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- PDB-27iq: Crystal structure of the mature form of human ASPRV1 bound to fil... -

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Basic information

Entry
Database: PDB / ID: 27iq
TitleCrystal structure of the mature form of human ASPRV1 bound to filaggrin peptide
ComponentsRetroviral-like aspartic protease 1
KeywordsHYDROLASE / Retroviral-like aspartic protease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / skin development / protein processing / aspartic-type endopeptidase activity / membrane
Similarity search - Function
Retroviral-like aspartic protease 1 / gag-polyprotein putative aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Retroviral-like aspartic protease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsChen, Z. / Feng, X. / Ding, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Biochim.Biophys.Sin. / Year: 2026
Title: Structure and enzymatic properties of human retroviral-like aspartic protease 1 and functional roles of disease-associated mutations.
Authors: Feng, X. / Chen, Z. / Lan, C. / Ding, J.
History
DepositionJun 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retroviral-like aspartic protease 1
B: Retroviral-like aspartic protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9744
Polymers30,8932
Non-polymers802
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-31 kcal/mol
Surface area12270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.004, 64.929, 76.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Retroviral-like aspartic protease 1 / Skin-specific retroviral-like aspartic protease / SASPase / Skin aspartic protease / TPA-inducible ...Skin-specific retroviral-like aspartic protease / SASPase / Skin aspartic protease / TPA-inducible aspartic proteinase-like protein / TAPS


Mass: 15446.690 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASPRV1, SASP / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q53RT3, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M calcium chloride dihydrate, 0.1 M sodium acetate trihydrate, pH 4.6, and 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jan 13, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.09→38.6 Å / Num. obs: 28780 / % possible obs: 97.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 38.94 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.6
Reflection shellResolution: 2.09→2.13 Å / Num. unique obs: 1419 / CC1/2: 0.89

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Processing

SoftwareName: PHENIX / Version: 1.21.2_5419 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→22.74 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 46.0802
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2922 2868 10.03 %
Rwork0.2616 25739 -
obs0.2646 28607 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.84 Å2
Refinement stepCycle: LAST / Resolution: 2.09→22.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 2 53 2110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852092
X-RAY DIFFRACTIONf_angle_d1.06942829
X-RAY DIFFRACTIONf_chiral_restr0.0645329
X-RAY DIFFRACTIONf_plane_restr0.0238358
X-RAY DIFFRACTIONf_dihedral_angle_d16.8027758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.130.46611410.40351274X-RAY DIFFRACTION97.32
2.13-2.170.3891440.37831294X-RAY DIFFRACTION99.72
2.17-2.210.42261440.36931287X-RAY DIFFRACTION99.72
2.21-2.250.37011470.32241293X-RAY DIFFRACTION99.52
2.25-2.30.32471420.32581298X-RAY DIFFRACTION99.52
2.3-2.350.30771430.32251281X-RAY DIFFRACTION99.44
2.35-2.410.29461520.31551302X-RAY DIFFRACTION99.18
2.41-2.480.29591400.29181271X-RAY DIFFRACTION99.65
2.48-2.550.32331420.27591345X-RAY DIFFRACTION99.93
2.55-2.630.43711390.2831273X-RAY DIFFRACTION99.51
2.63-2.730.34931420.27441278X-RAY DIFFRACTION99.23
2.73-2.840.28311460.25431311X-RAY DIFFRACTION99.73
2.84-2.970.26391420.2831294X-RAY DIFFRACTION99.51
2.97-3.120.35191440.25661290X-RAY DIFFRACTION99.51
3.12-3.320.32581450.26771299X-RAY DIFFRACTION99.79
3.32-3.570.31991430.23661294X-RAY DIFFRACTION99.52
3.57-3.930.2521330.23521288X-RAY DIFFRACTION99.23
3.93-4.490.2221520.2131298X-RAY DIFFRACTION99.72
4.5-5.650.20181480.23351286X-RAY DIFFRACTION99.45
5.65-22.740.33211390.24131183X-RAY DIFFRACTION91.42

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