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- PDB-4m92: Crystal structure of hN33/Tusc3-peptide 2 -

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Basic information

Entry
Database: PDB / ID: 4m92
TitleCrystal structure of hN33/Tusc3-peptide 2
Components
  • Interleukin-1 receptor accessory protein-like 1
  • Tumor suppressor candidate 3
KeywordsOXIDOREDUCTASE / thioredoxin-like fold / thiol/disulfide oxidoreductase / thiol/disulfide exchange reactions / redox-active protein
Function / homology
Function and homology information


trans-synaptic signaling by trans-synaptic complex / Asparagine N-linked glycosylation / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / presynaptic membrane assembly / synaptic membrane adhesion / magnesium ion transmembrane transporter activity ...trans-synaptic signaling by trans-synaptic complex / Asparagine N-linked glycosylation / Interleukin-38 signaling / Receptor-type tyrosine-protein phosphatases / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / presynaptic membrane assembly / synaptic membrane adhesion / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / positive regulation of dendritic spine morphogenesis / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity, cyclic ADP-ribose generating / protein N-linked glycosylation / regulation of postsynapse organization / positive regulation of synapse assembly / negative regulation of exocytosis / regulation of neuron projection development / regulation of presynapse assembly / transmembrane transport / cognition / neuron differentiation / Maturation of spike protein / postsynaptic membrane / cell surface receptor signaling pathway / signaling receptor binding / axon / dendrite / endoplasmic reticulum membrane / glutamatergic synapse / cell surface / mitochondrion / plasma membrane / cytoplasm
Similarity search - Function
IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Interleukin-1 receptor family / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TUSC3 / Interleukin-1 receptor accessory protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor suppressor candidate 3
B: Interleukin-1 receptor accessory protein-like 1


Theoretical massNumber of molelcules
Total (without water)20,9612
Polymers20,9612
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-4 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.850, 62.200, 64.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 19125.799 Da / Num. of mol.: 1 / Fragment: unp residues 44-194 / Mutation: C123S, C102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TUSC3, N33 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13454
#2: Protein/peptide Interleukin-1 receptor accessory protein-like 1 / IL-1-RAPL-1 / IL-1RAPL-1 / IL1RAPL-1 / Oligophrenin-4 / Three immunoglobulin domain-containing IL-1 ...IL-1-RAPL-1 / IL-1RAPL-1 / IL1RAPL-1 / Oligophrenin-4 / Three immunoglobulin domain-containing IL-1 receptor-related 2 / TIGIRR-2 / X-linked interleukin-1 receptor accessory protein-like 1


Mass: 1834.960 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 207-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1RAPL1, OPHN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZN1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 1.91 Å3/Da / Density % sol: 35.6 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→25.1 Å / Num. all: 21798 / Num. obs: 21733 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 9.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.637 / % possible all: 100

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Processing

SoftwareName: REFMAC / Version: 5.7.0032 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4M8G

4m8g


Resolution: 1.6→25.09 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.026 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23206 435 2 %RANDOM
Rwork0.19175 ---
obs0.19255 21196 99.1 %-
all-21196 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.668 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.88 Å2-0 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 0 243 1578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191373
X-RAY DIFFRACTIONr_bond_other_d0.0050.021289
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9321848
X-RAY DIFFRACTIONr_angle_other_deg0.8433.0012953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.15823.15173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.10915244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5351513
X-RAY DIFFRACTIONr_chiral_restr0.0990.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02359
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8821.38648
X-RAY DIFFRACTIONr_mcbond_other1.8711.374647
X-RAY DIFFRACTIONr_mcangle_it2.6372.053807
X-RAY DIFFRACTIONr_mcangle_other2.642.06808
X-RAY DIFFRACTIONr_scbond_it3.321.791725
X-RAY DIFFRACTIONr_scbond_other3.3171.796726
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0882.5331041
X-RAY DIFFRACTIONr_long_range_B_refined7.09214.0451839
X-RAY DIFFRACTIONr_long_range_B_other7.06412.9421701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 30 -
Rwork0.281 1533 -
obs--99.87 %

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