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- PDB-2bgg: The structure of a Piwi protein from Archaeoglobus fulgidus compl... -

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Basic information

Entry
Database: PDB / ID: 2bgg
TitleThe structure of a Piwi protein from Archaeoglobus fulgidus complexed with a 16nt siRNA duplex.
Components
  • 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
  • 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'
  • PROTEIN AF1318
KeywordsRNA-BINDING PROTEIN/RNA / RNA-BINDING PROTEIN-RNA COMPLEX / RNA-BINDING ARGONAUTE / PIWI DOMAIN / RNAI / RISC / PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


DNA binding / RNA binding / metal ion binding
Similarity search - Function
Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold ...Piwi domain profile. / Piwi domain / Piwi domain / Piwi / Response regulator / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / Piwi protein
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsParker, J.S. / Roe, S.M. / Barford, D.
Citation
Journal: Nature / Year: 2005
Title: Structural Insights Into Mrna Recognition from a Piwi Domain-Sirna Guide Complex
Authors: Parker, J.S. / Roe, S.M. / Barford, D.
#1: Journal: Embo J. / Year: 2004
Title: Crystal Structure of a Piwi Protein Suggests Mechanisms for Sirna Recognition and Slicer Activity.
Authors: Parker, J.S. / Roe, S.M. / Barford, D.
History
DepositionDec 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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_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 / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN AF1318
B: PROTEIN AF1318
P: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'
Q: 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
R: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'
S: 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7758
Polymers108,6656
Non-polymers1102
Water9,170509
1
A: PROTEIN AF1318
P: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'
Q: 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3874
Polymers54,3333
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-29.7 kcal/mol
Surface area18880 Å2
MethodPISA
2
B: PROTEIN AF1318
R: 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'
S: 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3874
Polymers54,3333
Non-polymers551
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-19.5 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.916, 61.206, 104.059
Angle α, β, γ (deg.)76.54, 76.14, 79.35
Int Tables number1
Space group name H-MP1
DetailsTHIS STRUCTURE CONTAINS A MONOMERIC PROTEIN, BOUND TO ARNA DUPLEX

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Components

#1: Protein PROTEIN AF1318 / PIWI


Mass: 49302.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O28951
#2: RNA chain 5'-R(*UP*UP*CP*GP*AP*CP*GP*CP)-3'


Mass: 2502.537 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: RNA chain 5'-R(*GP*UP*CP*GP*AP*AP*UP*UP)-3'


Mass: 2527.545 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE DESIGNED IN SILICO

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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: 2.6 Å3/Da / Density % sol: 52.7 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. obs: 58841 / % possible obs: 96.7 % / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.2 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W9H

1w9h


Resolution: 2.2→99.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.243 2972 5.1 %RANDOM
Rwork0.18 ---
obs0.183 55860 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å2-0.37 Å20.06 Å2
2--1.23 Å2-0.33 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→99.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6410 616 2 509 7537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227269
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0972.0719996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6965785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.0424.536291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.664151178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0931526
X-RAY DIFFRACTIONr_chiral_restr0.1570.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025191
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.23336
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24826
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2559
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2331.54094
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00826458
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.81133894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1214.53538
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 247 -
Rwork0.217 4122 -
obs--96.36 %
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)
10.95290.58430.00530.85060.07280.60750.0447-0.048-0.05270.0195-0.0227-0.09520.0611-0.009-0.022-0.07570.02030.0166-0.12020.0148-0.048910.977314.560672.6813
20.8488-0.08950.59230.85380.27711.8086-0.0260.1160.02910.00570.0558-0.0748-0.11960.0319-0.0299-0.1421-0.0154-0.0032-0.01360.0184-0.1345-14.28343.208328.9058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 427
2X-RAY DIFFRACTION1P1 - 8
3X-RAY DIFFRACTION1Q9 - 16
4X-RAY DIFFRACTION1A1428
5X-RAY DIFFRACTION2B10 - 427
6X-RAY DIFFRACTION2R1 - 8
7X-RAY DIFFRACTION2S9 - 13
8X-RAY DIFFRACTION2B1428

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