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- PDB-6d8p: Ternary RsAgo Complex Containing Guide RNA Paired with Target DNA -

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Basic information

Entry
Database: PDB / ID: 6d8p
TitleTernary RsAgo Complex Containing Guide RNA Paired with Target DNA
Components
  • DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')
  • RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
  • Uncharacterized protein
KeywordsRNA BINDING PROTEIN / Rhodobacter sphaerodes Argounaute (RsAgo) / guide RNA / target DNA / RNA-DNA heteroduplex / non-canonical base pairs and bulges
Function / homology
Function and homology information


clearance of foreign intracellular DNA / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain / Piwi domain profile. / Piwi domain / Piwi / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / DNA / DNA (> 10) / RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
Rhodobacter sphaeroides ATCC 17025 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLiu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Patel, D.J.
CitationJournal: Cell Rep / Year: 2018
Title: Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.
Authors: Liu, Y. / Esyunina, D. / Olovnikov, I. / Teplova, M. / Kulbachinskiy, A. / Aravin, A.A. / Patel, D.J.
History
DepositionApr 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
E: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
J: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')
B: Uncharacterized protein
C: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,31238
Polymers204,2956
Non-polymers2,01732
Water12,971720
1
A: Uncharacterized protein
E: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
J: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,59027
Polymers102,1483
Non-polymers1,44224
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-97 kcal/mol
Surface area33780 Å2
MethodPISA
2
B: Uncharacterized protein
C: RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')
G: DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,72211
Polymers102,1483
Non-polymers5758
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10330 Å2
ΔGint-75 kcal/mol
Surface area33230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.234, 119.216, 117.648
Angle α, β, γ (deg.)90.000, 95.620, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein / RNA chain / DNA chain , 3 types, 6 molecules ABECJG

#1: Protein Uncharacterized protein


Mass: 89038.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) (bacteria)
Strain: ATCC 17025 / ATH 2.4.3 / Gene: Rsph17025_3694 / Production host: Escherichia coli (E. coli) / References: UniProt: A4WYU7
#2: RNA chain RNA (5'-R(P*UP*UP*AP*CP*UP*GP*CP*AP*CP*AP*GP*GP*UP*GP*AP*CP*GP*A)-3')


Mass: 5772.491 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)
#3: DNA chain DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*TP*AP*AP*C)-3')


Mass: 7336.728 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)

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Non-polymers , 5 types, 752 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6AsO2
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 720 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 40% MPD, 30 mM magnesium acetate, 50 mM sodium cacodylate pH 5.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 101956 / % possible obs: 93.5 % / Redundancy: 3.4 % / Net I/σ(I): 27.1
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.1→42.336 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.2348 5085 4.99 %
Rwork0.1816 --
obs0.1843 101921 93.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.02 Å2 / Biso mean: 36.73 Å2 / Biso min: 12.62 Å2
Refinement stepCycle: final / Resolution: 2.1→42.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11551 1566 115 720 13952
Biso mean--68.69 37 -
Num. residues----1585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813697
X-RAY DIFFRACTIONf_angle_d1.218943
X-RAY DIFFRACTIONf_chiral_restr0.0782166
X-RAY DIFFRACTIONf_plane_restr0.0052205
X-RAY DIFFRACTIONf_dihedral_angle_d16.6265094
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1002-2.12410.32431300.24552722285279
2.1241-2.14910.31561600.23372898305884
2.1491-2.17530.28871640.23012961312586
2.1753-2.20280.27091630.22623008317187
2.2028-2.23180.27761410.23423080322190
2.2318-2.26240.31211440.23693141328590
2.2624-2.29470.3061750.2253136331191
2.2947-2.3290.28391570.22343127328492
2.329-2.36540.29041640.22693153331791
2.3654-2.40410.31571470.21353185333292
2.4041-2.44560.31661610.2043150331191
2.4456-2.490.2661810.21133172335393
2.49-2.53790.261650.20683223338892
2.5379-2.58970.28361720.20553187335994
2.5897-2.6460.26881760.2023187336393
2.646-2.70760.26231760.20753241341794
2.7076-2.77530.29561570.2143250340794
2.7753-2.85030.28541590.21213300345995
2.8503-2.93410.27661970.21413312350997
2.9341-3.02880.27131820.20993315349797
3.0288-3.13710.25941820.20353384356698
3.1371-3.26260.24961840.19363375355998
3.2626-3.4110.23331800.18113421360198
3.411-3.59080.2211880.16913376356499
3.5908-3.81560.20061820.15953422360499
3.8156-4.110.20731680.15333412358099
4.11-4.52320.18671740.13493465363999
4.5232-5.17670.17871980.14193405360399
5.1767-6.51830.20531910.17183463365499
6.5183-42.34480.21251670.1713365353295
Refinement TLS params.Method: refined / Origin x: 7.6656 Å / Origin y: -26.7551 Å / Origin z: 31.0675 Å
111213212223313233
T0.1438 Å2-0.0304 Å20.0011 Å2-0.1938 Å20.03 Å2--0.1613 Å2
L0.124 °20.0292 °20.0232 °2-0.3085 °20.1017 °2--0.1933 °2
S0.0553 Å °-0.0546 Å °-0.0134 Å °0.0822 Å °-0.074 Å °-0.0383 Å °0.035 Å °-0.1163 Å °0.0005 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA20 - 777
2X-RAY DIFFRACTION1allE1 - 18
3X-RAY DIFFRACTION1allF1
4X-RAY DIFFRACTION1allJ-13 - 5
5X-RAY DIFFRACTION1allB20 - 777
6X-RAY DIFFRACTION1allC1 - 18
7X-RAY DIFFRACTION1allD1 - 10
8X-RAY DIFFRACTION1allG-14 - 5
9X-RAY DIFFRACTION1allI1 - 882
10X-RAY DIFFRACTION1allH2 - 21
11X-RAY DIFFRACTION1allK1 - 4
12X-RAY DIFFRACTION1allL1

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