[English] 日本語
Yorodumi
- PDB-6n6i: Human REXO2 bound to pGG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6n6i
TitleHuman REXO2 bound to pGG
Components
  • RNA (5'-R(P*GP*G)-3')
  • RNA exonuclease 2 homolog,Small fragment nuclease
Keywordsrna binding protein/rna / 3'-5' exoribonuclease / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / Mitochondrial RNA degradation / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / Mitochondrial RNA degradation / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / 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 / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / RNA / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.431 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123609 United States
CitationJournal: Elife / Year: 2019
Title: A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.
Authors: Kim, S.K. / Lormand, J.D. / Weiss, C.A. / Eger, K.A. / Turdiev, H. / Turdiev, A. / Winkler, W.C. / Sondermann, H. / Lee, V.T.
History
DepositionNov 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*GP*G)-3')
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,26410
Polymers48,8694
Non-polymers3946
Water7,710428
1
A: RNA exonuclease 2 homolog,Small fragment nuclease
D: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5504
Polymers24,4352
Non-polymers1152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-24 kcal/mol
Surface area9550 Å2
MethodPISA
2
B: RNA exonuclease 2 homolog,Small fragment nuclease
C: RNA (5'-R(P*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7146
Polymers24,4352
Non-polymers2794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-20 kcal/mol
Surface area10060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.814, 87.289, 123.797
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ABDC

#1: Protein RNA exonuclease 2 homolog,Small fragment nuclease / REXO2


Mass: 23789.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*GP*G)-3')


Mass: 645.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 434 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M sodium malonate (pH 5.5) and 15-20% polyethylene glycol 3350, 25% gylcerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 11, 2018
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.431→45.814 Å / Num. all: 91458 / Num. obs: 91458 / % possible obs: 99 % / Redundancy: 7.6 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.107 / Rsym value: 0.099 / Net I/av σ(I): 6.5 / Net I/σ(I): 13.2 / Num. measured all: 691974
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.431-1.515.50.8580.9124700.3870.9450.85894
1.51-1.67.40.611.3126140.2390.6570.61100
1.6-1.7180.4271.8118790.160.4570.427100
1.71-1.857.90.2882.7110850.1090.3080.28899.9
1.85-2.0280.1784.3102140.0670.190.17899.9
2.02-2.2680.1136.792710.0420.1210.11399.8
2.26-2.618.10.0799.382070.030.0850.07999.8
2.61-3.28.10.05811.770100.0220.0620.05899.9
3.2-4.537.90.04214.855180.0160.0450.042100
4.53-45.8147.60.0413.931900.0150.0430.0499.8

-
Processing

Software
NameVersionClassification
XDSdata reduction
SCALA3.3.22data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6N6A

6n6a


Resolution: 1.431→42.966 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.38
RfactorNum. reflection% reflection
Rfree0.1781 2275 2.49 %
Rwork0.1581 --
obs0.1586 91345 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.02 Å2 / Biso mean: 18.3983 Å2 / Biso min: 6.94 Å2
Refinement stepCycle: final / Resolution: 1.431→42.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 94 29 461 3581
Biso mean--35.75 31.37 -
Num. residues----373
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4312-1.46230.28661230.27534802492587
1.4623-1.49630.24981400.24155471561198
1.4963-1.53370.24911420.215155615703100
1.5337-1.57520.21381400.200455595699100
1.5752-1.62160.19431430.185655515694100
1.6216-1.67390.18231420.16955885730100
1.6739-1.73370.16821410.162355605701100
1.7337-1.80310.17721440.158955695713100
1.8031-1.88520.17481430.155555855728100
1.8852-1.98460.1831450.155856195764100
1.9846-2.10890.16821400.146955895729100
2.1089-2.27180.15951440.143256105754100
2.2718-2.50030.16291440.149456305774100
2.5003-2.86210.18321450.155656925837100
2.8621-3.60570.17461460.139457205866100
3.6057-42.98550.1591530.146659646117100
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)
14.65641.61840.17942.32980.23090.78050.0456-0.0715-0.0494-0.0012-0.005-0.12740.04280.0247-0.04710.077-0.00350.00440.07790.00760.05374.24419.93915.3227
23.363-1.00231.89062.5703-1.28152.21850.06390.01510.0333-0.22840.01890.30410.1396-0.1504-0.10660.1157-0.0227-0.02260.1057-0.00560.1259-10.55074.84618.7464
30.44720.1231-0.14962.2068-0.57580.6670.01840.03650.0038-0.1411-0.0165-0.04820.0350.016-0.00070.0738-0.00040.00430.1016-0.00480.08215.419117.809315.8199
41.48661.72071.02552.6012.18433.3975-0.0050.348-0.1406-0.23160.2002-0.6289-0.26571.0056-0.11440.1372-0.02920.03930.2485-0.00130.189317.614932.693911.4058
54.14992.40593.15147.9175-3.93697.48610.04571.75261.5626-1.8006-0.0550.1489-1.5414-0.33120.01450.47360.0608-0.00510.33460.14590.3959-7.053242.514814.1789
61.5016-0.0381-0.56072.1974-0.67392.1702-0.0802-0.2068-0.15310.1917-0.0261-0.01410.1808-0.02220.080.0995-0.01780.00670.105-0.00270.0935-4.095526.529438.3948
71.3388-0.2852-0.20530.78210.28180.8426-0.0213-0.0920.03170.0332-0.00870.05560.0165-0.0620.03390.0722-0.0183-0.00650.0708-0.00110.0762-3.253328.406127.5965
84.62990.4102-2.82740.90650.88993.35510.0321-0.29060.1950.0020.0672-0.0967-0.13370.3533-0.05470.0945-0.0032-0.020.0815-0.01740.13049.419335.295628.7536
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:55)A4 - 55
2X-RAY DIFFRACTION2(chain A and resid 56:88)A56 - 88
3X-RAY DIFFRACTION3(chain A and resid 89:179)A89 - 179
4X-RAY DIFFRACTION4(chain A and resid 180:186)A180 - 186
5X-RAY DIFFRACTION5(chain B and resid 2:8)B2 - 8
6X-RAY DIFFRACTION6(chain B and resid 9:78)B9 - 78
7X-RAY DIFFRACTION7(chain B and resid 79:155)B79 - 155
8X-RAY DIFFRACTION8(chain B and resid 156:187)B156 - 187

+
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