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- PDB-1r6z: The Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion) -

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Basic information

Entry
Database: PDB / ID: 1r6z
TitleThe Crystal Structure of the Argonaute2 PAZ domain (as a MBP fusion)
ComponentsChimera of Maltose-binding periplasmic protein and Argonaute 2
KeywordsGENE REGULATION / deviant OB fold / RNAi
Function / homology
Function and homology information


detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
paz domain / paz domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Beta Complex / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...paz domain / paz domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Beta Complex / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / NICKEL (II) ION / : / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Drosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSong, J.J. / Liu, J. / Tolia, N.H. / Schneiderman, J. / Smith, S.K. / Martienssen, R.A. / Hannon, G.J. / Joshua-Tor, L.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes.
Authors: Song, J.J. / Liu, J. / Tolia, N.H. / Schneiderman, J. / Smith, S.K. / Martienssen, R.A. / Hannon, G.J. / Joshua-Tor, L.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Chimera of Maltose-binding periplasmic protein and Argonaute 2
A: Chimera of Maltose-binding periplasmic protein and Argonaute 2
Z: Chimera of Maltose-binding periplasmic protein and Argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,95615
Polymers169,4013
Non-polymers1,55512
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
P: Chimera of Maltose-binding periplasmic protein and Argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9855
Polymers56,4671
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Chimera of Maltose-binding periplasmic protein and Argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9855
Polymers56,4671
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
Z: Chimera of Maltose-binding periplasmic protein and Argonaute 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9855
Polymers56,4671
Non-polymers5184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.811, 89.811, 380.326
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chimera of Maltose-binding periplasmic protein and Argonaute 2 / Maltodextrin-binding protein / MMBP / CG7439-PB


Mass: 56466.988 Da / Num. of mol.: 3
Fragment: MBP (residues 28-392) fused with Argonaute2 PAZ domain (residues 591-726)
Source method: isolated from a genetically manipulated source
Details: The construct is a fusion of E.coli MBP (residues 28-392) and D.melanogaster Argonaute2 PAZ domain (residues 591-726).
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Drosophila melanogaster (fruit fly)
Genus: Escherichia, Drosophila / Species: , / Strain: , / Gene: MALE, Argonaute 2 CG7439-PB / Plasmid: modified pMAL_c2x / Production host: Escherichia coli (E. coli) / Strain (production host): BL21RIL
References: UniProt: P02928, GenBank: 23093413, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG2KMME, NiCl2, TrisHCl, NaF, meso-erythritol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %(w/v)PEG2000 MME1reservoir
210 mM1reservoirNiCl2
35 %(v/v)ethylene glycol1reservoir
4100 mM1reservoirNaF
530 mMmeso-erythritol1reservoir
6100 mMTris-HCl1reservoirpH8.5
715 mg/mlprotein1drop
8100 mMTris-HCl1droppH8.0
9100 mM1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 42457 / Num. obs: 41500 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 50.8 Å2 / Rsym value: 0.105 / Net I/σ(I): 12.74
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 1.756 / Num. unique all: 3383 / Rsym value: 0.548 / % possible all: 78.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. measured all: 172206 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 78.9 % / Num. unique obs: 3383 / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 1.76

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF(no sugar, no waters)

1anf


Resolution: 2.8→44.91 Å / Isotropic thermal model: Isotropic / Cross valid method: Rfree / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.281 1986 RANDOM
Rwork0.227 --
all-39344 -
obs-39344 -
Displacement parametersBiso mean: 48.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11699 0 78 57 11834
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0079
X-RAY DIFFRACTIONc_angle_deg1.32
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024
RfactorNum. reflection% reflection
Rfree0.393 266 -
Rwork0.336 --
obs-4842 72.4 %
Software
*PLUS
Name: CNS / Version: 1.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.801 Å / Lowest resolution: 50 Å / Num. reflection obs: 39394 / % reflection Rfree: 5 % / Rfactor Rfree: 0.2809 / Rfactor Rwork: 0.2268
Solvent computation
*PLUS
Displacement parameters
*PLUS

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