[English] 日本語
Yorodumi
- PDB-4oav: Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oav
TitleComplete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate.
Components
  • PROTEIN (RNase L)
  • RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
KeywordsHYDROLASE/RNA / HPC1 / 2-5A / 2' / 5'-oligoadenylate / interferon / dsRNA / kinase / RNase / RIDD / Ire1 / RNA decay / RNase L protein kinase / pseudokinase / KEN-domain containing / Regulated RNA decay / innate immune response / antiviral response / dsRNA response / 5'-linked oligoadenylates / 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 / RNA processing / ribonucleoprotein complex binding / 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 / RNA processing / ribonucleoprotein complex binding / regulation of mRNA stability / RNA endonuclease activity / positive regulation of D-glucose import / Interferon alpha/beta signaling / nuclear matrix / mRNA processing / rRNA processing / defense response to virus / protein kinase activity / rRNA binding / protein phosphorylation / mitochondrial matrix / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNase L, RNase domain / Ankyrin repeats (many copies) / KEN domain / 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 / Ankyrin repeats (many copies) / KEN domain / 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 / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-PUP / RNA / 2-5A-dependent ribonuclease
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_sheet / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_sheet.number_strands / _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
B: PROTEIN (RNase L)
A: RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
D: PROTEIN (RNase L)
C: RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,46611
Polymers161,8384
Non-polymers1,6287
Water16,412911
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-92 kcal/mol
Surface area58100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 160.700, 230.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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

#1: Protein PROTEIN (RNase L)


Mass: 79416.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q05823
#2: RNA chain RNA (5'-R(P*(PO4)P*(PO4)P*AP*AP*AP*AP*(PO4))-2')


Mass: 1502.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical synthesis

-
Non-polymers , 4 types, 918 molecules

#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PUP / (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate


Mass: 520.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H22N2O15P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 911 / 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: 3.41 Å3/Da / Density % sol: 63.95 %
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 MgCl2, 5 mM DTT, 2.8 mM ATP or AMP-PCP, and 10% glycerol) was mixed with 2-5A and RNA18 at molar ratio 1: ...Details: RNase L (21-719) (15 mg/ml in buffer containing 20 mM HEPES pH 7.5, 109 mM NaCl, 5 mM MgCl2, 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, 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 CHANNEL11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→46.7 Å / Num. all: 128179 / Num. obs: 128124 / % possible obs: 100 % / 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
Starting model: PDB ENTRY 4G8L

