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- PDB-6s1v: Crystal structure of dimeric M-PMV protease D26N mutant in comple... -

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Basic information

Entry
Database: PDB / ID: 6s1v
TitleCrystal structure of dimeric M-PMV protease D26N mutant in complex with inhibitor
Components
  • Gag-Pro-Pol polyprotein
  • PRO-0A1-VAL-PSA-ALA-MET-THR
KeywordsHYDROLASE / Mason-Pfizer Monkey Virus / M-PMV / retrovirus / retropepsin / aspartic protease / dimerization / inhibitor / flap structure
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding ...dUTP diphosphatase / dUTP diphosphatase activity / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / gag protein p24 N-terminal domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsWosicki, S. / Gilski, M. / Jaskolski, M. / Zabranska, H. / Pichova, I.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of SciencesRVO 61388963 Czech Republic
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Comparison of a retroviral protease in monomeric and dimeric states.
Authors: Wosicki, S. / Gilski, M. / Zabranska, H. / Pichova, I. / Jaskolski, M.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structure of a monomeric retroviral protease solved by protein folding game players.
Authors: Khatib, F. / DiMaio, F. / Cooper, S. / Kazmierczyk, M. / Gilski, M. / Krzywda, S. / Zabranska, H. / Pichova, I. / Thompson, J. / Popovic, Z. / Jaskolski, M. / Baker, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: High-resolution structure of a retroviral protease folded as a monomer.
Authors: Gilski, M. / Kazmierczyk, M. / Krzywda, S. / Zabranska, H. / Cooper, S. / Popovic, Z. / Khatib, F. / DiMaio, F. / Thompson, J. / Baker, D. / Pichova, I. / Jaskolski, M.
#3: Journal: Nature / Year: 1989
Title: Crystal structure of a retroviral protease proves relationship to aspartic protease family.
Authors: Miller, M. / Jaskolski, M. / Rao, J.K. / Leis, J. / Wlodawer, A.
#4: Journal: Science / Year: 1989
Title: Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease.
Authors: Wlodawer, A. / Miller, M. / Jaskolski, M. / Sathyanarayana, B.K. / Baldwin, E. / Weber, I.T. / Selk, L.M. / Clawson, L. / Schneider, J. / Kent, S.B.
History
DepositionJun 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
I: PRO-0A1-VAL-PSA-ALA-MET-THR


Theoretical massNumber of molelcules
Total (without water)26,8143
Polymers26,8143
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-31 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.947, 29.504, 85.390
Angle α, β, γ (deg.)90.00, 101.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 1 - 108 / Label seq-ID: 1 - 108

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Gag-Pro-Pol polyprotein / Pr180


Mass: 12963.964 Da / Num. of mol.: 2 / Mutation: D26N; ENGINEERED MUTATION
Source method: isolated from a genetically manipulated source
Details: Gaps in the sequence indicate residues that were not modeled because of poor electron density
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Plasmid: pBPS13ATG
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P07572, dUTP diphosphatase, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, ...References: UniProt: P07572, dUTP diphosphatase, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, Hydrolases; Acting on ester bonds
#2: Protein/peptide PRO-0A1-VAL-PSA-ALA-MET-THR


Mass: 886.065 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: In the standard definition used by Refmac, the Cgamma atom of the PSA residue is labeled as CA. In the PDB Validation Report this label is interpreted as Calpha causing geometrical alerts. ...Details: In the standard definition used by Refmac, the Cgamma atom of the PSA residue is labeled as CA. In the PDB Validation Report this label is interpreted as Calpha causing geometrical alerts. These alerts are false and should be ignored.
Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.378 Å3/Da / Density % sol: 46.54 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Protein solution: 5.0 mg/mL protein with 1.4-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir ...Details: Protein solution: 5.0 mg/mL protein with 1.4-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 5 mM TCEP, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M sodium citrate buffer, 25% propan-2-ol, 5 mM TCEP;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2013
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.64→48.91 Å / Num. obs: 30408 / % possible obs: 99.3 % / Redundancy: 3.65 % / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.05 / Net I/σ(I): 14.36
Reflection shellResolution: 1.64→1.74 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 4819 / CC1/2: 0.568 / Rrim(I) all: 0.97 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S1U, chain A

