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- PDB-1zbh: 3'-end specific recognition of histone mRNA stem-loop by 3'-exonu... -

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Basic information

Entry
Database: PDB / ID: 1zbh
Title3'-end specific recognition of histone mRNA stem-loop by 3'-exonuclease
Components
  • 3'-5' exonuclease ERI1
  • 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP*GP*G)-3'
KeywordsHYDROLASE/RNA / histone mRNA 3'-end-specific recognition / Structures of 3'-exonuclease and its RNA complex / HYDROLASE-RNA COMPLEX
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 / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation ...: / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / 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 / RNA / RNA (> 10) / 3'-5' exoribonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP*GP*G)-3'
E: 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP*GP*G)-3'
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)152,90718
Polymers151,3246
Non-polymers1,58312
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.386, 195.148, 87.966
Angle α, β, γ (deg.)90.00, 92.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13D
23A
14F
24E

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRARGARGAC126 - 34876 - 298
21TYRTYRARGARGDF126 - 34876 - 298
12ASPASPARGARGBD124 - 34874 - 298
22ASPASPARGARGCE124 - 34874 - 298
13ASPASPLEULEUDF60 - 11710 - 67
23ASPASPLEULEUAC60 - 11710 - 67
14GGCCFA6 - 213 - 18
24GGCCEB6 - 213 - 18

NCS ensembles :
ID
1
2
3
4

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Components

#1: RNA chain 5'-R(*CP*CP*GP*GP*CP*UP*CP*UP*UP*UP*UP*CP*AP*GP*AP*GP*CP*CP*GP*G)-3'


Mass: 6351.791 Da / Num. of mol.: 2 / Fragment: SL-RNA / Source method: obtained synthetically
#2: Protein
3'-5' exonuclease ERI1 / Eri-1 homolog / Histone mRNA 3' end-specific exoribonuclease / Protein 3'hExo / HEXO


Mass: 34655.047 Da / Num. of mol.: 4 / Fragment: 3'hExo / Mutation: H293N, W213L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERI1, 3'EXO / Plasmid: pGBO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: Q8IV48, Hydrolases; Acting on ester bonds
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorDate: Oct 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→19.92 Å / Num. obs: 33770

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.92 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.861 / SU B: 36.108 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2597 3225 10 %RANDOM
Rwork0.20922 ---
obs0.21426 29143 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.849 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å20.21 Å2
2---1.46 Å20 Å2
3---3.3 Å2
Refinement stepCycle: LAST / Resolution: 3→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8354 666 100 18 9138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0229376
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0942.08512820
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.74751024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10424.646396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15151622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4771548
X-RAY DIFFRACTIONr_chiral_restr0.0870.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.24269
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.26376
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1740.25
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1731.55317
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.30928400
X-RAY DIFFRACTIONr_scbond_it0.31834795
X-RAY DIFFRACTIONr_scangle_it0.5334.54420
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1810medium positional0.410.5
2B1824medium positional0.370.5
3D483medium positional0.30.5
4F333medium positional0.210.5
1A1810medium thermal0.112
2B1824medium thermal0.112
3D483medium thermal0.172
4F333medium thermal0.072
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 203 -
Rwork0.262 1902 -
obs--87.45 %
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)
14.1358-2.84830.53846.836-0.00132.438-0.064-0.21940.36530.31430.1521-0.28380.08820.1272-0.0881-0.40720.02320.0194-0.3177-0.0863-0.330110.112432.419931.5432
24.85881.06911.53865.05092.22643.38830.0979-0.03320.08040.0216-0.0497-0.17850.08310.0349-0.0482-0.29490.03410.0492-0.3698-0.0698-0.454928.737413.30612.8723
34.6412-1.7768-1.86923.92851.7213.06580.16790.0053-0.19930.1437-0.0988-0.3969-0.18250.0075-0.0691-0.3460.0217-0.0969-0.3595-0.1098-0.323625.3313-12.808173.6823
45.34013.3269-0.03548.23210.40561.8729-0.20650.4681-0.5769-0.72230.3237-0.5189-0.15190.0632-0.1171-0.3695-0.03450.0338-0.2913-0.1084-0.29116.5993-32.670355.8138
5000000000000000000000000
69.7535-2.3732.50322.6458-3.18673.8546-0.4505-1.33790.25941.70420.51191.3213-1.1626-0.8194-0.06150.64990.49180.17220.50350.24110.07380.391722.482557.3387
71.73231.45731.17192.0591-1.03345.6871-0.21030.8421.2787-1.48760.2875-0.53180.02170.3362-0.07721.0533-0.39190.45870.79770.11810.341613.8609-15.768430.0193
81.77672.1653-0.16233.6852-4.43417.1639-0.10352.0222-0.1479-1.2243-0.0421.18210.3234-0.02320.14551.0718-0.1245-0.07281.34360.01410.4224-2.218-25.380528.7309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AC60 - 11710 - 67
2X-RAY DIFFRACTION2AC126 - 34876 - 298
3X-RAY DIFFRACTION3BD124 - 34874 - 298
4X-RAY DIFFRACTION4CE124 - 34874 - 298
5X-RAY DIFFRACTION5DF60 - 11710 - 67
6X-RAY DIFFRACTION6DF126 - 34876 - 298
7X-RAY DIFFRACTION7FA6 - 213 - 18
8X-RAY DIFFRACTION8EB6 - 213 - 18

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