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- PDB-2hpl: Crystal structure of the mouse p97/PNGase complex -

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Basic information

Entry
Database: PDB / ID: 2hpl
TitleCrystal structure of the mouse p97/PNGase complex
Components
  • C-terminal of mouse p97/VCP
  • PNGase
KeywordsHYDROLASE / PUB domain / Winged helix / p97
Function / homology
Function and homology information


peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase / peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / glycoprotein catabolic process / collagen-containing extracellular matrix / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / PUB domain / PUB-like domain superfamily / PUB domain ...Peptide N glycanase, PAW domain / PAW domain superfamily / PNGase C-terminal domain, mannose-binding module PAW / PAW domain profile. / domain present in PNGases and other hypothetical proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2190 / : / PUB domain / PUB-like domain superfamily / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Papain-like cysteine peptidase superfamily / Galactose-binding-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFMAC 5.2.0005 / Resolution: 1.8 Å
AuthorsZhao, G. / Zhou, X. / Wang, L. / Li, G. / Lennarz, W. / Schindelin, H.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Studies on peptide:N-glycanase-p97 interaction suggest that p97 phosphorylation modulates endoplasmic reticulum-associated degradation.
Authors: Zhao, G. / Zhou, X. / Wang, L. / Li, G. / Schindelin, H. / Lennarz, W.J.
History
DepositionJul 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PNGase
B: C-terminal of mouse p97/VCP


Theoretical massNumber of molelcules
Total (without water)11,7802
Polymers11,7802
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.608, 52.420, 35.028
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number5
Space group name H-MC121
DetailsHeterodimer of mouse PNGase PUB and p97

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Components

#1: Protein PNGase / Peptide N-glycanase


Mass: 11198.752 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ngly1 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 Codon Plus RIL
References: UniProt: Q9JI78, peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
#2: Protein/peptide C-terminal of mouse p97/VCP


Mass: 581.574 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized. Occurs naturally in mus musculus (mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 281 K / pH: 8
Details: 18-22% PEG 5000 MME and 14-18% Tacsimate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 8764 / % possible obs: 87.7 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.314 / % possible all: 46.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
REFMAC5.2.0005phasing
RefinementMethod to determine structure: REFMAC 5.2.0005 / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.459 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 428 4.9 %RANDOM
Rwork0.146 ---
all-3033 --
obs-8753 87.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20.01 Å2
2---0.9 Å20 Å2
3----1.94 Å2
Refine analyzeLuzzati coordinate error free: 0.242 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 0 167 994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022839
X-RAY DIFFRACTIONr_bond_other_d0.0020.02780
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9971133
X-RAY DIFFRACTIONr_angle_other_deg0.8731816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6645103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05324.10339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38415151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.512157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02165
X-RAY DIFFRACTIONr_nbd_refined0.2290.2179
X-RAY DIFFRACTIONr_nbd_other0.20.2774
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2411
X-RAY DIFFRACTIONr_nbtor_other0.0890.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1850.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3130.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2321.5681
X-RAY DIFFRACTIONr_mcbond_other0.2581.5214
X-RAY DIFFRACTIONr_mcangle_it1.3962846
X-RAY DIFFRACTIONr_scbond_it2.5153351
X-RAY DIFFRACTIONr_scangle_it3.4944.5287
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 16 -
Rwork0.185 319 -
obs--46.4 %
Refinement TLS params.Method: refined / Origin x: 40.6055 Å / Origin y: 51.9203 Å / Origin z: 13.9924 Å
111213212223313233
T-0.0399 Å20.0127 Å2-0.0029 Å2--0.0407 Å20.0054 Å2---0.0506 Å2
L0.6876 °2-0.0694 °2-0.1333 °2-2.05 °20.484 °2--1.4068 °2
S0.0055 Å °0.0282 Å °0.0327 Å °0.0239 Å °-0.0434 Å °-0.0044 Å °0.0245 Å °-0.0204 Å °0.038 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 1111 - 100
2X-RAY DIFFRACTION1BB803 - 8062 - 5

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