[English] 日本語
Yorodumi
- PDB-27jq: Crystal structure of the mature form of human ASPRV1-14(R311P) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 27jq
TitleCrystal structure of the mature form of human ASPRV1-14(R311P)
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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 3, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retroviral-like aspartic protease 1
B: Retroviral-like aspartic protease 1
C: Retroviral-like aspartic protease 1


Theoretical massNumber of molelcules
Total (without water)44,7003
Polymers44,7003
Non-polymers00
Water2,612145
1
A: Retroviral-like aspartic protease 1

A: Retroviral-like aspartic protease 1


Theoretical massNumber of molelcules
Total (without water)29,8002
Polymers29,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2800 Å2
ΔGint-7 kcal/mol
Surface area11980 Å2
MethodPISA
2
B: Retroviral-like aspartic protease 1
C: Retroviral-like aspartic protease 1


Theoretical massNumber of molelcules
Total (without water)29,8002
Polymers29,8002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-6 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.222, 67.222, 154.618
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
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: 14900.019 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10 % (v/v) 2-propanol, and 26 % (v/v) PEG 400

-
Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→46.51 Å / Num. obs: 30344 / % possible obs: 99.9 % / Redundancy: 13.9 % / Biso Wilson estimate: 30.99 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 1089 / CC1/2: 0.849

