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- PDB-5awh: Rhodobacter sphaeroides Argonaute in complex with guide RNA/targe... -

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Basic information

Entry
Database: PDB / ID: 5awh
TitleRhodobacter sphaeroides Argonaute in complex with guide RNA/target DNA heteroduplex
Components
  • DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')
  • RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')
  • Uncharacterized protein
KeywordsRNA BINDING PROTEIN/DNA/RNA / Argonaute / RNA-guided DNA silencing / RNA BINDING PROTEIN-DNA-RNA complex
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
DNA / DNA (> 10) / RNA / RNA (> 10) / Protein argonaute
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMiyoshi, T. / Ito, K. / Murakami, R. / Uchiumi, T.
CitationJournal: Nat Commun / Year: 2016
Title: Structural basis for the recognition of guide RNA and target DNA heteroduplex by Argonaute.
Authors: Miyoshi, T. / Ito, K. / Murakami, R. / Uchiumi, T.
History
DepositionJul 3, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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
B: Uncharacterized protein
C: RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')
E: RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,8348
Polymers196,7856
Non-polymers492
Water11,458636
1
A: Uncharacterized protein
C: RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')
D: DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4174
Polymers98,3933
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8710 Å2
ΔGint-70 kcal/mol
Surface area35040 Å2
MethodPISA
2
B: Uncharacterized protein
E: RNA (5'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')
F: DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,4174
Polymers98,3933
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-72 kcal/mol
Surface area33540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.186, 118.303, 118.480
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uncharacterized protein / Argonaute


Mass: 87143.469 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 21-777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (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'-D(P*UP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*G)-3')


Mass: 5613.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*A)-3')


Mass: 5635.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 636 / 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: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.05 M sodium cacodylate trihydrlate (pH 7.0), 42% (v/v) 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 123866 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Χ2: 2.17 / Net I/av σ(I): 35.821 / Net I/σ(I): 15.3 / Num. measured all: 466156
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.033.80.41100
2.03-2.073.80.3341100
2.07-2.113.80.2971100
2.11-2.153.80.2521100
2.15-2.23.80.2131100
2.2-2.253.80.1811100
2.25-2.313.80.1591100
2.31-2.373.80.1381100
2.37-2.443.80.121100
2.44-2.523.80.1021100
2.52-2.613.80.091100
2.61-2.713.80.0811100
2.71-2.843.80.0741100
2.84-2.993.80.0661100
2.99-3.173.80.059199.9
3.17-3.423.80.055199.5
3.42-3.763.70.053198.1
3.76-4.313.60.05194.1
4.31-5.433.50.048188
5.43-503.40.047174.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.15data extraction
SHARPphasing
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→35.63 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.715 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.163 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 6232 5 %RANDOM
Rwork0.1842 ---
obs0.1866 117604 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 143.48 Å2 / Biso mean: 58.291 Å2 / Biso min: 27.72 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å2-0 Å20.12 Å2
2--3.85 Å2-0 Å2
3----1.15 Å2
Refinement stepCycle: final / Resolution: 2→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11669 1498 2 636 13805
Biso mean--40.06 52.47 -
Num. residues----1546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01813597
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212333
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.86218725
X-RAY DIFFRACTIONr_angle_other_deg0.968328346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.82751468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47722.532553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.51152049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.56815124
X-RAY DIFFRACTIONr_chiral_restr0.110.22031
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02114300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023214
X-RAY DIFFRACTIONr_mcbond_it2.873.3085890
X-RAY DIFFRACTIONr_mcbond_other2.873.3085889
X-RAY DIFFRACTIONr_mcangle_it3.9314.9457352
LS refinement shellResolution: 1.992→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 423 -
Rwork0.237 8259 -
all-8682 -
obs--92.25 %
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)
11.27880.04030.0750.8263-0.44360.90920.0445-0.1995-0.09080.094-0.0952-0.02050.007-0.13840.05070.1137-0.04410.01340.1036-0.03580.10175.7404-7.715646.603
21.48060.31620.78220.98220.95661.9125-0.08510.21120.0663-0.23180.02880.0823-0.36890.28160.05640.2102-0.0140.01970.09450.04650.104-10.00720.764-15.3335
30.9187-0.14690.05151.4688-0.38620.78580.1003-0.2116-0.1920.0097-0.1155-0.07210.139-0.20010.01520.1921-0.0582-0.01040.15530.00710.21185.1192-13.934744.2197
41.3440.2086-0.47010.72260.06391.18-0.0428-0.1319-0.14480.2-0.0107-0.08420.22-0.26030.05350.1339-0.05830.00290.1140.00650.09534.1714-13.925146.7185
52.22921.13291.01182.37951.30413.22120.04460.2602-0.2224-0.11780.01230.00520.0610.4877-0.05690.1540.07660.01830.1317-0.00580.0998-8.1318-6.741-14.6345
61.57940.25070.65411.52310.742.4493-0.01360.3364-0.086-0.23710.09420.07660.04550.6082-0.08070.14190.0570.02620.1922-0.01580.0455-7.2953-6.231-17.0531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 777
2X-RAY DIFFRACTION2B21 - 777
3X-RAY DIFFRACTION3C1 - 18
4X-RAY DIFFRACTION4D1 - 18
5X-RAY DIFFRACTION5E1 - 18
6X-RAY DIFFRACTION6F1 - 18

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