4g8l


Resolution: 2.1→46.622 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 6405 5 %RANDOM
Rwork0.198 ---
obs0.1995 128099 99.95 %-
all-128124 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10751 202 99 911 11963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411270
X-RAY DIFFRACTIONf_angle_d0.92215244
X-RAY DIFFRACTIONf_dihedral_angle_d20.8446924
X-RAY DIFFRACTIONf_chiral_restr0.0721677
X-RAY DIFFRACTIONf_plane_restr0.0031913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.31672080.2853945X-RAY DIFFRACTION100
2.1239-2.14890.30212130.2774042X-RAY DIFFRACTION100
2.1489-2.17510.31632110.26684037X-RAY DIFFRACTION100
2.1751-2.20260.32332080.26563935X-RAY DIFFRACTION100
2.2026-2.23160.30622130.25514047X-RAY DIFFRACTION100
2.2316-2.26210.29832130.24854046X-RAY DIFFRACTION100
2.2621-2.29450.29632080.2443949X-RAY DIFFRACTION100
2.2945-2.32870.29282120.23344034X-RAY DIFFRACTION100
2.3287-2.36510.28472120.24224028X-RAY DIFFRACTION100
2.3651-2.40390.28022110.23784016X-RAY DIFFRACTION100
2.4039-2.44530.28652120.23044036X-RAY DIFFRACTION100
2.4453-2.48980.29522100.22194003X-RAY DIFFRACTION100
2.4898-2.53770.25682140.22394049X-RAY DIFFRACTION100
2.5377-2.58950.26152110.22024020X-RAY DIFFRACTION100
2.5895-2.64580.28312120.21374021X-RAY DIFFRACTION100
2.6458-2.70730.22582120.21434025X-RAY DIFFRACTION100
2.7073-2.7750.2572130.21394045X-RAY DIFFRACTION100
2.775-2.850.25762110.21544024X-RAY DIFFRACTION100
2.85-2.93390.27832160.20984091X-RAY DIFFRACTION100
2.9339-3.02850.25532100.20654006X-RAY DIFFRACTION100
3.0285-3.13680.24822140.20744060X-RAY DIFFRACTION100
3.1368-3.26230.21732160.20514101X-RAY DIFFRACTION100
3.2623-3.41080.23392130.19744038X-RAY DIFFRACTION100
3.4108-3.59050.19382140.18384076X-RAY DIFFRACTION100
3.5905-3.81540.222150.1794089X-RAY DIFFRACTION100
3.8154-4.10980.19012160.16674101X-RAY DIFFRACTION100
4.1098-4.52310.1712180.1594146X-RAY DIFFRACTION100
4.5231-5.17680.16472170.15724124X-RAY DIFFRACTION100
5.1768-6.51940.2222220.19194200X-RAY DIFFRACTION100
6.5194-46.63340.1932300.17954360X-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)
10.60280.86110.04143.5428-0.38070.4215-0.0289-0.061-0.0636-0.01470.08630.00970.03040.0136-0.05180.3120.04320.0330.3882-0.00130.324913.7076-15.3912107.7443
24.44690.99711.60022.7710.69833.0227-0.04730.0927-0.0024-0.18120.1201-0.0492-0.00360.0369-0.0710.4404-0.0663-0.00180.3465-0.01610.254512.642711.977982.3975
32.64270.36381.01751.9443-0.26626.8643-0.06770.3197-0.0116-0.21030.09090.0373-0.1989-0.3621-0.01840.5571-0.0869-0.03380.5361-0.01080.33020.243812.684960.0183
43.5898-0.7616-0.97333.02210.06596.75730.1404-0.0528-0.0525-0.059-0.1885-0.0311-0.0845-0.16450.02760.5925-0.1224-0.04960.58130.03410.33325.68718.688928.5636
50.70050.81440.16962.35190.34710.3027-0.0653-0.08990.0798-0.03380.0370.2134-0.0027-0.04850.02650.28990.0243-0.02210.3556-0.0340.31118.512815.3748107.172
64.13730.4143-1.62772.7522-1.10783.1384-0.03680.0804-0.0942-0.03040.16710.1632-0.0859-0.1928-0.12270.4674-0.08090.00450.3717-0.02540.288311.5027-12.495682.5443
73.68310.0325-1.78122.05370.02687.18150.01080.2434-0.0347-0.1650.0291-0.07850.17920.3085-0.00750.4993-0.07660.0180.4342-0.02950.310126.5704-13.254361.88
83.3502-0.52850.63783.89420.34917.73830.02750.3432-0.0897-0.4595-0.07220.01590.30680.1460.04140.6183-0.04640.04470.69510.0080.320726.5898-9.153229.9256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )C1 - 6
2X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )C7
3X-RAY DIFFRACTION1( CHAIN C AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN D AND RESID 26:327 )D26 - 327
4X-RAY DIFFRACTION2( CHAIN D AND RESID 336:436 )D336 - 436
5X-RAY DIFFRACTION3( CHAIN D AND ( RESID 437:586 OR RESID 1001:1003 ) )D437 - 586
6X-RAY DIFFRACTION3( CHAIN D AND ( RESID 437:586 OR RESID 1001:1003 ) )D1001 - 1003
7X-RAY DIFFRACTION4( CHAIN D AND ( RESID 587:719 OR RESID 1004:1004 ) )D587 - 719
8X-RAY DIFFRACTION4( CHAIN D AND ( RESID 587:719 OR RESID 1004:1004 ) )D1004
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )A1 - 6
10X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )A7
11X-RAY DIFFRACTION5( CHAIN A AND ( RESID 1:6 OR RESID 7:7 ) ) OR ( CHAIN B AND RESID 24:327 )B24 - 327
12X-RAY DIFFRACTION6( CHAIN B AND RESID 336:436 )B336 - 436
13X-RAY DIFFRACTION7( CHAIN B AND ( RESID 437:586 OR RESID 801:803 ) )B437 - 586
14X-RAY DIFFRACTION7( CHAIN B AND ( RESID 437:586 OR RESID 801:803 ) )B801 - 803
15X-RAY DIFFRACTION8( CHAIN B AND ( RESID 587:717 OR RESID 1012:1014 ) )B587 - 717
16X-RAY DIFFRACTION8( CHAIN B AND ( RESID 587:717 OR RESID 1012:1014 ) )B1012 - 1014

+
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