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- PDB-4m8g: Crystal structure of Se-Met hN33/Tusc3 -

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Basic information

Entry
Database: PDB / ID: 4m8g
TitleCrystal structure of Se-Met hN33/Tusc3
ComponentsTumor suppressor candidate 3
KeywordsOXIDOREDUCTASE / thioredoxin-like fold / thiol/disulfide oxidoreductase / thiol/disulfide exchange reactions / redox-active protein
Function / homology
Function and homology information


Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / protein N-linked glycosylation via asparagine / magnesium ion transmembrane transporter activity / protein N-linked glycosylation / transmembrane transport / cognition / Maturation of spike protein ...Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / protein N-linked glycosylation via asparagine / magnesium ion transmembrane transporter activity / protein N-linked glycosylation / transmembrane transport / cognition / Maturation of spike protein / endoplasmic reticulum membrane / mitochondrion / plasma membrane
Similarity search - Function
Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Thioredoxin-like superfamily
Similarity search - Domain/homology
Tumor suppressor candidate 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.
CitationJournal: Structure / Year: 2014
Title: Structural basis of substrate specificity of human oligosaccharyl transferase subunit n33/tusc3 and its role in regulating protein N-glycosylation.
Authors: Mohorko, E. / Owen, R.L. / Malojcic, G. / Brozzo, M.S. / Aebi, M. / Glockshuber, R.
History
DepositionAug 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 20, 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_sheet
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_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor suppressor candidate 3
B: Tumor suppressor candidate 3


Theoretical massNumber of molelcules
Total (without water)38,9402
Polymers38,9402
Non-polymers00
Water2,018112
1
A: Tumor suppressor candidate 3


Theoretical massNumber of molelcules
Total (without water)19,4701
Polymers19,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tumor suppressor candidate 3


Theoretical massNumber of molelcules
Total (without water)19,4701
Polymers19,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.107, 64.456, 62.467
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor suppressor candidate 3 / Magnesium uptake/transporter TUSC3 / Protein N33


Mass: 19470.133 Da / Num. of mol.: 2 / Fragment: soluble domain of N33/Tusc3 / Mutation: C123S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: N33, TUSC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13454
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M KSCN, 10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9787 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2→64.45 Å / Num. obs: 20996 / % possible obs: 100 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 31.1
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.322 / Mean I/σ(I) obs: 11.4 / Rsym value: 0.322 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→44.836 Å / SU ML: 0.14 / σ(F): 0 / Phase error: 25.88 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2484 396 1.89 %
Rwork0.2286 --
obs0.229 20996 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 0 112 2381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012328
X-RAY DIFFRACTIONf_angle_d1.4753134
X-RAY DIFFRACTIONf_dihedral_angle_d15.555865
X-RAY DIFFRACTIONf_chiral_restr0.11320
X-RAY DIFFRACTIONf_plane_restr0.009411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.28950.24491420.22316784X-RAY DIFFRACTION99
2.2895-2.88440.26351370.24556841X-RAY DIFFRACTION100
2.8844-44.84770.24161170.22266975X-RAY DIFFRACTION100
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)
13.7702-1.1059-0.85442.53090.49723.17540.1145-0.03490.7670.5675-0.03640.2719-1.3769-0.64550.12210.39770.1181-0.00960.19790.00390.32044.065936.86660.1893
23.8055-0.0329-1.2581.11980.14442.3108-0.16930.12970.13950.0780.0966-0.0715-0.0133-0.0650.06470.13020.032-0.02650.083-0.010.136210.027128.099758.7676
38.5694-3.7806-1.27234.33570.34052.2572-0.02920.25340.7472-0.09410.0545-0.3488-0.0280.0963-0.09390.1184-0.0313-0.01130.1171-0.01360.18497.159231.810944.8436
44.18630.19350.27092.34240.56664.6354-0.1132-0.0826-0.06730.16540.1031-0.21760.0690.57250.00830.12680.0069-0.0040.136-0.01010.133911.910225.398656.4409
54.5616-0.6165-0.87245.12381.28036.7198-0.2151-0.4236-0.30090.60590.1799-0.08860.6556-0.05050.05910.16320.0064-0.00270.10910.02270.12282.09617.818857.0807
64.4635-2.4327-2.21254.43750.15884.23810.06320.06580.0127-0.2094-0.07670.40230.0386-0.2148-0.00660.1-0.0231-0.04660.1497-0.03620.1215-0.409423.262544.4692
70.93060.5490.8084.1728-0.06042.7030.59630.4423-0.3017-1.1207-0.2611.22461.2257-0.5474-0.17971.18570.219-0.3880.59720.11241.038213.30376.379995.5413
81.9982-0.4241-0.58410.62670.01613.4789-0.06190.0175-0.1808-0.03350.1149-0.08320.5240.1787-0.12990.26120.0213-0.01250.1399-0.02840.1526.963613.571694.2603
93.78191.55994.68891.31122.05365.16510.12550.3080.1135-0.0578-0.17310.07890.0427-0.11010.05330.181-0.0045-0.02290.1969-0.03520.1725-4.026615.729380.3278
103.63-4.7160.14366.4572-0.9823.0791-0.01080.3672-0.6988-0.05140.0991-0.05360.2670.176-0.03150.19610.030.00050.1775-0.06160.23547.455311.406176.217
111.84630.198-0.40122.11860.97234.27480.18140.07150.02040.2142-0.16610.02660.2343-0.25350.02270.18270-0.03670.1895-0.05730.20042.291117.86787.0626
124.4863-0.21092.50746.4873-0.38942.16850.1938-0.20810.14050.3219-0.0441-0.3244-0.76570.7245-0.05050.2027-0.00810.01620.2232-0.06490.157111.432125.987388.8095
134.9611-1.95881.3893.82740.20454.26710.0015-0.08480.228-0.28750.2238-0.2986-0.15770.3979-0.2280.09460.00780.04050.1784-0.0360.155614.599420.692376.7924
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 110 )
5X-RAY DIFFRACTION5chain 'A' and (resid 111 through 126 )
6X-RAY DIFFRACTION6chain 'A' and (resid 127 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 13 through 22 )
8X-RAY DIFFRACTION8chain 'B' and (resid 23 through 45 )
9X-RAY DIFFRACTION9chain 'B' and (resid 46 through 58 )
10X-RAY DIFFRACTION10chain 'B' and (resid 59 through 77 )
11X-RAY DIFFRACTION11chain 'B' and (resid 78 through 111 )
12X-RAY DIFFRACTION12chain 'B' and (resid 112 through 126 )
13X-RAY DIFFRACTION13chain 'B' and (resid 127 through 153 )

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