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- PDB-1j5o: CRYSTAL STRUCTURE OF MET184ILE MUTANT OF HIV-1 REVERSE TRANSCRIPT... -

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Basic information

Entry
Database: PDB / ID: 1j5o
TitleCRYSTAL STRUCTURE OF MET184ILE MUTANT OF HIV-1 REVERSE TRANSCRIPTASE IN COMPLEX WITH DOUBLE STRANDED DNA TEMPLATE-PRIMER
Components
  • (Reverse transcriptase) x 2
  • 5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3'
  • 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3'
  • ANTIBODY (HEAVY CHAIN)
  • ANTIBODY (LIGHT CHAIN)
KeywordsTRANSFERASE/IMMUNE SYSTEM/DNA / HIV / REVERSE TRANSCRIPTASE / MET184ILE / 3TC / PROTEIN-DNA COMPLEX / DRUG RESISTANCE / M184I / TRANSFERASE-IMMUNE SYSTEM-DNA COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / 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 / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / 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 / 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. / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Plaits / Immunoglobulins / Roll / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å
AuthorsSarafianos, S.G. / Das, K. / Arnold, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids.
Authors: Sarafianos, S.G. / Das, K. / Clark Jr., A.D. / Ding, J. / Boyer, P.L. / Hughes, S.H. / Arnold, E.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Structure and Functional Implications of the Polymerase Active Site Region in a Complex of HIV-1 RT with a Double-Stranded DNA template-primer and an Antibody Fab Fragment at 2.8 Angstroms Resolution
Authors: Ding, J. / Das, K. / Hsiou, Y. / Sarafianos, S.G. / Clark Jr., A.D. / Jacobo-Molina, A. / Tantillo, C. / Hughes, S.H. / Arnold, E.
#2: Journal: Chem.Biol. / Year: 1999
Title: Touching the Heart of HIV-1 Drug Resistance: The Fingers Close Down on the dNTP at the Polymerase Active Site
Authors: Sarafianos, S.G. / Das, K. / Ding, J. / Boyer, P.L. / Hughes, S.H. / Arnold, E.
History
DepositionMay 24, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionJun 14, 2002ID: 1C9R
Revision 1.0Jun 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: 5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3'
P: 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3'
A: Reverse transcriptase
B: Reverse transcriptase
L: ANTIBODY (LIGHT CHAIN)
H: ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)172,3116
Polymers172,3116
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.180, 169.180, 221.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

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DNA chain , 2 types, 2 molecules TP

#1: DNA chain 5'-D(*AP*TP*GP*GP*CP*GP*CP*CP*CP*GP*AP*AP*CP*AP*GP*GP*GP*AP*C)-3'


Mass: 5864.801 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*TP*CP*CP*CP*TP*GP*TP*TP*CP*GP*GP*GP*CP*GP*CP*CP*A)-3'


Mass: 5484.528 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 2 types, 2 molecules AB

#3: Protein Reverse transcriptase / / HIV-1 RT


Mass: 64256.613 Da / Num. of mol.: 1 / Mutation: M184I,C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase
#4: Protein Reverse transcriptase / / HIV-1 RT


Mass: 50263.723 Da / Num. of mol.: 1 / Mutation: M184I,C280S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Production host: Escherichia coli (E. coli) / References: UniProt: P03366, RNA-directed DNA polymerase

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Antibody , 2 types, 2 molecules LH

#5: Antibody ANTIBODY (LIGHT CHAIN)


Mass: 22984.068 Da / Num. of mol.: 1 / Fragment: FAB28 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: Antibody ANTIBODY (HEAVY CHAIN)


Mass: 23457.156 Da / Num. of mol.: 1 / Fragment: FAB28 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 10

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Sample preparation

CrystalDensity Matthews: 5.32 Å3/Da / Density % sol: 76.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30 % SATURATED AMMONIUM SULFATE, 100 MM CACODYLATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlprotein1drop
20.2 mMDNA1drop
3100 mMcacodylate1reservoirpH5.6
429-31 %satammonium sulfate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12771
21051
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS F110.918
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
FUJI1IMAGE PLATESep 10, 1996
MARRESEARCH2IMAGE PLATEJun 10, 1997
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
21.11
ReflectionResolution: 3.5→40 Å / Num. all: 46038 / Num. obs: 42062 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.91 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.2
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / % possible all: 83
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 91.5 %
Reflection shell
*PLUS
% possible obs: 83 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.843refinement
X-PLORphasing
RefinementResolution: 3.5→10 Å / σ(F): 1 / σ(I): 1
RfactorNum. reflection% reflection
Rfree0.338 1700 -
Rwork0.262 --
obs0.27 39033 91.5 %
all-46020 -
Refinement stepCycle: LAST / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10967 753 0 0 11720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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