[English] 日本語
Yorodumi
- PDB-1zbu: crystal structure of full-length 3'-exonuclease -

+
Open data


ID or keywords:

Loading...

-
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 / exoribonuclease II / 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 / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding ...histone pre-mRNA stem-loop binding / rRNA 3'-end processing / exoribonuclease II / 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 / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 3'-5' exonuclease activity / ribosome binding / 3'-5'-RNA exonuclease activity / rRNA binding / nucleolus / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Exonuclease / SAP domain superfamily / Exonuclease, RNase T/DNA polymerase III / EXOIII / SAP motif profile. / SAP domain ...: / : / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / Exonuclease / SAP domain superfamily / Exonuclease, RNase T/DNA polymerase III / EXOIII / SAP motif profile. / SAP domain / 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 / 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
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.06 %

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more