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- PDB-9d4s: Structure of G2L4 RT in complex with 15 nucleotide snapback substrate -

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Basic information

Entry
Database: PDB / ID: 9d4s
TitleStructure of G2L4 RT in complex with 15 nucleotide snapback substrate
Components
  • DNA
  • Group II intron-like 4 reverse transcriptase
KeywordsDNA BINDING PROTEIN / Reverse transcriptase / Microhomology-Mediated End-Joining / DNA repair.
Function / homology2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10)
Function and homology information
Biological speciesGammaproteobacteria (g-proteobacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsGuo, M. / Zhang, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35148356 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Structural basis for the evolution of a domesticated group II intron-like reverse transcriptase to function in host cell DNA repair.
Authors: Park, S.K. / Guo, M. / Stamos, J.L. / Kim, W. / Lee, S. / Zhang, Y.J. / Lambowitz, A.M.
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Group II intron-like 4 reverse transcriptase
C: DNA
B: Group II intron-like 4 reverse transcriptase
P: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3028
Polymers102,2584
Non-polymers1,0444
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12710 Å2
ΔGint-39 kcal/mol
Surface area37810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.398, 99.190, 157.276
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Group II intron-like 4 reverse transcriptase


Mass: 45650.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Genbank Accession:WP_071557413 REFERENCE 1 (residues 1 to 415) AUTHORS Xiong,Y. and Eickbush,T.H. TITLE Origin and evolution of retroelements based upon their reverse transcriptase sequences ...Details: Genbank Accession:WP_071557413 REFERENCE 1 (residues 1 to 415) AUTHORS Xiong,Y. and Eickbush,T.H. TITLE Origin and evolution of retroelements based upon their reverse transcriptase sequences JOURNAL EMBO J 9 (10), 3353-3362 (1990)
Source: (gene. exp.) Gammaproteobacteria (g-proteobacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: DNA chain DNA


Mass: 5478.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: 15 nucleotides single strand DNA / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 25% PEG3350, 0.2M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 18, 2022
RadiationMonochromator: Double-crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. obs: 26710 / % possible obs: 99.4 % / Redundancy: 7.2 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Χ2: 0.603 / Net I/σ(I): 3.6 / Num. measured all: 192211
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.77-2.826.80.83613190.7820.9370.3390.9040.41699.3
2.82-2.876.40.73512890.780.9360.3080.80.41599.2
2.87-2.926.60.70113100.7950.9410.290.760.42899.1
2.92-2.987.50.62613300.880.9680.2410.6720.41899.8
2.98-3.057.60.53813040.8910.9710.2070.5770.43599.8
3.05-3.127.50.42713350.9430.9850.1650.4580.44699.8
3.12-3.27.60.38612970.9460.9860.1490.4140.45299.7
3.2-3.287.40.31813500.9590.990.1230.3410.45899.6
3.28-3.387.50.26712920.9720.9930.1030.2870.483100
3.38-3.497.40.22413330.9790.9950.0870.2410.52299.2
3.49-3.617.30.18513220.9840.9960.0720.1990.55499.3
3.61-3.766.50.16312920.9780.9940.0680.1770.5999.3
3.76-3.937.20.14413460.990.9980.0560.1550.62699
3.93-4.147.70.12513420.9920.9980.0480.1340.73699.9
4.14-4.47.60.10813410.9930.9980.0420.1160.81999.8
4.4-4.747.50.113490.9940.9980.0390.1080.90299.6
4.74-5.217.20.09913370.9930.9980.0390.1070.85799
5.21-5.966.60.09713690.9920.9980.0390.1050.71599
5.96-7.517.40.08113870.9960.9990.0310.0870.752100
7.51-506.60.05214660.99810.0210.0570.96398.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→47.3 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2765 1963 7.5 %
Rwork0.2353 --
obs0.2384 26164 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.77→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6415 592 0 7 7014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117171
X-RAY DIFFRACTIONf_angle_d1.5029777
X-RAY DIFFRACTIONf_dihedral_angle_d17.3982721
X-RAY DIFFRACTIONf_chiral_restr0.0931099
X-RAY DIFFRACTIONf_plane_restr0.0381167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.830.33471310.31261582X-RAY DIFFRACTION91
2.84-2.910.41791380.31751657X-RAY DIFFRACTION95
2.91-30.37461360.30731695X-RAY DIFFRACTION96
3-3.090.32761340.27671681X-RAY DIFFRACTION97
3.09-3.20.31881400.25971707X-RAY DIFFRACTION98
3.2-3.330.36661390.26351715X-RAY DIFFRACTION98
3.33-3.480.31181380.26251719X-RAY DIFFRACTION98
3.48-3.670.31391390.24941735X-RAY DIFFRACTION98
3.67-3.90.31211390.23721712X-RAY DIFFRACTION98
3.9-4.20.29081440.22341761X-RAY DIFFRACTION99
4.2-4.620.23211420.19991771X-RAY DIFFRACTION99
4.62-5.290.23471420.22141771X-RAY DIFFRACTION99
5.29-6.660.25561470.23471799X-RAY DIFFRACTION98
6.66-47.30.19851540.19481896X-RAY DIFFRACTION99

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