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- PDB-2q2f: Structure of the human Selenoprotein S (VCP-interacting membrane ... -

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Basic information

Entry
Database: PDB / ID: 2q2f
TitleStructure of the human Selenoprotein S (VCP-interacting membrane protein)
ComponentsSelenoprotein S
KeywordsMEMBRANE PROTEIN / Anti-parallel coiled-coil / Endoplasmic reticulum / Membrane / Selenium / Selenocysteine / Transmembrane / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / : / very-low-density lipoprotein particle / negative regulation of D-glucose import / low-density lipoprotein particle / Derlin-1 retrotranslocation complex ...regulation of nitric oxide metabolic process / negative regulation of acute inflammatory response to antigenic stimulus / Derlin-1-VIMP complex / negative regulation of macrophage apoptotic process / negative regulation of glycogen biosynthetic process / : / very-low-density lipoprotein particle / negative regulation of D-glucose import / low-density lipoprotein particle / Derlin-1 retrotranslocation complex / response to redox state / retrograde protein transport, ER to cytosol / regulation of gluconeogenesis / ER overload response / ubiquitin-specific protease binding / cytoplasmic microtubule / antioxidant activity / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / response to glucose / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / endoplasmic reticulum unfolded protein response / ERAD pathway / cell redox homeostasis / establishment of protein localization / negative regulation of inflammatory response / cellular response to insulin stimulus / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / ATPase binding / cellular response to oxidative stress / cellular response to lipopolysaccharide / endoplasmic reticulum membrane / enzyme binding / endoplasmic reticulum / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2950 / Selenoprotein S / Selenoprotein S (SelS) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsWalker, J.R. / Paramanathan, R. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Human Selenoprotein S (VCP-interacting membrane protein).
Authors: Walker, J.R. / Paramanathan, R. / Butler-Cole, C. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionMay 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: Selenoprotein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9504
Polymers10,7871
Non-polymers1633
Water1,22568
1
A: Selenoprotein S
hetero molecules

A: Selenoprotein S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8998
Polymers21,5732
Non-polymers3266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y,-z+31
Buried area2740 Å2
ΔGint-55 kcal/mol
Surface area12270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.666, 18.705, 37.992
Angle α, β, γ (deg.)90.00, 93.36, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x+1/2, y+1/2, -z.

