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- PDB-7k9y: GsI-IIC RT Template-Switching Complex (twinned) -

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Basic information

Entry
Database: PDB / ID: 7k9y
TitleGsI-IIC RT Template-Switching Complex (twinned)
Components
  • DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')
  • RNA (5'-R(*U*UP*UP*UP*G)-3')
  • RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')
  • Trt
KeywordsRNA BINDING PROTEIN/RNA/DNA / Polymerase / Reverse transcriptase / RNA binding protein-RNA-DNA complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / defense response to virus / RNA binding
Similarity search - Function
RNA-directed DNA polymerase (reverse transcriptase), msDNA / Group II intron, maturase-specific / Group II intron reverse transcriptase/maturase / Group II intron, maturase-specific domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / Trt
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsStamos, J.L. / Lentzsch, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural basis for template switching by a group II intron-encoded non-LTR-retroelement reverse transcriptase.
Authors: Lentzsch, A.M. / Stamos, J.L. / Yao, J. / Russell, R. / Lambowitz, A.M.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trt
B: DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')
C: RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')
D: Trt
E: DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')
F: RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')
G: RNA (5'-R(*U*UP*UP*UP*G)-3')
H: RNA (5'-R(*U*UP*UP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,97515
Polymers115,6558
Non-polymers1,3197
Water0
1
A: Trt
B: DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')
C: RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')
G: RNA (5'-R(*U*UP*UP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5358
Polymers57,8284
Non-polymers7084
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-57 kcal/mol
Surface area23430 Å2
MethodPISA
2
D: Trt
E: DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')
F: RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')
H: RNA (5'-R(*U*UP*UP*UP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4397
Polymers57,8284
Non-polymers6123
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-40 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.380, 107.415, 71.973
Angle α, β, γ (deg.)90.000, 113.650, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARGAA2 - 4182 - 418
21ALAALAARGARGDD2 - 4182 - 418
12DCDCDCDCBB1 - 111 - 11
22DCDCDCDCEE1 - 111 - 11

NCS ensembles :
ID
1
2

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Components

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RNA chain , 2 types, 4 molecules CFGH

#3: RNA chain RNA (5'-R(*UP*UP*GP*CP*CP*UP*GP*GP*AP*G)-3')


Mass: 3193.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: RNA chain RNA (5'-R(*U*UP*UP*UP*G)-3')


Mass: 1524.912 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA chain , 2 types, 4 molecules ADBE

#1: Protein Trt


Mass: 49805.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: trt / Production host: Escherichia coli (E. coli) / References: UniProt: E2GM63
#2: DNA chain DNA (5'-D(*CP*TP*CP*CP*AP*GP*GP*CP*AP*AP*C)-3')


Mass: 3303.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 7 molecules

#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, sodium citrate tribasic dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11H+4/2L, -K, -L20.5
ReflectionResolution: 3.2→48.79 Å / Num. obs: 20707 / % possible obs: 99.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.033 / Rrim(I) all: 0.086 / Net I/σ(I): 15 / Num. measured all: 141221 / Scaling rejects: 22
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
3.2-3.4270.5812612037480.9490.2370.628399.8
9.05-48.7960.03255319230.9990.0140.03547.598

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AR3

6ar3


Resolution: 3.2→48.79 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 61.08 / SU ML: 0.491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3241 2073 10 %RANDOM
Rwork0.2705 ---
obs0.276 18631 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 231.34 Å2 / Biso mean: 115.561 Å2 / Biso min: 44.84 Å2
Baniso -1Baniso -2Baniso -3
1--119.13 Å2-0 Å2-90.83 Å2
2--69.39 Å20 Å2
3---49.74 Å2
Refinement stepCycle: final / Resolution: 3.2→48.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6898 1016 77 0 7991
Biso mean--123.15 --
Num. residues----893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0128258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177380
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.58911354
X-RAY DIFFRACTIONr_angle_other_deg1.2011.68417038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8316.0691066
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.35319.227440
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.332151312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1361597
X-RAY DIFFRACTIONr_chiral_restr0.0620.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028431
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021923
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A135350.11
12D135350.11
21B9220.04
22E9220.04
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 182 -
Rwork0.331 1336 -
all-1518 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.8381.50060.48190.6260.06510.599-0.0528-0.2690.0253-0.11-0.1747-0.05020.11590.14330.22760.5390.06730.23410.2671-0.01480.2074-102.80639.6083-16.8361
21.08740.34770.95690.9760.03582.26280.33450.1745-0.4349-0.06770.079-0.08520.20240.2369-0.41350.60750.06940.0910.2035-0.14030.3396-98.894816.6385-26.264
34.95180.40051.95491.30471.09721.46670.1355-0.28150.28320.1259-0.1311-0.11820.1154-0.1836-0.00450.3993-0.03120.12230.1275-0.06470.1045-133.039921.5626-43.9415
42.8217-0.37741.71310.1703-0.46861.5720.0851.13170.23560.3261-0.16640.0263-0.5580.73660.08141.034-0.02370.19750.5531-0.08970.4006-110.288834.7352-34.2989
54.2631-0.93491.65330.72760.15894.2619-0.24210.36840.1493-0.082-0.05750.04-0.28030.18470.29950.356-0.03760.06620.0733-0.04290.1355-110.47435.8059-33.8437
62.92061.04450.35070.46490.09190.104-0.00230.1593-0.0240.0015-0.0571-0.1404-0.1183-0.01190.05940.70550.06010.11830.29930.11690.2422-130.17451.4941-68.3719
70.19020.0469-0.00450.77990.70.668-0.22180.16350.218-0.1467-0.15710.36620.0266-0.14530.3790.6739-0.0240.01380.35460.2850.6713-129.861620.1906-75.4056
85.1777-1.00170.81070.759-0.71250.79950.1605-0.23780.2353-0.12680.03650.1790.03090.1131-0.19690.2801-0.0890.08670.1674-0.02250.1604-97.997120.9195-66.1845
90.62791.3688-0.35433.4466-0.51510.458-0.19490.12720.1595-0.3272-0.13130.84740.1791-0.05910.32610.8249-0.089-0.00040.8512-0.09380.777-111.85513.7056-73.6593
105.112-0.18793.7991.1842-0.24513.0855-0.0940.5402-0.1073-0.04580.3079-0.25550.14010.1703-0.2140.3785-0.1943-0.00790.3120.03190.1993-112.41383.0151-72.7252
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 91
2X-RAY DIFFRACTION2A92 - 300
3X-RAY DIFFRACTION2A501
4X-RAY DIFFRACTION2A503
5X-RAY DIFFRACTION3A301 - 426
6X-RAY DIFFRACTION4B1 - 11
7X-RAY DIFFRACTION5C1 - 10
8X-RAY DIFFRACTION5G2 - 5
9X-RAY DIFFRACTION6D2 - 108
10X-RAY DIFFRACTION7D109 - 236
11X-RAY DIFFRACTION7D501
12X-RAY DIFFRACTION7D503
13X-RAY DIFFRACTION8D237 - 419
14X-RAY DIFFRACTION9E1 - 11
15X-RAY DIFFRACTION10F1 - 10
16X-RAY DIFFRACTION10H2 - 5

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