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- PDB-8sw0: Puromycin sensitive aminopeptidase -

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Basic information

Entry
Database: PDB / ID: 8sw0
TitlePuromycin sensitive aminopeptidase
ComponentsPuromycin-sensitive aminopeptidase
KeywordsHYDROLASE / aminopeptidase / zinc metallopeptidase / M1 family / four domains
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 / nucleus / membrane / 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
1,4-DIETHYLENE DIOXIDE / Puromycin-sensitive aminopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsRodgers, D.W. / Sampath, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1364
Polymers101,8611
Non-polymers2763
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
  • 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
Unit cell
Length a, b, c (Å)70.684, 257.715, 60.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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
Source: (gene. exp.) Homo sapiens (human) / Gene: NPEPPS, PSA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P55786, cytosol alanyl aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 0.97182 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97182 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 47993 / % possible obs: 95.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.033 / Rrim(I) all: 0.073 / Χ2: 1.066 / Net I/σ(I): 12.8 / Num. measured all: 223462
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.384.60.58746800.750.3060.6640.90895.4
2.38-2.484.60.43146650.8550.2250.4880.95495.3
2.48-2.594.60.3146770.9180.1620.3510.99294.5
2.59-2.734.60.21647060.9550.1120.2441.06294.9
2.73-2.94.60.1646860.9740.0840.1811.20594.7
2.9-3.124.60.11446600.9850.060.1291.06894.5
3.12-3.444.60.0847140.9930.0410.091.07894.5
3.44-3.934.60.05548340.9970.0280.0621.11996
3.93-4.954.70.05350370.9960.0270.0591.10599.4
4.95-5050.03553340.9970.0170.0391.14399.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.2refinement
PDB_EXTRACT3.27data extraction
PHENIX1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z1W

1z1w


Resolution: 2.301→45.201 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2406 2036 4.25 %
Rwork0.2233 45878 -
obs0.224 47914 95.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.44 Å2 / Biso mean: 67.995 Å2 / Biso min: 13.71 Å2
Refinement stepCycle: final / Resolution: 2.301→45.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6856 0 15 184 7055
Biso mean--68.81 52.18 -
Num. residues----864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017030
X-RAY DIFFRACTIONf_angle_d0.4169538
X-RAY DIFFRACTIONf_chiral_restr0.0381052
X-RAY DIFFRACTIONf_plane_restr0.0031227
X-RAY DIFFRACTIONf_dihedral_angle_d9.4684207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3012-2.35470.3341290.3215289793
2.3547-2.41360.321300.309297794
2.4136-2.47880.34431320.3062299996
2.4788-2.55180.32671350.2919299395
2.5518-2.63410.33551330.2906299794
2.6341-2.72830.29721330.2897299995
2.7283-2.83750.30371310.2804299095
2.8375-2.96660.27221340.2864298695
2.9666-3.1230.3021320.2816298994
3.123-3.31860.25231340.2532301694
3.3186-3.57470.28081340.234303694
3.5747-3.93420.23091380.2014309297
3.9342-4.50310.21441420.1825320699
4.5031-5.67170.18881460.17213260100
5.6717-45.2010.17191530.17933441100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.65810.54360.22792.681-0.53441.13810.0798-0.53831.08350.3296-0.0343-0.3853-0.2332-0.0417-0.02390.4014-0.00210.01460.5157-0.26591.137939.5811105.946726.1273
22.49990.30040.2343.60440.51330.44710.06980.11160.3326-0.2116-0.0657-0.3913-0.06610.0043-0.00770.29110.02740.12570.3730.0560.272824.144278.61687.1197
32.4618-0.5395-0.45381.4002-0.18012.84350.0329-0.40310.46180.2385-0.0519-0.0781-0.52590.0850.05160.3958-0.0581-0.00220.4684-0.09990.3059-0.734483.982626.6776
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 367 )A51 - 367
2X-RAY DIFFRACTION2chain 'A' and (resid 368 through 611 )A368 - 611
3X-RAY DIFFRACTION3chain 'A' and (resid 612 through 914 )A612 - 914

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