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- PDB-4exh: The crystal structure of xmrv protease complexed with acetyl-pepstatin -

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Basic information

Entry
Database: PDB / ID: 4exh
TitleThe crystal structure of xmrv protease complexed with acetyl-pepstatin
Components
  • ACETYL-PEPSTATIN
  • Putative gag-pro-pol polyprotein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / BETA SHEET / DIMER / PROTEASE / ACETYL-PEPSTAIN / VIRUS / HYDROLASE-HYDROL INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination ...host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / plasma membrane
Similarity search - Function
Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein ...Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
ACETYL-PEPSTATIN / FORMIC ACID / Gag-Pol polyprotein
Similarity search - Component
Biological speciesDG-75 Murine leukemia virus
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsLi, M. / Wlodawer, A.
CitationJournal: Febs J. / Year: 2012
Title: Inhibition of XMRV and HIV-1 proteases by pepstatin A and acetyl-pepstatin.
Authors: Matuz, K. / Motyan, J. / Li, M. / Wlodawer, A.
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative gag-pro-pol polyprotein
B: Putative gag-pro-pol polyprotein
J: ACETYL-PEPSTATIN
M: ACETYL-PEPSTATIN
P: ACETYL-PEPSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6206
Polymers30,5745
Non-polymers461
Water84747
1
A: Putative gag-pro-pol polyprotein
B: Putative gag-pro-pol polyprotein
J: ACETYL-PEPSTATIN
M: ACETYL-PEPSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9925
Polymers29,9464
Non-polymers461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative gag-pro-pol polyprotein
B: Putative gag-pro-pol polyprotein
P: ACETYL-PEPSTATIN


Theoretical massNumber of molelcules
Total (without water)29,3183
Polymers29,3183
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.314, 65.210, 69.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative gag-pro-pol polyprotein


Mass: 14345.290 Da / Num. of mol.: 2 / Fragment: unp residues 533-657
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DG-75 Murine leukemia virus / Strain: PCDNA3.1-XMRV-VP63 / Gene: GAG-POL / Plasmid: PDEST-521 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)TONA PRARE / References: UniProt: Q9E7M1
#2: Protein/peptide ACETYL-PEPSTATIN


Type: Oligopeptide / Class: Inhibitor / Mass: 627.812 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Streptomyces (bacteria) / References: ACETYL-PEPSTATIN
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 1.72 Å3/Da / Density % sol: 28.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.5M naFormate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 20, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14051 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rsym value: 0.079 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 473 / Rsym value: 0.284 / % possible all: 64.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→47.54 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 9.779 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23808 719 5.1 %RANDOM
Rwork0.1958 ---
obs0.19787 13292 93.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.973 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---2.5 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 3 47 1859
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221869
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9972542
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.9623.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95515284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1661510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221370
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8961.51190
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.68921927
X-RAY DIFFRACTIONr_scbond_it2.4053679
X-RAY DIFFRACTIONr_scangle_it4.1174.5617
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 33 -
Rwork0.262 660 -
obs--64.95 %
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)
10.30320.2456-0.35591.1202-0.04821.1455-0.0159-0.0189-0.0206-0.05640.00270.01890.0325-0.040.01320.0345-0.0007-0.00050.02260.00960.0454-7.2641-7.649413.9801
20.6132-0.1082-0.06561.0873-0.33230.5229-0.0520.0296-0.03-0.0680.0353-0.05590.03560.03130.01670.0374-0.00480.00820.03050.00270.03423.55164.85830.3054
38.951-8.318611.30117.5702-5.646338.07270.273-0.6010.4188-0.21710.6367-0.60350.4188-0.0414-0.90960.0829-0.0285-0.00870.0783-0.02280.1825-8.74746.05213.8594
425.44214.462312.684912.89244.79373.9174-0.40231.16220.81760.0029-0.3196-0.1749-0.29840.77480.72190.0184-0.039-0.0710.320.040.2334-0.15472.543817.4069
57.8586-1.47654.50450.7391-2.47438.70390.49880.3694-0.14690.01440.09740.19550.00310.0843-0.59620.13320.04850.00950.21730.04530.1359-4.1193.804510.2718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 122
2X-RAY DIFFRACTION2B1 - 122
3X-RAY DIFFRACTION3J1 - 4
4X-RAY DIFFRACTION4M1 - 4
5X-RAY DIFFRACTION5P1 - 6

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