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- PDB-7bgt: Mason-Pfizer Monkey Virus Protease mutant C7A/D26N/C106A in compl... -

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Basic information

Entry
Database: PDB / ID: 7bgt
TitleMason-Pfizer Monkey Virus Protease mutant C7A/D26N/C106A in complex with peptidomimetic inhibitor
Components
  • Gag-Pro-Pol polyprotein
  • peptidomimetic inhibitor
KeywordsHYDROLASE / Mason-Pfizer Monkey Virus / M-PMV / retropepsin / active site inhibitor / active site mutant
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 / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / 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 / 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
Similarity search - Domain/homology
ACETATE ION / Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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: Protein Sci. / Year: 2021
Title: Crystal structures of inhibitor complexes of M-PMV protease with visible flap loops.
Authors: Wosicki, S. / Kazmierczyk, M. / Gilski, M. / Zabranska, H. / Pichova, I. / Jaskolski, M.
#1: 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.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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.
#5: 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.
History
DepositionJan 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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
C: Gag-Pro-Pol polyprotein
D: Gag-Pro-Pol polyprotein
G: peptidomimetic inhibitor
F: peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,07111
Polymers53,4186
Non-polymers6545
Water5,549308
1
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
F: peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0656
Polymers26,7093
Non-polymers3563
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-38 kcal/mol
Surface area10480 Å2
MethodPISA
2
C: Gag-Pro-Pol polyprotein
D: Gag-Pro-Pol polyprotein
G: peptidomimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0065
Polymers26,7093
Non-polymers2972
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-34 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.296, 67.618, 69.716
Angle α, β, γ (deg.)76.845, 83.875, 83.645
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 18 or resid 20...
d_2ens_1(chain "B" and (resid 1 through 18 or resid 20...
d_3ens_1(chain "C" and (resid 1 through 18 or resid 20 through 65 or resid 67 through 108))
d_4ens_1(chain "D" and (resid 1 through 18 or resid 20...
d_1ens_2(chain "F" and resid 1 through 7)
d_2ens_2chain "G"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1TRPASPA1 - 18
d_12ens_1METILEA22 - 57
d_13ens_1ASNSERA62 - 67
d_14ens_1TYRPROA69 - 110
d_21ens_1TRPASPC1 - 18
d_22ens_1METILEC20 - 55
d_23ens_1ASNSERC60 - 65
d_24ens_1TYRPROC69 - 110
d_31ens_1TRPASPE1 - 18
d_32ens_1METSERE20 - 61
d_33ens_1TYRPROE63 - 104
d_41ens_1TRPASPG1 - 18
d_42ens_1METILEG20 - 55
d_43ens_1ASNSERG60 - 65
d_44ens_1TYRPROG69 - 110
d_11ens_2PROHISJ1 - 7
d_21ens_2PROHISI1 - 7

NCS ensembles :
ID
ens_1
ens_2

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Components

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


Mass: 12899.834 Da / Num. of mol.: 4 / Mutation: C7A, D26N, C106A; ENGINEERED MUTATIONS
Source method: isolated from a genetically manipulated source
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 peptidomimetic inhibitor


Mass: 909.082 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: In the standard definition used by CCP4, 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 CCP4, 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.63 Å3/Da / Density % sol: 53.29 % / Description: plate
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: Protein solution: 4.7 mg/mL protein with 1.4-fold molar excess (relative to dimeric protein) of the inhibitor, 10 mM Tris buffer pH 7.4; Reservoir solution: 0.1 M imidazole buffer, 0.6 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: 0.82657 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 7, 2012
RadiationMonochromator: Double Crystal Monochromator, Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82657 Å / Relative weight: 1
ReflectionResolution: 1.929→32.42 Å / Num. obs: 37694 / % possible obs: 97 % / Redundancy: 2.22 % / Biso Wilson estimate: 27.22 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.095 / Net I/σ(I): 9.4
Reflection shellResolution: 1.929→2.05 Å / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 6043 / CC1/2: 0.555 / Rrim(I) all: 0.86 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6s1v, chain B

6s1v


Resolution: 1.93→32.42 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / Phase error: 22.67
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 999 2.65 %RANDOM
Rwork0.1773 36685 --
obs0.1782 37684 97.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.83 Å2
Refinement stepCycle: LAST / Resolution: 1.93→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 44 308 3897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083702
X-RAY DIFFRACTIONf_angle_d1.1055038
X-RAY DIFFRACTIONf_chiral_restr0.069566
X-RAY DIFFRACTIONf_plane_restr0.007621
X-RAY DIFFRACTIONf_dihedral_angle_d16.4851393
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.764186838559
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.03277314348
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.821634593181
ens_2d_2GX-RAY DIFFRACTIONTorsion NCS0.716288298668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.030.31771410.28315178X-RAY DIFFRACTION96.34
2.03-2.160.27941420.23665240X-RAY DIFFRACTION96.89
2.16-2.320.26531430.2165253X-RAY DIFFRACTION97
2.33-2.560.22451430.19495239X-RAY DIFFRACTION97.27
2.56-2.930.24431450.18715337X-RAY DIFFRACTION97.7
2.93-3.690.21151430.16625244X-RAY DIFFRACTION97.43
3.69-32.420.15131420.13795194X-RAY DIFFRACTION96.6

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