6s1u


Resolution: 1.64→48.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.119 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.094 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22018 1004 3.3 %RANDOM
Rwork0.1787 ---
obs0.18006 29403 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.063 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0 Å2-0.82 Å2
2---0.76 Å2-0 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.64→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 157 1890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131823
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171696
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.642496
X-RAY DIFFRACTIONr_angle_other_deg1.361.5743975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6195218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88225.40574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04615317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.397154
X-RAY DIFFRACTIONr_chiral_restr0.090.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7542.889876
X-RAY DIFFRACTIONr_mcbond_other2.7492.881875
X-RAY DIFFRACTIONr_mcangle_it4.1444.271089
X-RAY DIFFRACTIONr_mcangle_other4.1424.281090
X-RAY DIFFRACTIONr_scbond_it3.4633.292947
X-RAY DIFFRACTIONr_scbond_other3.4543.292947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2474.8071405
X-RAY DIFFRACTIONr_long_range_B_refined8.84634.7022065
X-RAY DIFFRACTIONr_long_range_B_other8.83134.2742035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3031 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.637→1.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 71 -
Rwork0.358 2075 -
obs--96.49 %
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)
17.82714.531-0.34739.73455.64374.8207-0.1221-0.50330.14361.0460.080.14480.93850.33130.04220.30020.1-0.02460.12510.03040.043523.5791-4.951922.1589
20.08360.1605-0.38820.4614-0.54493.5910.02110.0179-0.01970.0711-0.0465-0.03230.1564-0.01460.02540.1868-0.00320.01390.08660.00310.039912.6994-3.763130.2615
31.5662-0.8067-1.78671.22120.18312.76160.18450.1291-0.1497-0.1302-0.20750.2816-0.0882-0.07570.0230.1983-0.05920.05630.1365-0.07460.1078-0.07861.904533.1028
40.6860.5353-0.251315.2032-9.74816.263-0.34270.02960.20290.03140.43560.1876-0.0679-0.2748-0.09290.2156-0.0411-0.06080.17160.01460.1175-3.60397.300824.2011
53.87-0.6091.56941.3532-0.01060.6877-0.08060.12140.10540.2202-0.00820.08830.01820.0380.08880.2596-0.01370.06060.0447-0.03230.079411.40833.072438.587
60.6255-0.6601-0.54670.8180.79022.20550.00860.0463-0.06830.13070.0380.1162-0.13210.1819-0.04660.29590.00310.07320.10980.02630.063612.26382.470627.3876
73.15171.9947-4.2521.3322-2.70345.74210.0833-0.1685-0.12440.1006-0.2235-0.04-0.11440.24320.14020.1115-0.0707-0.0350.2165-0.03670.141825.45647.889119.7223
80.070.3112-0.0871.7495-0.55860.19260.02220.0167-0.01450.2286-0.0603-0.1285-0.0980.02980.03810.0764-0.01670.00490.1160.00880.142818.48589.53299.1592
90.53310.0019-0.06461.0610.33380.78680.05690.0480.08340.1124-0.01310.1089-0.0514-0.1197-0.04380.02850.00650.02440.13550.00660.125310.29734.58574.11
103.1264-1.35852.53211.1434-1.76382.84730.3315-0.2267-0.13520.07470.04260.28440.0032-0.1067-0.37410.1457-0.11560.07530.22290.01330.20610.5576-4.4989.2141
110.9978-0.0871-0.44690.6740.32190.33350.02590.0075-0.11150.0028-0.0407-0.0134-0.0185-0.05350.01480.01670.00890.01630.130.01190.140314.91351.14842.334
120.30460.0344-0.12481.12990.51810.59920.0384-0.11990.010.0420.0176-0.00430.09440.095-0.0560.07180.00050.02890.1426-0.00220.093119.66171.160514.4333
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 30
3X-RAY DIFFRACTION3A31 - 52
4X-RAY DIFFRACTION4A53 - 61
5X-RAY DIFFRACTION5A62 - 80
6X-RAY DIFFRACTION6A81 - 108
7X-RAY DIFFRACTION7B1 - 5
8X-RAY DIFFRACTION8B6 - 19
9X-RAY DIFFRACTION9B20 - 48
10X-RAY DIFFRACTION10B49 - 60
11X-RAY DIFFRACTION11B61 - 88
12X-RAY DIFFRACTION12B89 - 108

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