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- PDB-4m91: crystal structure of hN33/Tusc3-peptide 1 -

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Basic information

Entry
Database: PDB / ID: 4m91
Titlecrystal structure of hN33/Tusc3-peptide 1
Components
  • Protein cereblon
  • Tumor suppressor candidate 3
KeywordsOXIDOREDUCTASE / Thioredoxin-like fold / formation of mixed disulfides / endoplasmic reticulum
Function / homology
Function and homology information


Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / negative regulation of monoatomic ion transmembrane transport / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior ...Asparagine N-linked glycosylation / magnesium ion transport / oligosaccharyltransferase complex / Miscellaneous transport and binding events / negative regulation of monoatomic ion transmembrane transport / magnesium ion transmembrane transporter activity / protein N-linked glycosylation via asparagine / protein N-linked glycosylation / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / transmembrane transport / cognition / Maturation of spike protein / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / transmembrane transporter binding / protein ubiquitination / endoplasmic reticulum membrane / perinuclear region of cytoplasm / mitochondrion / metal ion binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain ...Oligosaccharyl transferase complex, subunit OST3/OST6 / OST3 / OST6 family, transporter family / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / Thioredoxin-like superfamily
Similarity search - Domain/homology
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit TUSC3 / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 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 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 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 1.4Nov 6, 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: Protein cereblon


Theoretical massNumber of molelcules
Total (without water)20,6212
Polymers20,6212
Non-polymers00
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.769, 62.235, 64.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailssubunit of the human oligosaccharyl tranferase complex

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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 Protein cereblon


Mass: 1494.762 Da / Num. of mol.: 1 / Fragment: unp residues 229-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.94 Å3/Da / Density % sol: 36.5 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.1→39.77 Å / Num. all: 68361 / Num. obs: 65763 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Rsym value: 0.052 / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4M8G

4m8g


Resolution: 1.1→33.88 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.719 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16023 2524 4 %RANDOM
Rwork0.13688 ---
obs0.1378 60538 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.656 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.1→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1309 0 0 194 1503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191441
X-RAY DIFFRACTIONr_bond_other_d0.0010.021344
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9261960
X-RAY DIFFRACTIONr_angle_other_deg1.2633.0013084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2325183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.40523.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7415256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8341515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211703
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02394
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_it1.7961.129677
X-RAY DIFFRACTIONr_mcbond_other1.7951.126676
X-RAY DIFFRACTIONr_mcangle_it1.9711.69855
X-RAY DIFFRACTIONr_mcangle_other2.1431.689856
X-RAY DIFFRACTIONr_scbond_it2.3871.45764
X-RAY DIFFRACTIONr_scbond_other2.4881.466766
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8172.081099
X-RAY DIFFRACTIONr_long_range_B_refined3.48510.9111850
X-RAY DIFFRACTIONr_long_range_B_other3.0149.9681739
X-RAY DIFFRACTIONr_rigid_bond_restr5.51432785
X-RAY DIFFRACTIONr_sphericity_free30.906537
X-RAY DIFFRACTIONr_sphericity_bonded8.68552894
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 145 -
Rwork0.245 3097 -
obs--67.43 %

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