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- PDB-7thb: Crystal structure of an RNA-5'/DNA-3' strand exchange junction -

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Basic information

Entry
Database: PDB / ID: 7thb
TitleCrystal structure of an RNA-5'/DNA-3' strand exchange junction
Components
  • DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')
  • DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')
  • RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')
KeywordsDNA-RNA HYBRID / strand exchange junction / DNA / RNA / DNA:DNA duplex / RNA:DNA hybrid / A-form/B-form junction / nucleic acid
Function / homologyDNA / DNA (> 10) / RNA
Function and homology information
Biological speciesSynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsCofsky, J.C. / Knott, G.J. / Gee, C.L. / Doudna, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817593 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Plos One / Year: 2022
Title: Crystal structure of an RNA/DNA strand exchange junction.
Authors: Cofsky, J.C. / Knott, G.J. / Gee, C.L. / Doudna, J.A.
History
DepositionJan 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,8999
Polymers23,8999
Non-polymers00
Water1,20767
1
A: DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')
B: RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')
C: DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,9663
Polymers7,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-5 kcal/mol
Surface area4730 Å2
MethodPISA
2
D: DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')
E: RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')
F: DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,9663
Polymers7,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-6 kcal/mol
Surface area4740 Å2
MethodPISA
3
G: DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')
H: RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')
I: DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,9663
Polymers7,9663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-4 kcal/mol
Surface area4790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.025, 43.586, 52.182
Angle α, β, γ (deg.)92.056, 103.722, 99.952
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: DNA chain DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')


Mass: 3671.418 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#2: RNA chain RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')


Mass: 2181.355 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')


Mass: 2113.410 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.5 uL of sample was combined with 0.5 uL reservoir solution (0.05 M sodium succinate (pH 5.3), 0.5 mM spermine, 20 mM magnesium chloride, 2.6 M ammonium sulfate) over 500 uL reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.637→35.34 Å / Num. obs: 24808 / % possible obs: 64.7 % / Redundancy: 6 % / Biso Wilson estimate: 41.63 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Net I/σ(I): 15.641
Reflection shell

Num. unique obs: 1240 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Rpim(I) allRrim(I) all% possible all
5.089-35.3355.70.02844.80.9990.0130.03197.7
1.637-1.7816.31.2931.50.4740.5561.4114.5

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISO3.339data scaling
PHASERphasing
Coot0.9.2model building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: see methods in primary citation

