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- PDB-4wyv: Crystal Structure of Human Translin in Open Conformation -

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Basic information

Entry
Database: PDB / ID: 4wyv
TitleCrystal Structure of Human Translin in Open Conformation
ComponentsTranslin
KeywordsRNA BINDING PROTEIN / Translin / Octomer / RNA / Open / Barrel
Function / homology
Function and homology information


endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / Hydrolases; Acting on ester bonds ...endoribonuclease complex / Small interfering RNA (siRNA) biogenesis / regulatory ncRNA-mediated post-transcriptional gene silencing / siRNA processing / male germ cell nucleus / single-stranded DNA binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / mRNA binding / endoplasmic reticulum / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Translin; domain 2 / Translin; domain 1 / Translin, N-terminal / Translin, C-terminal / Translin / Translin family / Translin superfamily / Translin family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDvir, H. / Eliahoo, E. / Alian, A.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: A novel open-barrel structure of octameric translin reveals a potential RNA entryway.
Authors: Eliahoo, E. / Marx, A. / Manor, H. / Alian, A.
History
DepositionNov 18, 2014Deposition site: RCSB / Processing site: PDBE
SupersessionNov 26, 2014ID: 4jhf
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 18, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Translin
B: Translin
C: Translin
D: Translin
E: Translin
F: Translin
G: Translin
H: Translin


Theoretical massNumber of molelcules
Total (without water)221,0048
Polymers221,0048
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21910 Å2
ΔGint-110 kcal/mol
Surface area72930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.308, 82.308, 635.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Translin / / Component 3 of promoter of RISC / C3PO


Mass: 27625.498 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSN / Production host: Escherichia coli (E. coli)
References: UniProt: Q15631, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.05M MES, 0.2M KCL, 0.01M MGCL2, 5% PEG8000, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2012
RadiationMonochromator: Si(111) Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→58.2 Å / Num. obs: 45180 / % possible obs: 98.4 % / Redundancy: 13.2 % / Rsym value: 0.113 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.16 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 3.3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j1j

1j1j


Resolution: 3→58 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.895 / SU B: 48.631 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27212 2272 5 %RANDOM
Rwork0.22551 ---
obs0.22786 42759 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20 Å2
2--0.23 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 3→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13917 0 0 18 13935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02214164
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.96719106
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.20251686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96223.177702
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.891152617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.53415128
X-RAY DIFFRACTIONr_chiral_restr0.0980.22195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210509
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7121.58443
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.401213678
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93335721
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4784.55428
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 158 -
Rwork0.315 2632 -
obs--84.6 %
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)
12.1776-0.5027-1.99121.48740.19183.9410.12150.15350.10330.0449-0.0755-0.5273-0.19680.3675-0.0460.1693-0.0523-0.14970.16590.02960.310119.424-6.72461.491
21.0933-0.6994-0.94243.6242.34474.4791-0.03730.073-0.15090.0895-0.1772-0.1810.35430.310.21450.240.0301-0.19090.13210.09390.325512.379-40.87560.549
31.03090.0206-0.77941.5366-2.70186.8027-0.06520.1157-0.05520.15230.09580.0359-0.3184-0.7097-0.03060.20030.0922-0.03690.1874-0.0350.0816-13.5585.11458.552
40.65490.68-0.94991.5608-2.55445.1012-0.05570.1123-0.0619-0.393-0.0114-0.030.2739-0.20670.06720.50670.1228-0.03870.1523-0.01110.1028-6.945-47.40119.231
50.1387-0.1111-0.11571.79022.28574.50120.07780.03340.1381-0.3231-0.0355-0.3305-0.56240.3291-0.04230.42430.04920.12680.34130.13780.354117.297-1.27225.125
61.6096-0.2286-1.47210.81760.26333.25080.0608-0.0905-0.0652-0.0643-0.0890.04990.1717-0.35390.02820.26660.0979-0.08920.52470.03940.0974-17.567-5.04523.822
70.56330.16461.1490.75690.42673.83430.07810.07260.0509-0.0562-0.1511-0.55080.240.50430.0730.39960.22410.00010.50120.18310.492225.192-35.50126.068
81.40040.34321.5381.16450.45916.06250.08120.08090.1495-0.2521-0.14190.2594-0.2488-0.51770.06060.18280.0534-0.06440.1885-0.0060.1804-21.26-38.66251.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 217
2X-RAY DIFFRACTION2B1 - 217
3X-RAY DIFFRACTION3C0 - 216
4X-RAY DIFFRACTION4D-1 - 217
5X-RAY DIFFRACTION5E0 - 217
6X-RAY DIFFRACTION6F0 - 217
7X-RAY DIFFRACTION7G1 - 217
8X-RAY DIFFRACTION8H1 - 216

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