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- PDB-6s1u: Crystal structure of dimeric M-PMV protease C7A/D26N/C106A mutant... -

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Basic information

Entry
Database: PDB / ID: 6s1u
TitleCrystal structure of dimeric M-PMV protease C7A/D26N/C106A 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 / RNA stem-loop binding / RNA-directed DNA polymerase activity ...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 / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / structural constituent of virion / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain 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: 1.9 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 9, 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

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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)26,6863
Polymers26,6863
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-25 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.603, 29.413, 85.533
Angle α, β, γ (deg.)90.00, 103.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

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
1BB
2AA

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Components

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


Mass: 12899.834 Da / Num. of mol.: 2 / Mutation: C7A, D26N, C106A; 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.: 149 / 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: 2.365 Å3/Da / Density % sol: 47.99 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Protein solution: 6.8 mg/mL protein with 1.2-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M ...Details: Protein solution: 6.8 mg/mL protein with 1.2-fold molar excess (relative to dimeric protein) of Pro-0A1-Val-PSA-Ala-Met-Thr (inhibitor), 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M imidazole buffer, 1.2 M sodium acetate;

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 22, 2012
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: 1.9→48.3 Å / Num. obs: 20007 / % possible obs: 99.1 % / Redundancy: 4.02 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.124 / Net I/σ(I): 11.49
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.67 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.53 / Num. unique obs: 3082 / CC1/2: 0.969 / Rrim(I) all: 1.146 / % possible all: 95.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0232refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3sqf, chain A

3sqf


Resolution: 1.9→48.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.787 / SU ML: 0.12 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.144 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23538 1001 5 %RANDOM
Rwork0.19286 ---
obs0.19499 19004 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.38 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å2-0.68 Å2
2--0.42 Å20 Å2
3----0.97 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 149 1875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0131773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171663
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.642424
X-RAY DIFFRACTIONr_angle_other_deg1.3091.5723882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.695209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.66825.14370
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.01315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.574154
X-RAY DIFFRACTIONr_chiral_restr0.0830.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021884
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02322
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_it2.4512.389858
X-RAY DIFFRACTIONr_mcbond_other2.3912.383857
X-RAY DIFFRACTIONr_mcangle_it3.7943.5141062
X-RAY DIFFRACTIONr_mcangle_other3.8023.5231063
X-RAY DIFFRACTIONr_scbond_it2.832.689915
X-RAY DIFFRACTIONr_scbond_other2.8282.691915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3983.9411362
X-RAY DIFFRACTIONr_long_range_B_refined8.29328.5812026
X-RAY DIFFRACTIONr_long_range_B_other8.23428.2232004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3110 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 68 -
Rwork0.35 1290 -
obs--91.69 %
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)
110.160.89653.43286.36775.87637.5980.0901-0.0831-0.16190.4158-0.058-0.33970.44130.0987-0.03210.23020.04210.00390.08610.06770.115921.4764-6.392221.2131
21.23910.0024-0.62052.14371.24153.34610.03480.1259-0.04270.1081-0.25030.27930.1565-0.37440.21540.2333-0.01660.04850.1053-0.02780.14666.0635-1.714132.3504
32.7611-0.78471.94280.2256-0.5511.3806-0.1256-0.09340.05470.01790.0471-0.0062-0.1517-0.10490.07850.50540.0702-0.02720.3336-0.06160.3828-2.9598.683123.6275
46.545-0.22523.01151.8435-0.2093.8663-0.0299-0.11140.2580.2715-0.16310.2399-0.0244-0.19630.19290.2737-0.02140.08550.1059-0.04330.17848.15262.396435.8454
51.74030.6913-0.6033.85180.74663.6157-0.0409-0.03830.0460.2603-0.04690.33850.00520.12170.08780.3080.00720.03570.13780.0070.15812.70141.601927.7347
61.5012-1.316-1.90533.53330.54648.4447-0.02770.13580.25580.15350.0425-0.2609-0.2112-0.098-0.01490.1207-0.0244-0.0230.18380.00230.125626.45623.218821.1202
77.2004-8.198-0.524312.22043.7923.58140.21290.19710.5291-0.5583-0.0364-0.7234-0.40030.2177-0.17650.2649-0.13390.02910.11710.03640.069123.79758.735421.0576
81.13091.3507-0.24881.68-0.53925.08820.1247-0.0549-0.04430.0981-0.0538-0.1518-0.1624-0.1394-0.07090.17-0.00770.05690.00750.00050.214218.42189.60087.2234
92.40780.08830.68270.07190.24531.25780.01160.06570.07990.0211-0.01170.0464-0.0652-0.07540.00010.17020.01810.03050.01140.01340.120710.06993.87063.294
107.9975-0.0972.10370.02470.00050.60020.2377-0.3418-0.29080.0438-0.0817-0.02530.1256-0.1943-0.15590.1887-0.2013-0.04380.33280.13320.20161.9629-6.18377.2856
113.43970.0585-0.35670.8011-0.24930.1266-0.0071-0.0637-0.2142-0.13910.0188-0.00770.0093-0.008-0.01160.17150.01650.02270.01120.01420.120115.24451.00632.0295
121.571-0.17370.10680.57881.38583.56780.0052-0.34320.0727-0.00060.117-0.04880.11310.2202-0.12210.2110.04840.01520.1233-0.01440.082120.2741.072914.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 9
2X-RAY DIFFRACTION2A10 - 49
3X-RAY DIFFRACTION3A50 - 61
4X-RAY DIFFRACTION4A62 - 87
5X-RAY DIFFRACTION5A88 - 102
6X-RAY DIFFRACTION6A103 - 108
7X-RAY DIFFRACTION7B1 - 7
8X-RAY DIFFRACTION8B8 - 24
9X-RAY DIFFRACTION9B25 - 47
10X-RAY DIFFRACTION10B48 - 59
11X-RAY DIFFRACTION11B60 - 88
12X-RAY DIFFRACTION12B89 - 109

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