_chiral_restr0.054292
X-RAY DIFFRACTIONf_plane_restr0.007344
X-RAY DIFFRACTIONf_dihedral_angle_d15.688715
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.8820.43631180.38742450256887
1.882-1.98120.39141270.297127422869100
1.9812-2.10530.27541470.245427602907100
2.1053-2.26790.2771400.222728052945100
2.2679-2.49610.25261320.219527702902100
2.4961-2.85720.25991320.221228032935100
2.8572-3.59930.22531440.185427782922100
3.5993-39.44160.18081550.15192811296699

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