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- PDB-1zbu: crystal structure of full-length 3'-exonuclease -

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Basic information

Entry
Database: PDB / ID: 1zbu
Titlecrystal structure of full-length 3'-exonuclease
Components3'-5' exonuclease ERI1
KeywordsHYDROLASE / 3'-exonuclease
Function / homology
Function and homology information


histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA 3'end processing complex / regulatory ncRNA-mediated gene silencing / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds ...histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone pre-mRNA 3'end processing complex / regulatory ncRNA-mediated gene silencing / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / Hydrolases; Acting on ester bonds / rRNA binding / nucleolus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Exonuclease, RNase T/DNA polymerase III ...: / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / 3'-5' exoribonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD, molecular replacement / Resolution: 2.998 Å
AuthorsCheng, Y. / Patel, D.J.
CitationJournal: To be Published
Title: Structural basis for 3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease, a human nuclease that also targets siRNA
Authors: Cheng, Y. / Patel, D.J.
History
DepositionApr 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3'-5' exonuclease ERI1
B: 3'-5' exonuclease ERI1
C: 3'-5' exonuclease ERI1
D: 3'-5' exonuclease ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,82616
Polymers162,2434
Non-polymers1,58312
Water66737
1
A: 3'-5' exonuclease ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9574
Polymers40,5611
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3'-5' exonuclease ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9574
Polymers40,5611
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3'-5' exonuclease ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9574
Polymers40,5611
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3'-5' exonuclease ERI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9574
Polymers40,5611
Non-polymers3963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)215.843, 215.843, 114.468
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein
3'-5' exonuclease ERI1 / E.C.3.1.-.- / Eri-1 homolog / Histone mRNA 3' end-specific exoribonuclease / Protein 3'hExo / HEXO


Mass: 40560.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERI1, 3'EXO / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IV48, Hydrolases; Acting on ester bonds
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 4.74 Å3/Da / Density % sol: 74.06 %

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Data collection

DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.998→19.96 Å / Num. all: 61407 / Num. obs: 53948 / % possible obs: 97.77 % / Observed criterion σ(I): 1.5

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Processing

SoftwareName: REFMAC / Version: 5.2 / Classification: refinement
RefinementMethod to determine structure: SAD, molecular replacement / Resolution: 2.998→19.96 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.898 / SU B: 18.934 / SU ML: 0.164 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.38 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22472 6085 10.1 %RANDOM
Rwork0.19852 ---
all0.20118 61407 --
obs0.20118 53948 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.379 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20.32 Å20 Å2
2--0.64 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 2.998→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7947 0 100 37 8084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228221
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.99311111
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.26124.543372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06151536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2721544
X-RAY DIFFRACTIONr_chiral_restr0.0830.21216
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026100
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2170.23519
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25719
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4260.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5431.55020
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87127993
X-RAY DIFFRACTIONr_scbond_it1.36533606
X-RAY DIFFRACTIONr_scangle_it2.2834.53118
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.998→3.074 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 390 -
Rwork0.33 3716 -
obs--93.28 %
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)
12.9758-0.6980.94861.8312-0.58991.6344-0.02240.0727-0.087-0.02750.07630.07960.0845-0.0872-0.0539-0.2441-0.06990.0358-0.22210.0079-0.28797.4021-68.6103-77.6648
24.2980.37481.41950.7290.06332.7539-0.0147-0.0011-0.05590.08070.09530.18730.0743-0.3887-0.0806-0.2179-0.07250.0572-0.11260.0699-0.207178.7628-78.2572-55.7707
33.8965-2.1150.84923.3937-0.64022.0447-0.0729-0.1291-0.0010.11050.070.2601-0.1634-0.25520.0029-0.01510.01610.023-0.2613-0.0023-0.1736105.1699-34.7391-51.268
43.82712.0099-0.97653.8707-1.3282.08440.08880.390.0732-0.0777-0.1154-0.03260.1472-0.2360.0266-0.154-0.1020.01740.0937-0.0336-0.076157.6392-83.0234-23.9212
55.4411-1.003-1.514910.1034-0.66258.9556-0.1568-0.1388-1.0048-0.2441-0.1525-0.2441.37640.36960.30930.70730.07950.05440.03250.02050.347499.826-104.8453-29.5255
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A126 - 349
2X-RAY DIFFRACTION2B126 - 349
3X-RAY DIFFRACTION3C126 - 349
4X-RAY DIFFRACTION4D126 - 349
5X-RAY DIFFRACTION5B51 - 119

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