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- PDB-6d92: Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-... -

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Basic information

Entry
Database: PDB / ID: 6d92
TitleTernary RsAgo Complex with Guide RNA and Target DNA Containing A-A non-canonical pair at position 3
Components
  • DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')
  • DNA (5'-D(P*TP*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*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 / 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: 1.81 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 27, 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
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*AP*AP*AP*C)-3')
F: Uncharacterized protein
H: 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*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,23813
Polymers201,8356
Non-polymers4037
Water15,277848
1
A: 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*AP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7436
Polymers100,6013
Non-polymers1423
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9270 Å2
ΔGint-66 kcal/mol
Surface area34150 Å2
MethodPISA
2
F: Uncharacterized protein
H: 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*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4957
Polymers101,2343
Non-polymers2614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-69 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.237, 118.942, 118.559
Angle α, β, γ (deg.)90.000, 95.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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DNA chain , 2 types, 2 molecules GJ

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


Mass: 5789.762 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)
#4: DNA chain DNA (5'-D(P*TP*GP*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*TP*GP*CP*AP*GP*AP*AP*AP*C)-3')


Mass: 6423.161 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)

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Protein / RNA chain , 2 types, 4 molecules AFCH

#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)

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Non-polymers , 4 types, 855 molecules

#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 848 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
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: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.81→70 Å / Num. obs: 160184 / % possible obs: 93.8 % / Redundancy: 4.3 % / Net I/σ(I): 15.8
Reflection shellResolution: 1.81→1.87 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.81→42.81 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.377 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.138
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 8084 5 %RANDOM
Rwork0.1975 ---
obs0.1996 152066 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 133.36 Å2 / Biso mean: 40.667 Å2 / Biso min: 19.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å2-0.17 Å2
2--0.88 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.81→42.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11684 1589 26 848 14147
Biso mean--60.67 43.69 -
Num. residues----1592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01813745
X-RAY DIFFRACTIONr_bond_other_d0.0030.0212195
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.85619013
X-RAY DIFFRACTIONr_angle_other_deg0.901327936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.31751516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.34722.576528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.518151905
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11115114
X-RAY DIFFRACTIONr_chiral_restr0.090.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023248
LS refinement shellResolution: 1.809→1.855 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 534 -
Rwork0.35 10361 -
all-10895 -
obs--86.05 %

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