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- PDB-3qir: Crystal structure of PIWIL2 PAZ domain -

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Basic information

Entry
Database: PDB / ID: 3qir
TitleCrystal structure of PIWIL2 PAZ domain
ComponentsPiwi-like protein 2
KeywordsRNA BINDING PROTEIN / Structural Genomics Consortium / SGC / PAZ domain / RNAi / RNA binding
Function / homology
Function and homology information


siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / retrotransposon silencing by heterochromatin formation / positive regulation of meiosis I ...siRNA-mediated retrotransposon silencing by heterochromatin formation / perinucleolar chromocenter / retrotransposon silencing by mRNA destabilization / PET complex / pi-body / secondary piRNA processing / piRNA-mediated retrotransposon silencing by heterochromatin formation / piRNA binding / retrotransposon silencing by heterochromatin formation / positive regulation of meiosis I / : / germ-line stem cell population maintenance / negative regulation of circadian rhythm / chromatoid body / dense body / P granule / regulatory ncRNA-mediated gene silencing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / oogenesis / PIWI-interacting RNA (piRNA) biogenesis / RNA endonuclease activity / positive regulation of translation / meiotic cell cycle / rhythmic process / spermatogenesis / mRNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
paz domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily ...paz domain / paz domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsDong, A. / Xu, C. / Bian, C. / Wernimont, A.K. / Kania, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of PIWIL2 PAZ domain
Authors: Xu, C. / Dong, A. / Bian, C. / Wernimont, A.K. / Kania, J. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Min, J.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Piwi-like protein 2
B: Piwi-like protein 2
C: Piwi-like protein 2
D: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)69,7034
Polymers69,7034
Non-polymers00
Water0
1
A: Piwi-like protein 2

A: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)34,8522
Polymers34,8522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1970 Å2
ΔGint-23 kcal/mol
Surface area13250 Å2
MethodPISA
2
B: Piwi-like protein 2
C: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)34,8522
Polymers34,8522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-28 kcal/mol
Surface area11760 Å2
MethodPISA
3
D: Piwi-like protein 2

D: Piwi-like protein 2


Theoretical massNumber of molelcules
Total (without water)34,8522
Polymers34,8522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area2310 Å2
ΔGint-32 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.548, 139.291, 224.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Piwi-like protein 2 / Cancer/testis antigen 80 / CT80


Mass: 17425.859 Da / Num. of mol.: 4 / Fragment: PAZ domain, rsidues 386-533
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIWIL2, HILI / Plasmid: pet28-MHL / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) Codon plus RIL (Stratagene)
References: UniProt: Q8TC59

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaI, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28286 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28286 Å / Relative weight: 1
ReflectionResolution: 2.45→100 Å / Num. all: 24387 / Num. obs: 24387 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 72.91 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 38.6
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.854 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1112 / Rsym value: 0.854 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.8.0refinement
Coot0.6model building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.75 Å / Cor.coef. Fo:Fc: 0.9181 / Cor.coef. Fo:Fc free: 0.8984 / Isotropic thermal model: 3O7X / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 1006 4.15 %RANDOM
Rwork0.2416 ---
all0.2428 24387 --
obs0.2428 24246 --
Displacement parametersBiso mean: 83.44 Å2
Baniso -1Baniso -2Baniso -3
1--16.9174 Å20 Å20 Å2
2---4.3153 Å20 Å2
3---21.2326 Å2
Refine analyzeLuzzati coordinate error obs: 0.573 Å
Refinement stepCycle: LAST / Resolution: 2.45→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 0 0 3290
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0133592
X-RAY DIFFRACTIONt_angle_deg1.0845792
X-RAY DIFFRACTIONt_dihedral_angle_d10722
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes852
X-RAY DIFFRACTIONt_gen_planes4965
X-RAY DIFFRACTIONt_it335920
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion18.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4665
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact34814
LS refinement shellResolution: 2.45→2.56 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3007 123 4.51 %
Rwork0.2789 2607 -
all0.2798 2730 -
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)
10.0666-0.4603-2.89062.1619-0.42517.4745-0.55660.3720.2184-0.12290.53180.33931.0885-0.50410.02480.2837-0.3040.00450.00690.068-0.3602-1.9905-34.224340.7769
21.4469-0.4212.82020.72971.53249.69280.4899-0.0735-0.05730.0522-0.0234-0.13460.68710.0319-0.46650.0193-0.10960.0125-0.2010.0136-0.185.7705-18.151515.0225
31.1546-1.58073.55491.0555-3.25068.7080.53260.2286-0.0698-0.5456-0.29660.27120.34340.7202-0.23590.05080.19740.027-0.1827-0.0228-0.23790.0774-16.402-16.4003
40.4399-0.02283.61560.80490.55918.2761-0.0880.1793-0.03130.02140.04580.0113-0.11410.44080.0422-0.12490.077-0.0321-0.1352-0.0186-0.0957-16.9165-0.3998-39.0422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }0
2X-RAY DIFFRACTION2{ B|* }0
3X-RAY DIFFRACTION3{ C|* }0
4X-RAY DIFFRACTION4{ D|* }0

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