Resolution: 1.64→35.34 Å / SU ML: 0.2983 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 50.1152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2841 1223 4.95 %
Rwork0.2369 23496 -
obs0.2391 24719 64.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.75 Å2
Refinement stepCycle: LAST / Resolution: 1.64→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1584 0 67 1651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01441770
X-RAY DIFFRACTIONf_angle_d1.41572721
X-RAY DIFFRACTIONf_chiral_restr0.0917324
X-RAY DIFFRACTIONf_plane_restr0.015978
X-RAY DIFFRACTIONf_dihedral_angle_d27.5301786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.70.218110.3798227X-RAY DIFFRACTION5.61
1.7-1.780.3861370.3721960X-RAY DIFFRACTION23.39
1.78-1.870.3895880.37871582X-RAY DIFFRACTION39.07
1.87-1.990.37721180.35182228X-RAY DIFFRACTION55.37
1.99-2.150.45241870.36732957X-RAY DIFFRACTION73.68
2.15-2.360.39942120.36923747X-RAY DIFFRACTION93.17
2.36-2.70.34391770.34643958X-RAY DIFFRACTION97.2
2.7-3.40.32532090.27743873X-RAY DIFFRACTION95.89
3.41-35.340.20831840.16683964X-RAY DIFFRACTION97.39
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)
14.7529823813-0.372657452220.9491749267673.69928184868-2.481106798675.969944776850.2683708054040.262244540666-0.373316695567-0.3682482664120.2143717158540.1544919948610.50277093202-1.09148730482-0.2889015581340.566157330094-0.01718240090650.06876777281850.748419770096-0.01037754923850.639716845416-18.1225574291-1.50308527387-3.58795662268
26.11145035390.4196545353840.6994827256423.63843868429-0.3832703453046.18570323076-0.3124817292931.209294864721.01830863588-0.812831481390.2320064499660.567013838137-0.12127404664-0.6637339068340.04400633776010.4834464808710.0010270333666-0.07447887468650.674500578860.2017931669990.650500978226-14.34690596199.63656249138-13.1167235645
34.38593741221-0.105067876890.01670206883092.53790497733-0.2551305622684.32580481528-0.3179397859710.3467725754680.368754691974-0.05702432777730.07835746902750.0146921165643-0.3087912874470.03633340480840.2345884416270.343033908794-0.07024698056-0.051903229550.4420640603750.001956501448870.4015561902831.272974442839.90586930685-12.7509583072
44.38280326680.00283842832748-0.2434775412673.73818357815-1.048481149054.717824784-0.0391453772129-0.3284853377740.234293061990.3665646232410.1228457096830.9650611686150.312924283607-1.72747580815-0.05953211809310.3237092001990.02272473402410.01091032720340.6337715426890.003435925794990.582047877496-18.51674659996.83466482627-2.91875749086
54.266283218910.515125916228-1.62651115433.53887534684-0.8100472903987.47418148355-0.1631508766431.11052700543-0.771675118683-0.5206052526590.3610227116280.2045552902210.986880073613-0.19223005811-0.2402391998660.3288347034110.01005602754930.008960330014460.431836415343-0.008819798431060.28418628478-2.974066265025.45630142131-13.1861777878
64.741896837921.52151898999-4.329757523946.846765972820.4140225443157.85663002406-0.595380242233-0.803010531859-0.8826447822770.6155371436850.320247205633-0.1195622955720.9458145106671.010065135510.280010296820.4447225813410.002834643899590.04926005204751.058051683310.3732858583550.82549644781514.0839924977-3.4076610679511.0070708341
72.559190714340.8139662259850.228302593640.272643311525-0.1730321390424.011520582830.15556428695-0.8594035476480.1492230172490.839859730881-0.151152644934-0.6811046513940.2336589499651.68713347921-0.01592377772330.613969798323-0.243737572328-0.1342503820141.511573789790.09948881262380.48245941234511.85171948524.5995790434423.5764264029
83.75661404447-1.1329541155-3.539081306593.44218759548-0.8918494161919.343522346730.163793692662-0.2325840962270.4878188388790.198064875242-0.0391017888863-0.048338259085-0.8158139188240.187049823582-0.1360713383610.5100236565050.01541309580760.02102463997060.501301905361-0.01879800466590.388675478258-3.89007998527.1164421362223.1914006539
94.83336547023-1.56398188569-1.848969308483.831701271620.4664020034790.7116293980650.380910167534-0.439136994677-0.1208993349740.03098346052940.214251349726-1.333726068780.009960330837321.91705313129-0.3498339101690.333800909291-0.0193029524574-0.02467249520621.07675536082-0.01501935917980.4472588347115.92093172924.3833670909912.892888703
104.332746946640.822190815889-4.250456445922.226066692521.234996453268.72810963836-0.236377241152-0.884794334477-0.3601673594470.441058423058-0.0881889969897-0.0333202552840.6719504591290.6801383234280.3577464263840.3323932036760.0260390001916-0.007443936001520.4367368863910.02767852890230.2463005844930.3104983590942.3976999480422.6701036808
113.98958901928-0.8363902622941.099517163065.35326444459-3.879039760414.20618197436-0.198205290399-0.767629653733-0.8796323541310.7758652665590.5093070267960.1590631120880.8989566293220.070544542142-0.218369623970.8039737180780.1663740131870.03106172316480.422405410481-0.06143050580740.683658744035-9.1530608973338.62888434266.98574733955
120.189235203794-0.1910898697-0.05809469269980.6030348905050.4243901096430.34624629195-0.3201344299170.0846486403428-0.448481409827-0.489941580461-0.08289258083920.268209909980.850179747328-0.2421189687880.237702402361.394075713760.504660381442-0.204681835332-0.229475448138-0.05396361824411.79980354828-8.6295622832426.0138170525-1.29777595189
132.11989524033-0.5121816362280.3315902255074.4228974007-2.909226485442.721081344240.6890587630430.309011106613-0.157074955935-0.766773053091-0.876637515263-0.325487110040.3393720000990.9700752061150.431284856191.517498458180.2103034071530.1501010126670.4459686325480.2352233021791.038887527143.6782870196917.10441000362.81463552575
140.880106626988-1.517908960730.02043985680542.70728030018-0.2648713949781.90304978810.009816271315540.279353997067-0.676478104015-0.752706230786-0.372903557358-0.2498474111360.8249724742560.3686737394140.1335659391030.5862966258970.1977042633290.07021174515490.08096304472710.07014742502481.01285189033-7.7107814389337.0906209647-1.0644603101
152.92580884672-2.286431698721.502609276722.14728844733-1.242190628623.565047713250.313444228077-0.7662412848130.118977763803-0.164313598261-0.642601426354-0.1432064057560.2474601256440.2168311675060.2308897643581.24009613490.1792617091840.0537096290520.457436101933-0.02524232381521.20704058711-0.930994245122.0657970345.99815581377
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:4)AA1 - 4
2X-RAY DIFFRACTION2(chain A and resid 5:8)AA5 - 8
3X-RAY DIFFRACTION3(chain A and resid 9:12)AA9 - 12
4X-RAY DIFFRACTION4(chain B and resid 1:7)BB1 - 7
5X-RAY DIFFRACTION5(chain C and resid 1:7)CC1 - 7
6X-RAY DIFFRACTION6(chain D and resid 1:4)DD1 - 4
7X-RAY DIFFRACTION7(chain D and resid 5:8)DD5 - 8
8X-RAY DIFFRACTION8(chain D and resid 9:12)DD9 - 12
9X-RAY DIFFRACTION9(chain E and resid 1:7)EE1 - 7
10X-RAY DIFFRACTION10(chain F and resid 1:7)FF1 - 7
11X-RAY DIFFRACTION11(chain G and resid 1:4)GG1 - 4
12X-RAY DIFFRACTION12(chain G and resid 5:8)GG5 - 8
13X-RAY DIFFRACTION13(chain G and resid 9:12)GG9 - 12
14X-RAY DIFFRACTION14(chain H and resid 1:7)HH1 - 7
15X-RAY DIFFRACTION15(chain I and resid 1:7)II1 - 7

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