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- PDB-2xde: Crystal structure of the complex of PF-3450074 with an engineered... -

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Basic information

Entry
Database: PDB / ID: 2xde
TitleCrystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal domain
ComponentsGAG POLYPROTEIN
KeywordsVIRAL PROTEIN / AIDS
Function / homology
Function and homology information


viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / telomerase activity / viral penetration into host nucleus / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral capsid / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / symbiont entry into host cell / viral translational frameshifting / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / : / gag protein p24 N-terminal domain / Reverse transcriptase connection / Reverse transcriptase connection 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. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 knuckle / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1B0 / Gag-Pol polyprotein / Gag protein
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBrown, D.G. / Irving, S.L. / Anderson, M. / Bazin, R.
CitationJournal: Plos Pathog. / Year: 2010
Title: HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention.
Authors: Blair, W.S. / Pickford, C. / Irving, S.L. / Brown, D.G. / Anderson, M. / Bazin, R. / Cao, J. / Ciaramella, G. / Isaacson, J. / Jackson, L. / Hunt, R. / Kjerrstrom, A. / Nieman, J. / Patick, ...Authors: Blair, W.S. / Pickford, C. / Irving, S.L. / Brown, D.G. / Anderson, M. / Bazin, R. / Cao, J. / Ciaramella, G. / Isaacson, J. / Jackson, L. / Hunt, R. / Kjerrstrom, A. / Nieman, J. / Patick, A.K. / Perros, M. / Scott, A.D. / Whitby, K. / Wu, H. / Butler, S.L.
History
DepositionApr 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Version format compliance
Revision 2.0May 22, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / pdbx_database_proc ...atom_site / pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAG POLYPROTEIN
B: GAG POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2864
Polymers32,4352
Non-polymers8512
Water6,882382
1
A: GAG POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6432
Polymers16,2171
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GAG POLYPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6432
Polymers16,2171
Non-polymers4261
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.756, 71.035, 41.419
Angle α, β, γ (deg.)90.00, 90.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99996, 0.00158, 0.00824), (0.00158, -1, -0.00032), (0.00824, 0.00033, -0.99997)
Vector: -20.02343, -0.06061, 20.69016)

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Components

#1: Protein GAG POLYPROTEIN / HIV-1 CAPSID


Mass: 16217.491 Da / Num. of mol.: 2 / Fragment: N TERMINAL DOMAIN, RESIDUES 1-146 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9IQV5, UniProt: P12497*PLUS
#2: Chemical ChemComp-1B0 / N-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE


Mass: 425.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H27N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 1.8 Å3/Da / Density % sol: 31.78 % / Description: NONE
Crystal growpH: 8
Details: 2ULOF PROTEIN (30MG/ML)AND 2UL OF WELL SOLUTION (20% PEG 8000, 100 MM PHOSPHATE-CITRATE PH 4.2 AND 200 MM SODIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 20, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 44735 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRUNCATED MODEL OF N TERMINAL CAPSID

Resolution: 1.4→20.72 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 1.176 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -5 %RANDOM
Rwork0.19546 ---
obs0.19546 44702 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.093 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20.24 Å2
2---0.05 Å20 Å2
3---1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.4→20.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2124 0 64 382 2570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222242
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9813050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.52125.31994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06115372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7381510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021704
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.21371
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21614
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.2157
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.284
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.51376
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36822206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2323986
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7484.5844
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.348 3291 -
obs--100 %

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