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- PDB-27iv: Crystal structure of the mature form of human ASPRV1 bound to sel... -

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Basic information

Entry
Database: PDB / ID: 27iv
TitleCrystal structure of the mature form of human ASPRV1 bound to self-cleavage 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: 1.95 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,2786
Polymers31,1172
Non-polymers1604
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-55 kcal/mol
Surface area12400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.130, 61.265, 76.295
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: 15558.745 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.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.99 Å3/Da / Density % sol: 34.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M HEPES sodium, pH 7.5, and 28% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.95→47.77 Å / Num. obs: 17760 / % possible obs: 100 % / Redundancy: 12.6 % / Biso Wilson estimate: 23.62 Å2 / CC1/2: 1 / Net I/σ(I): 22.3
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1241 / CC1/2: 0.915

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Processing

SoftwareName: PHENIX / Version: 1.21.2_5419 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→32.38 Å / SU ML: 0.2256 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3854
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1826 10.32 %
Rwork0.1913 15867 -
obs0.1963 17693 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.95→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 4 161 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662101
X-RAY DIFFRACTIONf_angle_d0.83812840
X-RAY DIFFRACTIONf_chiral_restr0.0593330
X-RAY DIFFRACTIONf_plane_restr0.0059362
X-RAY DIFFRACTIONf_dihedral_angle_d13.6026767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.28441470.2351200X-RAY DIFFRACTION100
2-2.060.24421350.22371196X-RAY DIFFRACTION99.92
2.06-2.130.2821400.19331193X-RAY DIFFRACTION100
2.13-2.20.27851380.20561200X-RAY DIFFRACTION100
2.2-2.290.27221430.19151206X-RAY DIFFRACTION100
2.29-2.40.23451330.18891215X-RAY DIFFRACTION99.63
2.4-2.520.27641200.2111214X-RAY DIFFRACTION99.93
2.52-2.680.26981440.20821209X-RAY DIFFRACTION99.93
2.68-2.890.27251390.21741214X-RAY DIFFRACTION100
2.89-3.180.26951210.19471247X-RAY DIFFRACTION100
3.18-3.640.2281340.17581242X-RAY DIFFRACTION100
3.64-4.580.17021530.15451244X-RAY DIFFRACTION99.93
4.58-32.380.23091790.1961287X-RAY DIFFRACTION99.39
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)
11.29641790486-0.328806960531-1.652940889250.8185899230540.4650323661436.883319208940.01437188438050.3216492634080.0987720769464-0.07653497861480.01706033491870.2243233843670.113025095686-0.5385524833260.05317511044210.18599488888-0.00933664098985-0.01491811828450.174658600144-0.02045069247720.1644118531721.23208662814-18.779824555-19.8524773775
21.184229218550.333847595349-0.8431868619711.16766641198-0.2665183216481.64536991440.145848329291-0.1944960215790.350042532507-0.02081865279880.02768127390140.0906387967221-0.3380222197090.189429014214-0.01682425722820.180850572789-0.02172511856350.04695729462020.170735673131-0.0559312317980.2237829899886.18107572647-8.01549062431-6.10915596141
32.176000483711.43052252262-0.3965789584743.733142777870.6367702773861.03222504340.135012153562-0.07467798218940.08719924291620.0427011679336-0.04615257125350.349487077184-0.1247487704360.0123763728311-0.057959793870.162685070115-0.0205318446530.01322896820960.172281307877-0.01581936055690.2069377316324.34461743671-15.2630986356-4.83181138536
