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- PDB-1x3z: Structure of a peptide:N-glycanase-Rad23 complex -

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Basic information

Entry
Database: PDB / ID: 1x3z
TitleStructure of a peptide:N-glycanase-Rad23 complex
Components
  • UV excision repair protein RAD23
  • peptide PHQ-Val-Ala-Asp-CF0
  • peptide: N-glycanase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding ...PNGase complex / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / nucleotide-excision repair factor 2 complex / ubiquitin-dependent glycoprotein ERAD pathway / nucleotide-excision repair, DNA damage recognition / protein deglycosylation / proteasome binding / protein quality control for misfolded or incompletely synthesized proteins / polyubiquitin modification-dependent protein binding / ERAD pathway / ubiquitin binding / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / damaged DNA binding / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #90 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #270 / XPC-binding domain / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues ...Rna Polymerase Sigma Factor; Chain: A - #90 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #270 / XPC-binding domain / Rad4 transglutaminase-like domain / UV excision repair protein Rad23 / XPC-binding domain / XPC-binding domain superfamily / XPC-binding domain / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Heat shock chaperonin-binding / Heat shock chaperonin-binding motif. / Rna Polymerase Sigma Factor; Chain: A / N-terminal domain of TfIIb - #10 / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / N-terminal domain of TfIIb / UBA-like superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Single Sheet / Helix non-globular / Papain-like cysteine peptidase superfamily / Special / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide / sucrose / : / UV excision repair protein RAD23 / Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLee, J.-H. / Choi, J.M. / Lee, C. / Yi, K.J. / Cho, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.
Authors: Lee, J.H. / Choi, J.M. / Lee, C. / Yi, K.J. / Cho, Y.
History
DepositionMay 11, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: peptide: N-glycanase
B: UV excision repair protein RAD23
I: peptide PHQ-Val-Ala-Asp-CF0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0936
Polymers47,3433
Non-polymers7503
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-20 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.801, 128.801, 128.376
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is protein-protein complex in the asymmetric unit

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein peptide: N-glycanase


Mass: 39425.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: GenBank: 6325161, UniProt: Q02890*PLUS, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Protein UV excision repair protein RAD23


Mass: 7445.399 Da / Num. of mol.: 1 / Fragment: XPC binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P32628

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Protein/peptide / Sugars , 2 types, 3 molecules I

#3: Protein/peptide peptide PHQ-Val-Ala-Asp-CF0


Type: Peptide-like / Class: Inhibitor / Mass: 471.907 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized
References: N-[(benzyloxy)carbonyl]-L-valyl-N-[(1S)-1-(carboxymethyl)-3-fluoro-2-oxopropyl]-L-alaninamide
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 30 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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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: 6.7 Å3/Da / Density % sol: 81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium chloride, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.0721 Å
DetectorType: KODAK / Detector: CCD / Date: Feb 21, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 30868 / Num. obs: 30868 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.8→2.9 Å / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.906 / SU B: 28.524 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1471 4.9 %RANDOM
Rwork0.23572 ---
all0.23737 28388 --
obs0.23737 28388 97.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.515 Å2
Baniso -1Baniso -2Baniso -3
1-3.34 Å21.67 Å20 Å2
2--3.34 Å20 Å2
3----5.01 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3121 0 47 29 3197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223239
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9684385
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.145377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75624.706170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.36615569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8021519
X-RAY DIFFRACTIONr_chiral_restr0.1240.2477
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022457
X-RAY DIFFRACTIONr_nbd_refined0.2790.21882
X-RAY DIFFRACTIONr_nbtor_refined0.3340.22235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2151
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.24
X-RAY DIFFRACTIONr_mcbond_it1.0441.51934
X-RAY DIFFRACTIONr_mcangle_it1.89123064
X-RAY DIFFRACTIONr_scbond_it3.45431470
X-RAY DIFFRACTIONr_scangle_it3.2814.51321
X-RAY DIFFRACTIONr_rigid_bond_restr4.22233404
X-RAY DIFFRACTIONr_sphericity_free3.905330
X-RAY DIFFRACTIONr_sphericity_bonded1.73733168
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 94 -
Rwork0.424 1872 -
obs--90.14 %

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