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

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Basic information

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


host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase activity / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination ...host cell late endosome membrane / virion assembly / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / telomerase 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 / Resolution: 1.65 Å
AuthorsGeorgiadis, M.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1939086 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*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
G: DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)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*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')
G: DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')

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


Theoretical massNumber of molelcules
Total (without water)70,0266
Polymers70,0266
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_475-x-1,-y+2,z1
Unit cell
Length a, b, c (Å)54.854, 146.480, 46.656
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-391-

HOH

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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*(IGU)P*(1WA)P*(1WA)P*(IGU)P*(IGU))-3')


Mass: 2502.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*(JSP)P*(JSP)P*(1W5)P*(1W5)P*(JSP)P*AP*AP*G)-3')


Mass: 2486.672 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.: 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: 2.68 Å3/Da / Density % sol: 54.05 %
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→73.24 Å / Num. obs: 46199 / % possible obs: 99.9 % / Redundancy: 12.5 % / Biso Wilson estimate: 24.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 14.7 / Num. measured all: 578693 / Scaling rejects: 215
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.65-1.6811.61.3392610722550.6970.4081.4022.3
9.04-73.2410.30.05835943490.9970.0170.0629.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MIK

6mik


Resolution: 1.65→30.46 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2213 4.8 %
Rwork0.2221 43915 -
obs0.2233 46128 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.37 Å2 / Biso mean: 33.2227 Å2 / Biso min: 13.31 Å2
Refinement stepCycle: final / Resolution: 1.65→30.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1989 334 0 154 2477
Biso mean---30.28 -
Num. residues----264
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.690.37191170.358827192836
1.69-1.730.31421580.304226992857
1.73-1.770.30571410.277826882829
1.77-1.820.29921440.248727082852
1.82-1.870.30981250.24827102835
1.87-1.930.22311210.233927312852
1.93-20.26911310.227227142845
2-2.080.27511240.235727292853
2.08-2.170.26031340.223627352869
2.17-2.290.24231290.218927312860
2.29-2.430.28561460.221827312877
2.43-2.620.2311480.224927532901
2.62-2.880.29271360.242127672903
2.88-3.30.27441490.236727532902
3.3-4.150.21731620.203927882950
4.16-30.460.20071480.193529593107

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