41.547696760610.34729752892-0.6889908370211.73835468706-0.1635073461631.044819452520.08026917107540.0469592193897-0.148767701283-0.235463208575-0.05643973355210.0883039481282-0.0106657682719-0.124775969598-0.01762805195410.198382632218-0.007508866732740.001785200587750.139927670366-0.01071645547290.1418472165056.66189562985-25.0080019196-14.9951489312
51.09771021439-0.156525899774-1.59986305680.621010883425-0.1139729600835.75672713229-0.169524575063-0.2235330657890.0907352904665-0.109240759327-0.0594439220462-0.1463531160340.3536998636910.3207732520690.01200170280940.206291179173-0.02297880569520.02830832764380.1934012532120.01088441494770.18560730292122.2585255375-18.4802838037-18.4569952883
61.670078311120.166493726359-0.9561491642150.684414033864-0.1044333867631.51658281078-0.083810022886-0.00092641678190.132803070478-0.03952171299490.03130264252160.0434745954935-0.06957682191980.343932163781-0.001563912199450.153232076665-0.03969182004370.02163097216240.1955383084710.01043534636440.13978812494419.4030795942-14.2211605967-27.8067382625
72.20880479029-0.566193445787-0.9081725334611.644653661650.4113718155892.25157403390.1260460549190.0561884291693-0.144036114386-0.296546495353-0.070376928569-0.116060534352-0.416564849159-0.0571149298739-0.0478756566910.1713618275610.002893541876970.03593128075160.1940088768530.0699185959820.2666505620817.7130404628-5.95780436677-38.1092008925
81.1491963660.293945434946-0.1701575551230.3379066176130.1033878990021.619795320190.0514611376620.03115975557660.104041409534-0.1261768142990.1769461163990.0752209835644-0.255001720087-0.140716242966-0.04805885290030.213086499423-0.02301451387890.02552003323170.218757591580.02889976591350.17397213214714.3361993849-8.07202339722-31.2660706246
92.28160398305-2.178486907130.1082544733776.84245040770.2672171372841.465042296750.2075543704880.314368363644-0.240479895717-0.4541893788890.00306654169129-0.2159056034930.0343723542380.196436385893-0.01009415649410.1899239408090.01136382457040.01652424105530.315795665272-0.04268753213790.2241442021318.2576548529-18.5322131411-35.1294245224
101.59546028498-0.1383719047240.04479804416352.02764183247-0.06067874592711.826963675370.03661724044490.0859734481268-0.001901294744170.1658725482580.0128687003905-0.177765084962-0.03338234694760.2536895777980.002777510351220.1869842459930.00712867634172-0.007976459158490.156411872571-0.01475694630850.1393496362715.6679105821-20.95483675-24.0345593898
112.084715097730.9468164900921.577507561363.175132474662.449192075953.567309625210.3176294515910.0661101660426-0.292105554451-0.143901389270.103497081824-0.5279561085440.4231173779070.242382155181-0.16919750070.2884680497950.08250117415040.01571948121920.2682739215340.0252545552360.26640861311621.7798729376-27.0655902854-23.2092996956
122.02890552549-0.2891445718542.109075352861.05990908474-0.8780120430644.276694967680.11525725145-0.2404540414210.3925963268360.0227392197263-0.168141688948-0.145366932914-0.0915178344217-0.1255853497980.1332145748030.264081434408-0.04430124579950.01247285514040.308599138055-0.003760191941150.29458580597715.9465055999-9.22435181771-15.4934432886
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 190 through 202 )BA190 - 2021 - 13
22chain 'B' and (resid 203 through 254 )BA203 - 25414 - 65
33chain 'B' and (resid 255 through 281 )BA255 - 28166 - 92
44chain 'B' and (resid 282 through 316 )BA282 - 31693 - 127
55chain 'A' and (resid 190 through 202 )AB190 - 2021 - 13
66chain 'A' and (resid 203 through 221 )AB203 - 22114 - 32
77chain 'A' and (resid 222 through 244 )AB222 - 24433 - 55
88chain 'A' and (resid 245 through 263 )AB245 - 26356 - 74
99chain 'A' and (resid 264 through 275 )AB264 - 27575 - 86
1010chain 'A' and (resid 276 through 305 )AB276 - 30587 - 116
1111chain 'A' and (resid 306 through 315 )AB306 - 315117 - 126
1212chain 'A' and (resid 316 through 331 )AB316 - 331127 - 142

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