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- PDB-3nr6: Crystal structure of xenotropic murine leukemia virus-related vir... -

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Basic information

Entry
Database: PDB / ID: 3nr6
TitleCrystal structure of xenotropic murine leukemia virus-related virus (XMRV) protease
ComponentsProtease p14
KeywordsHYDROLASE/INHIBITOR / DIMER / PROTEASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / 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 / membrane / identical protein binding
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
: / PHOSPHATE ION / Gag-Pol polyprotein
Similarity search - Component
Biological speciesXenotropic MuLV-related virus VP62
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsLubkowski, J. / Li, M. / Gustchina, A. / Zhou, D. / Dauter, Z. / Wlodawer, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Crystal structure of XMRV protease differs from the structures of other retropepsins.
Authors: Li, M. / Dimaio, F. / Zhou, D. / Gustchina, A. / Lubkowski, J. / Dauter, Z. / Baker, D. / Wlodawer, A.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protease p14
B: Protease p14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8254
Polymers28,6912
Non-polymers1342
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-13 kcal/mol
Surface area11290 Å2
MethodPISA
2
A: Protease p14
B: Protease p14
hetero molecules

A: Protease p14
B: Protease p14
hetero molecules

A: Protease p14
B: Protease p14
hetero molecules

A: Protease p14
B: Protease p14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,29916
Polymers114,7628
Non-polymers5368
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area15020 Å2
ΔGint-57 kcal/mol
Surface area37980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.915, 63.915, 106.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number89
Space group name H-MP422

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Components

#1: Protein Protease p14


Mass: 14345.290 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RETROVIRAL PROTEASE FROM XMRV / Source: (gene. exp.) Xenotropic MuLV-related virus VP62 / 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: A1Z651, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.9 Å3/Da / Density % sol: 35.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PROTEIN CONCENTRATION: 10 MG/ML PRECIPITANT: 0.06 M KH2PO4, 1.34 M NA2HPO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 10, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 16141 / Num. obs: 16141 / % possible obs: 98.5 % / Observed criterion σ(F): -1.74 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.044 / Rsym value: 0.044 / Net I/σ(I): 32.1
Reflection shellResolution: 1.97→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.23 / Num. unique all: 667 / Rsym value: 0.257 / % possible all: 82.1

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
Rosettamodel building
REFMAC5.5.0104refinement
HKL-3000data reduction
HKL-3000data scaling
Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ASSEMBLY OF RETROVIRAL PROTEASES

Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 8.324 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23322 815 5 %RANDOM
Rwork0.19568 ---
all0.19737 ---
obs0.19737 15336 98.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--0.48 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 6 66 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221863
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9752538
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6035231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57824.21176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84415302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.21510
X-RAY DIFFRACTIONr_chiral_restr0.1450.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0221408
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_it2.73921168
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.06231898
X-RAY DIFFRACTIONr_scbond_it3.6762695
X-RAY DIFFRACTIONr_scangle_it5.0663639
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.965→2.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 60 -
Rwork0.224 920 -
obs-980 83.76 %
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)
13.23870.4637-1.42354.0084-0.94114.52-0.07320.023-0.1454-0.03540.01430.11280.1332-0.14350.05890.05450.0191-0.01310.0701-0.00940.040611.112221.355414.6024
26.7048-1.32692.12632.91770.4855.557-0.1293-0.3786-0.16420.25650.07930.15730.0569-0.24620.04990.11540.04890.03620.09010.0470.0489.374822.838238.6955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2B1 - 125

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