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- PDB-8sw1: Puromycin-sensitive aminopeptidase with bound peptide -

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Basic information

Entry
Database: PDB / ID: 8sw1
TitlePuromycin-sensitive aminopeptidase with bound peptide
Components
  • Polyglutamine peptide
  • Puromycin-sensitive aminopeptidase
KeywordsHYDROLASE / aminopeptidase / zinc metallopeptidase / M1 family / four domains / polyglutamine peptide
Function / homology
Function and homology information


cytosol alanyl aminopeptidase / positive regulation of protein targeting to mitochondrion / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to hypoxia / proteolysis ...cytosol alanyl aminopeptidase / positive regulation of protein targeting to mitochondrion / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / peptide binding / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to hypoxia / proteolysis / extracellular space / extracellular exosome / zinc ion binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / : / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / : / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Puromycin-sensitive aminopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsRodgers, D.W. / Madabushi, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS38041 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130954 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)DA02243 United States
CitationJournal: Plos One / Year: 2023
Title: Structure of puromycin-sensitive aminopeptidase and polyglutamine binding.
Authors: Madabushi, S. / Chow, K.M. / Song, E.S. / Goswami, A. / Hersh, L.B. / Rodgers, D.W.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Puromycin-sensitive aminopeptidase
B: Polyglutamine peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5613
Polymers103,4962
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, Yamamoto, Y, Li, HL, ushiyama, I, Nishimura, A, Ohkubo, I, Nishi, K. (2000) Forensic Sci. Int. 113, 143-146.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-41 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.745, 256.562, 60.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Puromycin-sensitive aminopeptidase / PSA / Cytosol alanyl aminopeptidase / AAP-S


Mass: 101860.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal 33 residues and C-terminal 5 residues of expressed protein not located in crystal structure. The N-terminal sequence includes a polyhistidine tag and TEV cleavage sequence. The ...Details: N-terminal 33 residues and C-terminal 5 residues of expressed protein not located in crystal structure. The N-terminal sequence includes a polyhistidine tag and TEV cleavage sequence. The entire sequence shown was present in the crystallized protein.
Source: (gene. exp.) Homo sapiens (human) / Gene: NPEPPS, PSA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P55786, cytosol alanyl aminopeptidase
#2: Protein/peptide Polyglutamine peptide


Mass: 1635.006 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Polyglutamine peptide: KKQQQQQQQQQQQQQQQKK. Six residues modeled as polyalanine.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Sequence detailsThe polyglutamine peptide, KKQQQQQQQQQQQQQQQKK, was modeled as six alanine residues.

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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: 2.69 Å3/Da / Density % sol: 54.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 5-8 mg/ml PSA mixed 1:1 with 15% PEG 4K, 0.1 M Tris (pH 8.5), 0.5 M sodium chloride, and 1.5% v/v dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.65→50 Å / Num. obs: 13423 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.079 / Rrim(I) all: 0.156 / Χ2: 1.085 / Net I/σ(I): 6.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.65-3.843.60.56718760.6970.9060.3460.6691.08299.7
3.84-4.083.70.44218880.8470.9580.2640.5181.11699.6
4.08-4.43.70.30418700.9250.980.180.3551.02699.6
4.4-4.843.70.20718850.9630.9910.1220.2421.12799.3
4.84-5.543.70.16319460.9730.9930.0960.1911.09699.5
5.54-6.983.60.1418990.9840.9960.0820.1631.09698.6
6.98-503.40.07120590.9930.9980.0420.0831.05198

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
PHENIX1.20.1_4487phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.65→47.52 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.295 1273 10 %
Rwork0.2565 --
obs0.2603 12728 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.65→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6886 0 1 0 6887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027046
X-RAY DIFFRACTIONf_angle_d0.4389562
X-RAY DIFFRACTIONf_dihedral_angle_d11.5312583
X-RAY DIFFRACTIONf_chiral_restr0.0391058
X-RAY DIFFRACTIONf_plane_restr0.0041232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-3.80.41771400.36161254X-RAY DIFFRACTION99
3.8-3.970.35321390.31471254X-RAY DIFFRACTION100
3.97-4.180.32941390.3051255X-RAY DIFFRACTION100
4.18-4.440.33991400.30881249X-RAY DIFFRACTION99
4.44-4.780.38231360.29521251X-RAY DIFFRACTION99
4.78-5.260.29371410.261260X-RAY DIFFRACTION99
5.26-6.020.28151430.28871277X-RAY DIFFRACTION99
6.02-7.580.29551440.25911293X-RAY DIFFRACTION98
7.59-47.520.22481510.18031362X-RAY DIFFRACTION98

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