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- PDB-7uyo: Crystal structure of B-form alien DNA 5'-CTTSSPBZPSZBBAAG in a ho... -

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Basic information

Entry
Database: PDB / ID: 7uyo
TitleCrystal structure of B-form alien DNA 5'-CTTSSPBZPSZBBAAG in a host-guest complex with the N-terminal fragment of Moloney murine leukemia virus reverse transcriptase
Components
  • DNA (5'-D(*CP*TP*TP*(JSP)P*(JSP)P*(1WA)P*(IGU)P*(1W5))-3')
  • DNA (5'-D(P*(1WA)P*(JSP)P*(1W5)P*(IGU)P*(IGU)P*AP*AP*G)-3')
  • reverse transcriptase
KeywordsDNA BINDING PROTEIN/DNA / unnatural DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


host cell late endosome membrane / virion assembly / virion component / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination ...host cell late endosome membrane / virion assembly / virion component / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / structural constituent of virion / 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 / plasma 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. / 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 / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain 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 / Resolution: 1.65 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)193908 United States
CitationJournal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2023
Title: Crystal structures of 'ALternative Isoinformational ENgineered' DNA in B-form.
Authors: Shukla, M.S. / Hoshika, S. / Benner, S.A. / Georgiadis, M.M.
History
DepositionMay 6, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(JSP)P*(JSP)P*(1WA)P*(IGU)P*(1W5))-3')
G: DNA (5'-D(P*(1WA)P*(JSP)P*(1W5)P*(IGU)P*(IGU)P*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)35,0133
Polymers35,0133
Non-polymers00
Water2,774154
1
A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(JSP)P*(JSP)P*(1WA)P*(IGU)P*(1W5))-3')
G: DNA (5'-D(P*(1WA)P*(JSP)P*(1W5)P*(IGU)P*(IGU)P*AP*AP*G)-3')

A: reverse transcriptase
B: DNA (5'-D(*CP*TP*TP*(JSP)P*(JSP)P*(1WA)P*(IGU)P*(1W5))-3')
G: DNA (5'-D(P*(1WA)P*(JSP)P*(1W5)P*(IGU)P*(IGU)P*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)70,0266
Polymers70,0266
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_475-x-1,-y+2,z1
Unit cell
Length a, b, c (Å)55.305, 145.928, 46.904
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*(JSP)P*(JSP)P*(1WA)P*(IGU)P*(1W5))-3')


Mass: 2452.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*(1WA)P*(JSP)P*(1W5)P*(IGU)P*(IGU)P*AP*AP*G)-3')


Mass: 2536.696 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.05 M 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: 31-ID / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.65→145.93 Å / Num. obs: 46528 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.022 / Rrim(I) all: 0.055 / Net I/σ(I): 17 / Num. measured all: 301349 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.65-1.686.70.8511537323020.7670.3520.9222.299.9
9.04-145.935.40.0418583410.9980.0180.0433597.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MIK

6mik


Resolution: 1.65→27.652 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 2236 4.81 %
Rwork0.2266 44207 -
obs0.2281 46443 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.26 Å2 / Biso mean: 41.938 Å2 / Biso min: 17.8 Å2
Refinement stepCycle: final / Resolution: 1.65→27.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1982 334 0 154 2470
Biso mean---36.58 -
Num. residues----263
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.68590.33621230.29672753100
1.6859-1.72510.28751550.26542693100
1.7251-1.76820.26311500.24442705100
1.7682-1.8160.32761400.22782730100
1.816-1.86950.26561370.2452728100
1.8695-1.92980.26781150.2342734100
1.9298-1.99870.261360.23082748100
1.9987-2.07870.28011160.23982781100
2.0787-2.17330.30161410.2332271499
2.1733-2.28780.25321330.23182763100
2.2878-2.43110.24721420.23582765100
2.4311-2.61870.23121500.23122769100
2.6187-2.8820.28341350.2471276099
2.882-3.29840.2861490.23492808100
3.2984-4.15340.23991660.221279699
4.1534-27.6520.23611480.203296099

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