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- PDB-6d9k: Ternary RsAgo Complex with Guide RNA and Target DNA Containing A-... -

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Basic information

Entry
Database: PDB / ID: 6d9k
TitleTernary RsAgo Complex with Guide RNA and Target DNA Containing A-G Non-canonical Pair
Components
  • DNA (5'-D(P*TP*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*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/RNA/DNA / guide RNA / target DNA / RNA-DNA heteroduplex / non-canonical base pairs and bulges / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


clearance of foreign intracellular DNA / DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 30, 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*GP*GP*CP*AP*GP*TP*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*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,80713
Polymers204,3456
Non-polymers4627
Water6,377354
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*GP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3746
Polymers102,1733
Non-polymers2023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9480 Å2
ΔGint-74 kcal/mol
Surface area33030 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*CP*GP*TP*CP*AP*CP*CP*TP*GP*GP*GP*CP*AP*GP*TP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4337
Polymers102,1733
Non-polymers2614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9700 Å2
ΔGint-73 kcal/mol
Surface area33240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.119, 119.130, 118.134
Angle α, β, γ (deg.)90.000, 95.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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

#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*GP*GP*CP*AP*GP*TP*AP*AP*C)-3')


Mass: 7361.741 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Rhodobacter sphaeroides ATCC 17025 (bacteria)

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Non-polymers , 4 types, 361 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. obs: 123233 / % possible obs: 97.4 % / Redundancy: 3.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.067 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.591 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.663 / % possible all: 90.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.362 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.168
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2416 6206 5 %RANDOM
Rwork0.1953 ---
obs0.1976 116985 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.34 Å2 / Biso mean: 54.031 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å2-0.41 Å2
2--1.97 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: final / Resolution: 2→43.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11482 1591 30 354 13457
Biso mean--62.46 51.9 -
Num. residues----1589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01813535
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211900
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.85318756
X-RAY DIFFRACTIONr_angle_other_deg0.949327218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.03251510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14822.566495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.667151797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.55715102
X-RAY DIFFRACTIONr_chiral_restr0.1050.22089
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114397
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023183
LS refinement shellResolution: 1.999→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 394 -
Rwork0.309 7744 -
all-8138 -
obs--87.26 %

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