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- PDB-1mu2: CRYSTAL STRUCTURE OF HIV-2 REVERSE TRANSCRIPTASE -

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Basic information

Entry
Database: PDB / ID: 1mu2
TitleCRYSTAL STRUCTURE OF HIV-2 REVERSE TRANSCRIPTASE
Components(HIV-2 RT) x 2
KeywordsTRANSFERASE / HIV-2 REVERSE TRANSCRIPTASE / AIDS / POLYMERASE / DRUG DESIGN
Function / homology
Function and homology information


HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body ...HIV-2 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / 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 / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA 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 / gag protein p24 N-terminal domain / 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 ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / gag protein p24 N-terminal domain / 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. / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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 / 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 / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRen, J. / Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Stuart, D.I. / Stammers, D.K.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of HIV-2 reverse transcriptase at 2.35-A resolution and the mechanism of resistance to non-nucleoside inhibitors
Authors: Ren, J. / Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Stuart, D.I. / Stammers, D.K.
#1: Journal: To be Published
Title: Cloning, Expression, Purification, and Crystallisation of HIV-2 Reverse Transcriptase
Authors: Bird, L.E. / Chamberlain, P.P. / Stewart-Jones, G.B. / Ren, J. / Stuart, D.I. / Stammers, D.K.
History
DepositionSep 23, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIV-2 RT
B: HIV-2 RT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,92529
Polymers114,3512
Non-polymers2,57427
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10970 Å2
ΔGint-286 kcal/mol
Surface area44300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.77, 107.81, 82.16
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 HIV-2 RT / Reverse transcriptase


Mass: 64169.555 Da / Num. of mol.: 1 / Mutation: R286S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Strain: pROD / Gene: POL / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P04584, RNA-directed DNA polymerase
#2: Protein HIV-2 RT / Reverse transcriptase


Mass: 50181.730 Da / Num. of mol.: 1 / Fragment: residues 6-431 / Mutation: R286S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 2 / Genus: Lentivirus / Strain: pROD / Gene: POL / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P04584, RNA-directed DNA polymerase
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.57 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: (NH4)2SO4, TRIS, DMSO, GLYCEROL, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Method: unknown
Details: Bird, L.E., (2003) Protein EExpression Purif., 27, 12.

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 56142 / % possible obs: 100 % / Observed criterion σ(I): -1.5 / Redundancy: 11.3 % / Biso Wilson estimate: 53.7 Å2 / Rmerge(I) obs: 0.128 / Net I/σ(I): 16
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.1 / Num. unique all: 5520 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 631721 / Rmerge(I) obs: 0.128
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 5520 / Rmerge(I) obs: 0.747

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1hmv, 1rtj

1hmv

1rtj


Resolution: 2.35→29.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2050186.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2838 5.1 %RANDOM
Rwork0.192 ---
obs-56074 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9425 Å2 / ksol: 0.343704 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2--1.15 Å20 Å2
3----0.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-30 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7742 0 140 286 8168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it4.184
X-RAY DIFFRACTIONc_mcangle_it6.497
X-RAY DIFFRACTIONc_scbond_it9.98
X-RAY DIFFRACTIONc_scangle_it13.6712
LS refinement shellResolution: 2.35→2.43 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.341 306 5.5 %
Rwork0.295 5211 -
obs-5221 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMCNS_PROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 53236 / Rfactor obs: 0.189 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0081
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
LS refinement shell
*PLUS
Rfactor Rfree: 0.341 / Rfactor Rwork: 0.295

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