-
Processing

SoftwareName: PHENIX / Version: 1.21.2_5419 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.51 Å / SU ML: 0.2585 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3197
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2319 1594 5.27 %
Rwork0.1866 28670 -
obs0.1889 30264 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.06 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 0 145 3051
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692960
X-RAY DIFFRACTIONf_angle_d0.87484007
X-RAY DIFFRACTIONf_chiral_restr0.0684467
X-RAY DIFFRACTIONf_plane_restr0.0052508
X-RAY DIFFRACTIONf_dihedral_angle_d13.50271074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.39431310.30412562X-RAY DIFFRACTION99.37
2.01-2.080.32731310.27472575X-RAY DIFFRACTION99.85
2.08-2.170.27371470.242555X-RAY DIFFRACTION99.85
2.17-2.270.2631410.20812568X-RAY DIFFRACTION99.82
2.27-2.390.25681710.19692529X-RAY DIFFRACTION99.89
2.39-2.540.22681360.20032609X-RAY DIFFRACTION100
2.54-2.730.32211570.19942585X-RAY DIFFRACTION100
2.73-3.010.29751260.19232621X-RAY DIFFRACTION100
3.01-3.440.22731460.18952628X-RAY DIFFRACTION100
3.44-4.340.21321300.15812672X-RAY DIFFRACTION100
4.34-46.510.17091780.15972766X-RAY DIFFRACTION99.33
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)
10.3203512167640.1418071172930.7069057675590.797761602849-0.001454264947767.930378421870.1751879760550.0926622508717-0.0520768155736-0.09056304984260.119610872377-0.05709277175740.1137525371060.405912873455-0.03152434962150.212234441827-0.00755848271445-0.007142003050140.2431985046430.0001639433819370.218970041026.72756335212-9.245986278711.36194375884
21.807966184180.1220823692090.09863870465020.8822291300490.2180590017761.834076080680.0731577900567-0.045550824568-0.08005917745450.0166980771107-0.00615146522347-0.02092417943840.0731821168689-0.0664597924775-0.007142586763960.163886372544-0.00876350406684-0.01341350337590.1934666980870.002797529910790.184903854238-3.3092204254-11.947475293115.6833201502
31.46314654721.15095726523-1.682463716233.34549431789-1.219466919171.87421413318-0.4697507160.505113333674-0.42598263846-0.1987430858560.234833689461-0.5361291414140.4033021092090.2167776017060.02770689472990.256346220340.004162773908250.02192190982890.251380085066-0.03751978183950.210021419978-2.09523768748-15.26184785748.34959785389
41.82063336067-0.6916238738351.114370180061.27886457641-0.4611944454691.31542379750.008491746079760.2098249533940.197386682111-0.0922947511201-0.0179487496791-0.0860516092622-0.3177830633750.215179964199-0.03043620575840.235830964288-0.0752086599627-0.001590478033130.2750160661340.001617289087640.1889452580495.034300257040.2206010400974.5804977678
53.898575155560.7009474796392.117255639052.686684319350.02186864878461.903573881760.187121763246-0.7080027758510.3178662151820.147639134638-0.4626126417570.616282326697-0.380478601127-0.8520457744990.03238261745730.1833369674020.04336363476640.07852684776120.5861889346510.008815048387690.4059018469-40.0410683574-12.919707678926.041722552
62.236125491470.4566112408131.957897015982.438514874841.944600684796.423397187480.0167489522868-0.6671893848320.4753296664270.494586562289-0.1064633731680.699369379939-0.123340421384-0.6353550397890.1499924015530.3470167648540.05407591613250.04988509422180.637337145412-0.06085629352760.344113193345-32.4616538215-8.5684013574332.224652675
71.715970702910.954435936680.1569309733040.710680851790.5451634103261.6030803325-0.1667013253820.207072115420.0182984214083-0.1794930044180.1091408564060.323379695589-0.0909780743052-0.1121897796960.04909880630120.185583790797-0.006121343452670.0009954273103950.356538560670.02319725494890.324223104245-28.9549602359-13.060811054619.7885456821
83.385927879880.002566196515310.6133265140141.70776893862-0.2666562098562.19058484996-0.17966548702-0.6214218091760.798005975980.566541214983-0.0386923132132-0.00331289728838-0.3255537572240.1983411648840.02892130036460.3400572832870.06100867330120.03206256880970.473163837466-0.08125276611050.357265639957-20.3035623371-1.7220960021731.6464050959
92.560367832030.2347372810581.190516062030.6598428308140.0274975556052.71869275402-0.1542273995160.0794586871496-0.0795308939510.1282345293620.1723214753280.0233333349113-0.2010846119130.12137446716-2.42812029933E-50.232893045554-0.0002614183341740.01765210851120.3201181286270.004792567927320.239516526732-17.1860149587-8.067678658816.7585454301
103.013755455543.269433302172.9039258735.577107020594.143754482473.98845032681-0.04788285119670.522733091292-0.10958415218-0.2757787446650.1543951368290.339558686423-0.247287572671-0.3112003860620.03273934586770.323170136264-0.0419350478269-0.05282759820440.42092649776-0.0002703531635210.289746324978-22.8211468773-8.5325349928512.4420602216
111.855396112460.676497081945-1.119686300671.7308745673-0.3016958767021.396290051140.00868033278275-0.574152802635-0.1554595312740.279923656488-0.04913700450850.03224226556080.02920765376440.3025941043130.03742420816150.219826566135-0.001681409106250.01807503699520.403954102480.07263609088580.241516347945-23.6133652148-14.102753404830.9331211479
122.626773224851.78400346553-0.2798102621913.53794353655-0.6385001552150.139826610799-0.1708459355310.07734609814270.552476781396-0.1173524341370.3461699763330.958736756155-0.16775301922-0.757396501561-0.06118365608640.3011256581710.0287282425681-0.002601625135720.3780438112210.0529021380510.365844464465-30.2851087992-6.8821678009121.5199823739
131.384726735310.580292638543-0.1719314396531.03733631170.07638062350261.232575109890.230103580815-0.299180758945-0.1146537141390.155807979681-0.05273048117290.2106980177750.237666369438-0.2355443471420.009363409603420.245042398562-0.06820456420920.014468879650.387482759960.1272041812820.441763289315-35.2945578915-23.638238339425.7109822815
142.60031951517-2.073987519941.462203160323.820405025681.099564426523.19470317557-0.00972299598426-0.358806097102-0.90192902787-0.04041556256970.103831143282-0.3716292815870.7850638484790.3984825104650.1585985605490.302840875134-0.04515744164690.1118534832270.6851136122320.2941006711170.58442542221-35.5622829691-23.991217701333.9662534419
152.76761996721-1.575857048712.813687216177.17883788037-3.565969606645.926299540610.532654656665-0.896680374986-0.6002799563940.32080737998-0.298807106031-0.222228901815-0.554788660086-1.05297406502-0.108942289920.302379216202-0.02509262010010.004880735050930.6686229995570.06682538023550.428023656386-44.2828468853-12.474022262325.2480260928
161.831677700870.4339498465650.3394128573350.717034485683-0.3682987393241.141401174870.005591347821560.807121213382-0.453549157741-0.03623531836060.003187348267750.05746629202380.262456618463-0.0615307058256-0.09485499467060.217457926857-0.0268060952877-0.0642864518350.660792041761-0.1713907082190.412290262294-38.9384090323-21.76476069863.35352525029
173.296730022760.101647411510.5291285573381.22489977126-0.2561013727613.65654898919-0.04212148928240.492350838379-0.4908289915690.1818899094340.0196074304352-0.153190412242-0.197624117804-0.1773731219730.002749605881810.18465719834-0.0711031483121-0.04362822153930.444174367459-0.03905916280980.402899388083-42.3500464814-20.73227400649.63384580404
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 190 through 202 )AA190 - 2021 - 13
22chain 'A' and (resid 203 through 274 )AA203 - 27414 - 85
33chain 'A' and (resid 275 through 285 )AA275 - 28586 - 96
44chain 'A' and (resid 286 through 317 )AA286 - 31797 - 128
55chain 'B' and (resid 191 through 202 )BB191 - 2021 - 12
66chain 'B' and (resid 203 through 210 )BB203 - 21013 - 20
77chain 'B' and (resid 211 through 221 )BB211 - 22121 - 31
88chain 'B' and (resid 222 through 235 )BB222 - 23532 - 45
99chain 'B' and (resid 236 through 246 )BB236 - 24646 - 56
1010chain 'B' and (resid 247 through 254 )BB247 - 25457 - 64
1111chain 'B' and (resid 255 through 274 )BB255 - 27465 - 84
1212chain 'B' and (resid 275 through 285 )BB275 - 28585 - 95
1313chain 'B' and (resid 286 through 305 )BB286 - 30596 - 115
1414chain 'B' and (resid 306 through 311 )BB306 - 311116 - 121
1515chain 'B' and (resid 312 through 317 )BB312 - 317122 - 127
1616chain 'C' and (resid 190 through 235 )CC190 - 2351 - 46
1717chain 'C' and (resid 236 through 316 )CC236 - 31647 - 127

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more