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- PDB-6tju: X-ray structure of C-terminal domain of human T-cell lymphotropic... -

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Basic information

Entry
Database: PDB / ID: 6tju
TitleX-ray structure of C-terminal domain of human T-cell lymphotropic virus type 1 (HTLV-1)
ComponentsPol protein
KeywordsTRANSFERASE / HTLV-1 / integrase / deltaretrovirus / DNA-binding
Function / homology
Function and homology information


DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / DNA recombination / nucleic acid binding / zinc ion binding
Similarity search - Function
Integrase Zinc binding domain / 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. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. ...Integrase Zinc binding domain / 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. / 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. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman T-cell leukemia virus type I
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBarski, M. / Maertens, G.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust107005 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of the deltaretroviral intasome in complex with the PP2A regulatory subunit B56γ.
Authors: Michał S Barski / Jordan J Minnell / Zuzana Hodakova / Valerie E Pye / Andrea Nans / Peter Cherepanov / Goedele N Maertens /
Abstract: Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor ...Human T-cell lymphotropic virus type 1 (HTLV-1) is a deltaretrovirus and the most oncogenic pathogen. Many of the ~20 million HTLV-1 infected people will develop severe leukaemia or an ALS-like motor disease, unless a therapy becomes available. A key step in the establishment of infection is the integration of viral genetic material into the host genome, catalysed by the retroviral integrase (IN) enzyme. Here, we use X-ray crystallography and single-particle cryo-electron microscopy to determine the structure of the functional deltaretroviral IN assembled on viral DNA ends and bound to the B56γ subunit of its human host factor, protein phosphatase 2 A. The structure reveals a tetrameric IN assembly bound to two molecules of the phosphatase via a conserved short linear motif. Insight into the deltaretroviral intasome and its interaction with the host will be crucial for understanding the pattern of integration events in infected individuals and therefore bears important clinical implications.
History
DepositionNov 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Pol protein


Theoretical massNumber of molelcules
Total (without water)7,6101
Polymers7,6101
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.408, 97.408, 97.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11AAA-109-

HOH

21AAA-129-

HOH

31AAA-141-

HOH

41AAA-143-

HOH

51AAA-147-

HOH

61AAA-154-

HOH

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Components

#1: Protein Pol protein


Mass: 7609.704 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human T-cell leukemia virus type I / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: A0A1Y1CAU9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.53 Å3/Da / Density % sol: 51.45 % / Description: rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.2 M ammonium tartrate dibasic, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→39.77 Å / Num. obs: 41483 / % possible obs: 100 % / Redundancy: 5.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.055 / Rrim(I) all: 0.095 / Χ2: 0.89 / Net I/σ(I): 7.4
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2513 / CC1/2: 0.354 / Rpim(I) all: 0.503

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Cootmodel building
PHASERphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LLJ

5llj


Resolution: 1.8→39.77 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.952 / SU B: 12.671 / SU ML: 0.144 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.117
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2464 418 5.489 %
Rwork0.1771 --
all0.181 --
obs-7615 99.987 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 51.44 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms425 0 0 57 482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.012441
X-RAY DIFFRACTIONr_bond_other_d0.0150.017398
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.637604
X-RAY DIFFRACTIONr_angle_other_deg1.471.569918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.055553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7142020
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.1051558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2153
X-RAY DIFFRACTIONr_chiral_restr0.0830.254
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02101
X-RAY DIFFRACTIONr_nbd_refined0.1870.261
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.2328
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2189
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2208
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.130.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.330.28
X-RAY DIFFRACTIONr_nbd_other0.2430.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.5440.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_mcbond_it8.0395.282218
X-RAY DIFFRACTIONr_mcbond_other7.9615.275217
X-RAY DIFFRACTIONr_mcangle_it9.277.853268
X-RAY DIFFRACTIONr_mcangle_other9.2927.858269
X-RAY DIFFRACTIONr_scbond_it8.0625.547223
X-RAY DIFFRACTIONr_scbond_other8.0465.553224
X-RAY DIFFRACTIONr_scangle_it9.3678.179335
X-RAY DIFFRACTIONr_scangle_other9.3548.186336
X-RAY DIFFRACTIONr_lrange_it10.22758.308478
X-RAY DIFFRACTIONr_lrange_other9.95757.139465
X-RAY DIFFRACTIONr_rigid_bond_restr4.7043837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.8470.37300.389518X-RAY DIFFRACTION100
1.847-1.8980.369320.351505X-RAY DIFFRACTION100
1.898-1.9530.4240.352487X-RAY DIFFRACTION100
1.953-2.0130.358220.315491X-RAY DIFFRACTION100
2.013-2.0790.312320.285457X-RAY DIFFRACTION100
2.079-2.1520.248340.257450X-RAY DIFFRACTION100
2.152-2.2330.386200.286430X-RAY DIFFRACTION100
2.233-2.3240.328310.233415X-RAY DIFFRACTION100
2.324-2.4270.223240.197397X-RAY DIFFRACTION100
2.427-2.5460.313170.194401X-RAY DIFFRACTION100
2.546-2.6830.396230.2366X-RAY DIFFRACTION100
2.683-2.8460.23180.187358X-RAY DIFFRACTION100
2.846-3.0420.333200.163338X-RAY DIFFRACTION100
3.042-3.2850.219170.15308X-RAY DIFFRACTION100
3.285-3.5980.169190.135291X-RAY DIFFRACTION100
3.598-4.0210.25150.123261X-RAY DIFFRACTION100
4.021-4.640.185120.11241X-RAY DIFFRACTION100
4.64-5.6770.187140.118203X-RAY DIFFRACTION100
5.677-8.0010.15990.161169X-RAY DIFFRACTION100
8.001-39.770.22250.229111X-RAY DIFFRACTION100

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