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- PDB-7sr6: Human Endogenous Retrovirus (HERV-K) reverse transcriptase ternar... -

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Basic information

Entry
Database: PDB / ID: 7sr6
TitleHuman Endogenous Retrovirus (HERV-K) reverse transcriptase ternary complex with dsDNA template Primer and dNTP
Components
  • DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')
  • Polymerase
KeywordsREPLICATION / reverse transcriptase RT dCTP dTTP dsDNA template primer
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase activity / DNA-templated DNA replication / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / metal ion binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily ...Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / 1,4-DIETHYLENE DIOXIDE / : / Chem-PG6 / THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / Polymerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.62 Å
AuthorsBaldwin, E.T. / Nichols, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT) structure and biochemistry reveals remarkable similarities to HIV-1 RT and opportunities for HERV-K-specific inhibition.
Authors: Baldwin, E.T. / Gotte, M. / Tchesnokov, E.P. / Arnold, E. / Hagel, M. / Nichols, C. / Dossang, P. / Lamers, M. / Wan, P. / Steinbacher, S. / Romero, D.L.
History
DepositionNov 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polymerase
B: Polymerase
D: DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')
E: DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')
F: Polymerase
G: Polymerase
H: DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')
I: DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,82871
Polymers308,2948
Non-polymers5,53563
Water5,116284
1
A: Polymerase
B: Polymerase
D: DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')
E: DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,76134
Polymers154,1474
Non-polymers2,61430
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18040 Å2
ΔGint11 kcal/mol
Surface area49750 Å2
MethodPISA
2
F: Polymerase
G: Polymerase
H: DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')
I: DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,06837
Polymers154,1474
Non-polymers2,92133
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18360 Å2
ΔGint-22 kcal/mol
Surface area49490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.697, 177.697, 117.414
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABFG

#1: Protein
Polymerase


Mass: 70136.945 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: V9H0F6

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DNA chain , 2 types, 4 molecules DHEI

#2: DNA chain DNA (5'-D(P*GP*GP*GP*AP*CP*CP*TP*GP*AP*AP*AP*GP*CP*GP*AP*AP*AP*GP*GP*GP*AP*AP*A)-3')


Mass: 7510.884 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*TP*TP*TP*CP*CP*CP*TP*TP*TP*CP*GP*CP*TP*TP*TP*CP*AP*GP*GP*T)-3')


Mass: 6362.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 9 types, 347 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#6: Chemical...
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C4H8O2
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: K
#9: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#10: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG400, 50 mM MES pH 6.0, 2 mM MgCl2 and 100 mM KCl)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.49993 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.49993 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11-h,-k,l20.501
ReflectionResolution: 2.62→88.9 Å / Num. obs: 114382 / % possible obs: 91.8 % / Redundancy: 10.7 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 17.6
Reflection shellResolution: 2.62→2.71 Å / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2 / Num. unique obs: 5724 / CC1/2: 0.78 / Rpim(I) all: 0.35 / % possible all: 49.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.62→88.848 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.303 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.052
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 5628 4.92 %RANDOM
Rwork0.1679 108753 --
all0.17 ---
obs-114381 91.771 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.451 Å20 Å20 Å2
2--3.451 Å20 Å2
3----6.902 Å2
Refinement stepCycle: LAST / Resolution: 2.62→88.848 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15773 1770 343 284 18170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01318617
X-RAY DIFFRACTIONr_bond_other_d0.0320.01517056
X-RAY DIFFRACTIONr_ext_dist_refined_d0.0070.0125452
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.65725579
X-RAY DIFFRACTIONr_angle_other_deg2.1921.5739437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4055.4842460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27723.441741
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.146152760
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg28.154152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5521570
X-RAY DIFFRACTIONr_chiral_restr0.1350.2072686
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0221694
X-RAY DIFFRACTIONr_gen_planes_other0.0170.023885
X-RAY DIFFRACTIONr_nbd_refined0.2260.24241
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2390.216538
X-RAY DIFFRACTIONr_nbtor_refined0.1840.28680
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.28206
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.2524
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1360.222
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.216
X-RAY DIFFRACTIONr_nbd_other0.3580.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.23
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_paralell_plane_angle_deg6.0490.6104
X-RAY DIFFRACTIONr_mcbond_it6.926.9898033
X-RAY DIFFRACTIONr_mcbond_other6.9196.9898032
X-RAY DIFFRACTIONr_mcangle_it9.64910.49510052
X-RAY DIFFRACTIONr_mcangle_other9.64910.49510053
X-RAY DIFFRACTIONr_scbond_it7.2977.3810584
X-RAY DIFFRACTIONr_scbond_other7.2977.3810584
X-RAY DIFFRACTIONr_scangle_it10.00411.03115523
X-RAY DIFFRACTIONr_scangle_other10.00411.0315524
X-RAY DIFFRACTIONr_lrange_it14.394167.2646092
X-RAY DIFFRACTIONr_lrange_other14.395167.29246076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.6880.2922210.2064024X-RAY DIFFRACTION45.9565
2.688-2.7620.3362140.2095938X-RAY DIFFRACTION68.6991
2.762-2.8420.273960.1896635X-RAY DIFFRACTION80.2717
2.842-2.9290.274270.1797324X-RAY DIFFRACTION91.8256
2.929-3.0250.2413980.1817860X-RAY DIFFRACTION99.9516
3.025-3.1310.2543700.1877606X-RAY DIFFRACTION100
3.131-3.2490.253600.1867271X-RAY DIFFRACTION100
3.249-3.3820.2694180.1876988X-RAY DIFFRACTION100
3.382-3.5320.2163020.1956782X-RAY DIFFRACTION99.9859
3.532-3.7040.2543200.1886451X-RAY DIFFRACTION100
3.704-3.9040.2243260.1786099X-RAY DIFFRACTION99.9689
3.904-4.140.2153300.1675768X-RAY DIFFRACTION100
4.14-4.4250.192960.155415X-RAY DIFFRACTION100
4.425-4.7790.1952760.1415066X-RAY DIFFRACTION100
4.779-5.2340.1922130.1434687X-RAY DIFFRACTION100
5.234-5.8490.1812450.1594182X-RAY DIFFRACTION100
5.849-6.750.231860.173717X-RAY DIFFRACTION100
6.75-8.2560.1991360.1493178X-RAY DIFFRACTION100
8.256-11.630.1641340.1262440X-RAY DIFFRACTION99.9612

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