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Components

#1: Protein Selenoprotein S / VCP-interacting membrane protein


Mass: 10786.705 Da / Num. of mol.: 1 / Fragment: Coiled-coil Domain, Residues 52-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SELS, VIMP, AD-015, SBBI8 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BQE4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.97 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: Protein buffer: 100mM NaCl, 50mM Tris-HCl pH 8.0, 1mM EDTA, 2mM CaCl2, 5mM Beta-mercaptoethanol. Crystallization buffer: 13% PEG2000 MME, 0.1M Sodium acetate pH 4.6, 0.1M KSCN. Cryo: 30% ...Details: Protein buffer: 100mM NaCl, 50mM Tris-HCl pH 8.0, 1mM EDTA, 2mM CaCl2, 5mM Beta-mercaptoethanol. Crystallization buffer: 13% PEG2000 MME, 0.1M Sodium acetate pH 4.6, 0.1M KSCN. Cryo: 30% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97927 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2007
RadiationMonochromator: double crystal and K-B pair of biomorph mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.5→31.2 Å / Num. all: 13654 / Num. obs: 13654 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 19.86 Å2 / Rsym value: 0.085 / Net I/σ(I): 25.08
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 1216 / Rsym value: 0.325 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→31.2 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.658 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21434 668 4.9 %RANDOM
Rwork0.18135 ---
all0.18291 ---
obs0.18291 12947 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å22.12 Å2
2---0.46 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms577 0 8 68 653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022641
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.984858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.675582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9922.66730
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95615142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7021510
X-RAY DIFFRACTIONr_chiral_restr0.0990.292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02478
X-RAY DIFFRACTIONr_nbd_refined0.2170.2292
X-RAY DIFFRACTIONr_nbtor_refined0.2860.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.219
X-RAY DIFFRACTIONr_mcbond_it1.8563411
X-RAY DIFFRACTIONr_mcangle_it2.3564636
X-RAY DIFFRACTIONr_scbond_it4.7715255
X-RAY DIFFRACTIONr_scangle_it6.4537222
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 39 -
Rwork0.18 816 -
obs--84.4 %
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)
15.94821.10382.03830.63460.7165.2116-0.17320.16920.23570.22020.0005-0.1566-0.470.32290.17270.1136-0.0488-0.03090.09420.0590.083135.57839.332415.0445
20.07570.8181-0.73169.0769-8.7119.8449-0.0884-0.02360.00590.0342-0.2071-0.06270.020.40130.29550.113-0.0193-0.04480.10680.02730.052333.10332.666919.5414
32.66430.5103-1.70051.2835-1.92068.53850.1086-0.02580.05720.0177-0.14750.0037-0.14720.01060.03890.12020.004-0.03310.0730.01110.062130.7237-1.430425.2265
43.6051.1063-5.42633.3224-3.35979.1303-0.2602-0.1133-0.1661-0.32280.1109-0.11440.5219-0.05520.14930.1136-0.0114-0.01230.07740.00690.063130.5435-9.085133.4654
51.24392.6621-0.27725.9938-1.02220.6827-0.25280.0418-0.005-0.02920.21820.00470.0612-0.00740.03460.0675-0.006-0.02790.09110.00090.091725.2222-8.946339.8312
65.5306-0.4778-3.24221.1259-0.6933.09680.0460.11320.0196-0.0232-0.0930.1513-0.1344-0.17620.0470.0711-0.00080.00270.0806-0.01390.107518.2802-11.500345.2245
724.1225-1.8224-11.364311.55711.20215.86140.2598-0.30710.4205-0.1556-0.20630.0481-0.2009-0.5047-0.05340.01180.01630.01680.1269-0.03460.075412.738-10.683451.0636
830.66025.0544-10.57252.5851-4.23487.1904-0.4106-0.6096-0.5909-0.00250.01250.04570.19270.17780.3980.0240.02570.0430.1532-0.00240.09336.0279-14.20755.446
926.68410.3141-10.02742.05881.62666.15990.0069-0.59380.0421-0.11930.03060.0601-0.43760.2225-0.0375-0.08150.02660.12750.17290.03420.0341-1.3768-14.432360.3777
1020.32933.2243-12.170812.1557-10.941830.7241-0.0129-1.2932-0.84020.6382-0.3629-0.50520.59451.1540.37580.08280.0307-0.00210.240.04080.1419-7.2911-17.10166.4458
1129.073713.3046-20.32588.4209-11.745323.53040.5071-1.24660.6570.1547-0.6460.3888-0.15111.56340.1389-0.0359-0.04110.06580.2093-0.00610.08-15.4327-17.355771.4811
1231.1953.6741-11.508711.2599-14.647920.56481.4451-1.65850.7222-0.2521-0.07050.8866-0.83590.2641-1.37460.0159-0.06520.07770.11950.02730.1406-23.7756-19.614277.0238
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA51 - 5818 - 25
2X-RAY DIFFRACTION2AA59 - 6226 - 29
3X-RAY DIFFRACTION3AA63 - 6930 - 36
4X-RAY DIFFRACTION4AA70 - 7637 - 43
5X-RAY DIFFRACTION5AA77 - 8144 - 48
6X-RAY DIFFRACTION6AA82 - 8749 - 54
7X-RAY DIFFRACTION7AA88 - 9255 - 59
8X-RAY DIFFRACTION8AA93 - 9860 - 65
9X-RAY DIFFRACTION9AA99 - 10466 - 71
10X-RAY DIFFRACTION10AA105 - 10972 - 76
11X-RAY DIFFRACTION11AA110 - 11777 - 84
12X-RAY DIFFRACTION12AA118 - 12285 - 89

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