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- PDB-8pol: Crystal structure of Plasmodium falciparum Sub1 protease -

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Basic information

Entry
Database: PDB / ID: 8pol
TitleCrystal structure of Plasmodium falciparum Sub1 protease
ComponentsSubtilisin-like protease 1
KeywordsHYDROLASE / Protease / Plasmodium falciparum / merozoite egress / pH-dependent dimerization
Function / homology
Function and homology information


merozoite dense granule / exoneme / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / symbiont-containing vacuolar space / symbiont-containing vacuole / subtilisin / membrane protein ectodomain proteolysis / serine-type peptidase activity / protein processing / serine-type endopeptidase activity ...merozoite dense granule / exoneme / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / symbiont-containing vacuolar space / symbiont-containing vacuole / subtilisin / membrane protein ectodomain proteolysis / serine-type peptidase activity / protein processing / serine-type endopeptidase activity / proteolysis / membrane / metal ion binding
Similarity search - Function
Peptidase S8A, subtilisin-like peptidase 1, plasmodium / SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site ...Peptidase S8A, subtilisin-like peptidase 1, plasmodium / SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
PHOSPHATE ION / Subtilisin-like protease 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsMartinez, M. / Bouillon, A. / Haouz, A. / Barale, J.C. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Mbio / Year: 2024
Title: Prodomain-driven enzyme dimerization: a pH-dependent autoinhibition mechanism that controls Plasmodium Sub1 activity before merozoite egress.
Authors: Martinez, M. / Bouillon, A. / Brule, S. / Raynal, B. / Haouz, A. / Alzari, P.M. / Barale, J.-.C.
History
DepositionJul 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin-like protease 1
B: Subtilisin-like protease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,29215
Polymers155,4972
Non-polymers79513
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-87 kcal/mol
Surface area36970 Å2
Unit cell
Length a, b, c (Å)86.576, 107.163, 137.682
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 37 through 40 or resid 42...
d_2ens_1(chain "B" and (resid 37 through 40 or resid 42...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLNGLNALAALAAA37 - 4037 - 40
d_12LYSLYSTHRTHRAA42 - 14842 - 148
d_13PROPROPROPROAA150 - 160150 - 160
d_14VALVALLEULEUAA162 - 185162 - 185
d_15GLUGLUILEILEAA187 - 531187 - 531
d_16LYSLYSLYSLYSAA533 - 629533 - 629
d_17VALVALLYSLYSAA631 - 668631 - 668
d_18CACACACAAC701
d_19CACACACAAD702
d_110CACACACAAE703
d_21GLNGLNALAALABB37 - 4037 - 40
d_22LYSLYSTHRTHRBB42 - 14842 - 148
d_23PROPROPROPROBB150 - 160150 - 160
d_24VALVALLEULEUBB162 - 185162 - 185
d_25GLUGLUASPASPBB187 - 217187 - 217
d_26PROPROILEILEBB330 - 531330 - 531
d_27LYSLYSLYSLYSBB533 - 629533 - 629
d_28VALVALLYSLYSBB631 - 668631 - 668
d_29CACACACABI701
d_210CACACACABJ702
d_211CACACACABK703

NCS oper: (Code: givenMatrix: (-0.560595051275, -0.0161776716599, 0.827932045174), (-0.032082878164, -0.998634184339, -0.0412365711304), (0.827468354328, -0.0496794606406, 0.559310355505)Vector: 96. ...NCS oper: (Code: given
Matrix: (-0.560595051275, -0.0161776716599, 0.827932045174), (-0.032082878164, -0.998634184339, -0.0412365711304), (0.827468354328, -0.0496794606406, 0.559310355505)
Vector: 96.4604807997, -0.961185811712, -51.0975286751)

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Components

#1: Protein Subtilisin-like protease 1 / PfSUB1


Mass: 77748.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: SUB1, PF3D7_0507500 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I0V0, subtilisin
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
Has ligand of interestN

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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

Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 1.6 M NaH2PO4 / 0.4 M K2HPO4, 0.1 M phosphate-citrate, pH 5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.0717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0717 Å / Relative weight: 1
ReflectionResolution: 3.09→43.3 Å / Num. obs: 24055 / % possible obs: 99.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 71.49 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.06 / Net I/σ(I): 11.1
Reflection shellResolution: 3.09→3.3 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4147 / CC1/2: 0.837 / Rpim(I) all: 0.317 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.09→43.25 Å / SU ML: 0.4357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.8721
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2284 1217 5.07 %
Rwork0.1701 22779 -
obs0.173 23996 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.41 Å2
Refinement stepCycle: LAST / Resolution: 3.09→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7523 0 33 0 7556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00447671
X-RAY DIFFRACTIONf_angle_d0.698210367
X-RAY DIFFRACTIONf_chiral_restr0.04871164
X-RAY DIFFRACTIONf_plane_restr0.0051350
X-RAY DIFFRACTIONf_dihedral_angle_d5.32351009
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.705132601497 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.210.35041400.28622359X-RAY DIFFRACTION94.41
3.21-3.360.3231430.23022512X-RAY DIFFRACTION99.89
3.36-3.530.27781320.2132490X-RAY DIFFRACTION99.92
3.53-3.760.29421290.20552522X-RAY DIFFRACTION99.92
3.76-4.040.20371240.14342526X-RAY DIFFRACTION99.92
4.04-4.450.17821440.12742537X-RAY DIFFRACTION99.93
4.45-5.090.16661430.11892555X-RAY DIFFRACTION99.89
5.1-6.410.22541360.17582568X-RAY DIFFRACTION99.85
6.42-43.250.2291260.17362710X-RAY DIFFRACTION99.44
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)
11.235770846710.08297825974690.8191009971870.899626841845-0.2223473806552.59763145503-0.0707186051809-0.08188182866310.195022520711-0.0302205446348-0.0764304245350.0379207715274-0.2227874635090.1890083355750.1365013589150.739554135969-0.0780828920819-0.01000701649660.738405427626-0.05497468924030.82344727865547.01190132-2.817194939242.62838698313
22.324642296141.014735683350.8527007893431.15813952280.4965449265372.35500114014-0.0752876588965-0.02503887179580.299006272977-0.0347572997424-0.1536636319180.312904732771-0.10973419136-0.08140873817280.2550353498350.5429632536330.0171935935225-0.03944902622530.514369557649-0.08238213148910.75523475967231.8129329421-6.20482375482-10.0784624389
33.287727726160.734204351640.9842361772991.98506179690.6975301100022.574372444620.2288373631190.013115436924-0.2132004801610.081595696445-0.177671287727-0.1157748831830.2126290698160.123177060466-0.0654942894150.559331167470.00111497367295-0.04565038606290.454826315235-0.04948514066620.60053282400940.4027742399-20.6249588745-9.86355118929
42.213315145860.6400167848590.4487621717631.04761000513-0.1363233155412.354334262970.144214054455-0.640775781736-0.3736667485970.184345802066-0.239634927326-0.3146453610240.08031933334670.3053483802770.04191265680360.697373145251-0.0853970296511-0.0381857120710.9111591973120.2098347789860.73937031172672.2811660929-0.0522246753826-10.748627006
51.85209458023-0.0718335749669-0.07329595092511.56259332014-0.6534110504612.780765393040.0457848392811-0.118466661578-0.00425405035745-0.246272522653-0.124108837937-0.08861047528160.2508923713790.1104061237020.06051084527940.585343756010.000695884772552-0.007493382651470.458071830170.09526950962940.56923285517170.15848520414.77191712545-30.2877736645
62.562633168990.0266620123318-0.3309889584572.89515320584-1.009263763013.148745302440.0397515439211-0.2896544236540.2598977340110.17494330616-0.1347066003530.00230359480987-0.373934084266-0.01246345986360.09839422714780.571209064321-0.0212327886413-0.03251368092740.5384572469060.008696813502150.59103735893765.924613050918.9268559403-22.155207758
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 37 through 203 )AA37 - 2031 - 128
22chain 'A' and (resid 204 through 482 )AA204 - 482129 - 295
33chain 'A' and (resid 483 through 668 )AA483 - 668296 - 477
44chain 'B' and (resid 37 through 203 )BF37 - 2031 - 128
55chain 'B' and (resid 204 through 482 )BF204 - 482129 - 297
66chain 'B' and (resid 483 through 668 )BF483 - 668298 - 479

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