[English] 日本語
Yorodumi
- PDB-4oau: Complete human RNase L in complex with biological activators. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oau
TitleComplete human RNase L in complex with biological activators.
Components
  • 2-5A-dependent ribonuclease
  • RNA (5'-R(P*A*AP*A)-2')
KeywordsHYDROLASE/RNA / RNase L / RNASEL / 2-5A / 2' / 5'-oligoadenylate / interferon / KEN / pseudokinase / kinase / inflammation / Ire1 / RIDD / regulated RNA decay / splicing cleavage / HPC1 / hereditary prostate cancer 1 / RNase L kinase-homology and KEN domain-containing / innate immunity / interferon response / antiviral response / 2-5A (2' / 5'-linked oligoadenylate)and RNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / ribonucleoprotein complex binding / RNA processing / regulation of mRNA stability / RNA endonuclease activity / positive regulation of D-glucose import ...OAS antiviral response / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / negative regulation of viral genome replication / fat cell differentiation / RNA nuclease activity / ribonucleoprotein complex binding / RNA processing / regulation of mRNA stability / RNA endonuclease activity / positive regulation of D-glucose import / nuclear matrix / mRNA processing / rRNA processing / Interferon alpha/beta signaling / defense response to virus / rRNA binding / protein kinase activity / mitochondrial matrix / protein phosphorylation / positive regulation of transcription by RNA polymerase II / RNA binding / ATP binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
RNase L, RNase domain / KEN domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / de novo design (two linked rop proteins) / Ankyrin repeat-containing domain ...RNase L, RNase domain / KEN domain / Ankyrin repeats (many copies) / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / de novo design (two linked rop proteins) / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Ankyrin repeat-containing domain superfamily / Alpha Horseshoe / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / RNA / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHan, Y. / Donovan, J. / Rath, S. / Whitney, G. / Chitrakar, A. / Korennykh, A.
CitationJournal: Science / Year: 2014
Title: Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response.
Authors: Han, Y. / Donovan, J. / Rath, S. / Whitney, G. / Chitrakar, A. / Korennykh, A.
History
DepositionJan 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / 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_conn_type.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
C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8355
Polymers80,3592
Non-polymers4763
Water2,504139
1
C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules

C: 2-5A-dependent ribonuclease
A: RNA (5'-R(P*A*AP*A)-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,67010
Polymers160,7184
Non-polymers9526
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12060 Å2
ΔGint-55 kcal/mol
Surface area60980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.130, 116.600, 162.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

-
Components

#1: Protein 2-5A-dependent ribonuclease / 2-5A-dependent RNase / Ribonuclease 4 / Ribonuclease L / RNase L


Mass: 79416.344 Da / Num. of mol.: 1 / Fragment: UNP residues 21-719 / Mutation: H672N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNASEL, RNS4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q05823, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: RNA chain RNA (5'-R(P*A*AP*A)-2')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemical synthesis
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl 2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio ...Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl 2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio 1:1.5:1.5, VAPOR DIFFUSION, temperature 277K

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.6→53.442 Å / Num. all: 28957 / Num. obs: 28947 / % possible obs: 99.87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→53.442 Å / SU ML: 0.37 / σ(F): 1.99 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1798 5 %RANDOM
Rwork0.2113 ---
obs0.2133 -99.87 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→53.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 67 29 139 5774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035747
X-RAY DIFFRACTIONf_angle_d0.7887761
X-RAY DIFFRACTIONf_dihedral_angle_d20.9913594
X-RAY DIFFRACTIONf_chiral_restr0.061853
X-RAY DIFFRACTIONf_plane_restr0.003990
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67030.3431370.32472594X-RAY DIFFRACTION100
2.6703-2.74890.34571360.32392583X-RAY DIFFRACTION100
2.7489-2.83760.3751350.31242574X-RAY DIFFRACTION100
2.8376-2.9390.32921360.29192585X-RAY DIFFRACTION100
2.939-3.05670.32351380.27152604X-RAY DIFFRACTION100
3.0567-3.19580.30341360.24632600X-RAY DIFFRACTION100
3.1958-3.36420.30361380.24022611X-RAY DIFFRACTION100
3.3642-3.5750.25421360.2012594X-RAY DIFFRACTION100
3.575-3.85090.25151390.18682630X-RAY DIFFRACTION100
3.8509-4.23830.20841380.17772626X-RAY DIFFRACTION100
4.2383-4.85130.22581400.15882651X-RAY DIFFRACTION100
4.8513-6.11070.21381420.20112691X-RAY DIFFRACTION100
6.1107-53.45350.20731470.19192801X-RAY DIFFRACTION99
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)
11.95280.0566-2.24910.512-0.23713.6844-0.07120.18310.0541-0.07230.05370.09610.0847-0.31130.030.4256-0.0337-0.08390.44070.04310.3948-2.1477-7.8617-17.183
29.03260.2735-0.86277.21871.49754.65730.0714-0.1739-0.0632-0.0653-0.36490.16080.4149-0.22580.23160.73260.05370.00380.4646-0.03310.3941-2.0124-32.987112.3325
34.9714-1.28531.36037.7501-0.83342.37040.01-0.2132-0.82290.4748-0.0342-0.65030.50470.3231-0.01181.10170.18080.06590.4811-0.01220.781512.0602-55.022713.8441
43.47940.77860.06110.63380.24912.3859-0.3026-0.0162-0.4112-0.11380.18450.59860.5937-0.0360.25771.83470.16140.21950.58530.02841.55899.1432-86.22069.0501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain C and (resid 25:330)
5X-RAY DIFFRACTION1chain A and (resid 1:3)
2X-RAY DIFFRACTION2chain C and resid 331:437
3X-RAY DIFFRACTION3chain C and (resid 438:584 or resid 801 or resid 802:803)
4X-RAY DIFFRACTION4chain C and resid 585:719

+
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