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- PDB-3o6e: Crystal Structure of human Hiwi1 PAZ domain (residues 277-399) in... -

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Basic information

Entry
Database: PDB / ID: 3o6e
TitleCrystal Structure of human Hiwi1 PAZ domain (residues 277-399) in complex with 14-mer RNA (12-bp + 2-nt overhang) containing 2'-OCH3 at its 3'-end
Components
  • Piwi-like protein 1
  • RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))-3')
KeywordsRNA BINDING PROTEIN/RNA / Piwi / PAZ / RNA silencing / pi-RNA / Hiwi1 / Hili / PAZ domain / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing ...primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / dense body / regulatory ncRNA-mediated gene silencing / P granule / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / PIWI-interacting RNA (piRNA) biogenesis / spermatid development / RNA endonuclease activity / meiotic cell cycle / regulation of translation / spermatogenesis / single-stranded RNA binding / mRNA binding / protein kinase binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain ...GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / paz domain / paz domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Piwi-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsTian, Y. / Simanshu, D.K. / Ma, J.-B. / Patel, D.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Inaugural Article: Structural basis for piRNA 2'-O-methylated 3'-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains.
Authors: Tian, Y. / Simanshu, D.K. / Ma, J.B. / Patel, D.J.
History
DepositionJul 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Piwi-like protein 1
A: RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))-3')


Theoretical massNumber of molelcules
Total (without water)19,0642
Polymers19,0642
Non-polymers00
Water1086
1
X: Piwi-like protein 1
A: RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))-3')

X: Piwi-like protein 1
A: RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))-3')


Theoretical massNumber of molelcules
Total (without water)38,1284
Polymers38,1284
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+3/41
Buried area5940 Å2
ΔGint-31 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.013, 44.013, 147.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Piwi-like protein 1


Mass: 14625.195 Da / Num. of mol.: 1 / Fragment: PAZ domain (UNP Residues 277-399)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIWI, Piwi-like protein 1, PIWIL1 / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96J94
#2: RNA chain RNA (5'-R(*GP*CP*GP*AP*AP*UP*AP*UP*UP*CP*GP*CP*UP*(OMU))-3')


Mass: 4438.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1-5% PEG3350, 50 mM NaCl, 50 mM Na-acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2009 / Details: vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 3451 / % possible obs: 95.3 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.083 / Χ2: 1.29 / Net I/σ(I): 32.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.9-36.20.2094.82450.52172.3
3-3.127.20.1883150.62590
3.12-3.279.50.1463200.71492.8
3.27-3.4410.50.1333360.80796.3
3.44-3.6511.40.1223630.974100
3.65-3.9312.20.0983461.164100
3.93-4.3312.20.0833531.397100
4.33-4.9511.90.0753701.697100
4.95-6.2311.40.0793801.738100
6.23-3010.10.0574232.13699.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O7V

3o7v


Resolution: 2.904→15 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.866 / WRfactor Rfree: 0.2717 / WRfactor Rwork: 0.2279 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7753 / SU B: 51.553 / SU ML: 0.418 / SU R Cruickshank DPI: 0.4752 / SU Rfree: 0.5689 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.569 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3051 305 9 %RANDOM
Rwork0.2515 ---
obs0.2562 3384 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 101.65 Å2 / Biso mean: 61.5548 Å2 / Biso min: 33.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å20 Å20 Å2
2--2.55 Å20 Å2
3----5.1 Å2
Refinement stepCycle: LAST / Resolution: 2.904→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms855 293 0 6 1154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221200
X-RAY DIFFRACTIONr_angle_refined_deg0.8422.2711691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2115105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.20825.36641
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42915147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.725152
X-RAY DIFFRACTIONr_chiral_restr0.050.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021800
X-RAY DIFFRACTIONr_mcbond_it0.1311.5534
X-RAY DIFFRACTIONr_mcangle_it0.2582863
X-RAY DIFFRACTIONr_scbond_it0.3383666
X-RAY DIFFRACTIONr_scangle_it0.5224.5828
LS refinement shellResolution: 2.904→2.977 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 12 -
Rwork0.332 154 -
all-166 -
obs--67.76 %
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)
12.97810.08990.42854.81420.66993.83220.147-0.2495-0.07410.3084-0.10010.34320.1743-0.4318-0.04680.13340.0243-0.01340.250.00230.134211.283924.338363.0024
22.6964-1.8196-1.42532.32050.96720.7537-0.159-0.29860.40470.17590.3628-0.58860.09190.1599-0.20380.27570.00680.00150.2757-0.08540.416232.051436.541158.497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X-10 - 9999
2X-RAY DIFFRACTION2A-10 - 9999

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