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- PDB-8dw1: Crystal structure of a host-guest complex with 5'-CTTAGTTATAACTAAG-3' -

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Basic information

Entry
Database: PDB / ID: 8dw1
TitleCrystal structure of a host-guest complex with 5'-CTTAGTTATAACTAAG-3'
Components
  • DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')
  • reverse transcriptase
KeywordsDNA BINDING PROTEIN/DNA / Host-guest complex DNA structure B-form DNA Moloney murine leukemia virus reverse transcriptase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / DNA integration / host multivesicular body / 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 / DNA integration / host multivesicular body / 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-mediated suppression of host gene expression / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / 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. / 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. / 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
Similarity search - Domain/homology
DNA / Gag-Pol polyprotein
Similarity search - Component
Biological speciesMoloney murine leukemia virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.849 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
American Cancer Society United States
CitationJournal: Bioorg.Med.Chem. / Year: 2023
Title: Two distinct rotations of bithiazole DNA intercalation revealed by direct comparison of crystal structures of Co(III)•bleomycin A 2 and B 2 bound to duplex 5'-TAGTT sites.
Authors: Goodwin, K.D. / Lewis, M.A. / Long, E.C. / Georgiadis, M.M.
History
DepositionJul 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: reverse transcriptase
D: DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
G: DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)34,8753
Polymers34,8753
Non-polymers00
Water3,765209
1
A: reverse transcriptase
D: DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
G: DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')

A: reverse transcriptase
D: DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')
G: DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)69,7506
Polymers69,7506
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)55.126, 145.786, 46.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein reverse transcriptase


Mass: 30023.531 Da / Num. of mol.: 1 / Fragment: N-terminal fragment (UNP residues 683-937)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UN00
#2: DNA chain DNA (5'-D(*CP*TP*TP*AP*GP*TP*TP*A)-3')


Mass: 2416.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*AP*AP*CP*TP*AP*AP*G)-3')


Mass: 2434.643 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5 mM magnesium acetate, 50 mM ADA, pH 6.5, 9% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 32812 / % possible obs: 98.7 % / Redundancy: 5 % / Biso Wilson estimate: 22.42 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.062 / Net I/σ(I): 15.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.85-1.923.10.47229361.031190.5
1.92-1.994.20.33932081.037198.7
1.99-2.0850.25832691.096199.9
2.08-2.195.40.18932921.074199.9
2.19-2.335.50.14632881.073199.7
2.33-2.515.50.09732921.051199.9
2.51-2.765.50.06833150.9561100
2.76-3.165.40.04633261.0721100
3.16-3.995.30.03733751.054199.9
3.99-505.10.02235111.155198.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX(phenix.refine)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZTW

1ztw


Resolution: 1.849→43.968 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.06 / Phase error: 23.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1603 5.09 %
Rwork0.1997 29913 -
obs0.2017 31516 94.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.478 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 147.07 Å2 / Biso mean: 35.01 Å2 / Biso min: 6.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.2401 Å20 Å2-0 Å2
2--1.4009 Å2-0 Å2
3----3.641 Å2
Refinement stepCycle: final / Resolution: 1.849→43.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1945 325 0 211 2481
Biso mean---32.45 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062387
X-RAY DIFFRACTIONf_angle_d1.1013324
X-RAY DIFFRACTIONf_chiral_restr0.066371
X-RAY DIFFRACTIONf_plane_restr0.005373
X-RAY DIFFRACTIONf_dihedral_angle_d21.005915
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.849-1.90840.3521000.2803214976
1.9084-1.97660.31981330.2491250289
1.9766-2.05570.28111630.2208262494
2.0557-2.14930.25341380.2105273097
2.1493-2.26260.23691280.199277097
2.2626-2.40430.22771500.2027273297
2.4043-2.590.26351560.2012280098
2.59-2.85050.25131560.2048281899
2.8505-3.26290.2121580.1993286499
3.2629-4.11050.23321640.17942892100
4.1105-43.9680.19841570.173303298

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