[English] 日本語
Yorodumi
- PDB-6xjq: Crystal structure of a self-alkylating ribozyme - alkylated form ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xjq
TitleCrystal structure of a self-alkylating ribozyme - alkylated form with biotinylated epoxide substrate
Components
  • Fab HAVx Heavy Chain
  • Fab HAVx Light Chain
  • Self-alkylating ribozyme (58-MER)
KeywordsRNA/IMMUNE SYSTEM / Self-alkylating ribozyme / Antibody-assisted RNA crystallography / RNA catalysis / RNA-Immune System complex
Function / homologyChem-V4J / RNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Aeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.708 Å
AuthorsKoirala, D. / Piccirilli, J.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI081987 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM102489 United States
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.
Authors: Krochmal, D. / Shao, Y. / Li, N.S. / DasGupta, S. / Shelke, S.A. / Koirala, D. / Piccirilli, J.A.
History
DepositionJun 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 13, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Self-alkylating ribozyme (58-MER)
B: Self-alkylating ribozyme (58-MER)
C: Fab HAVx Heavy Chain
D: Fab HAVx Light Chain
H: Fab HAVx Heavy Chain
L: Fab HAVx Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0048
Polymers145,2276
Non-polymers7772
Water15,043835
1
A: Self-alkylating ribozyme (58-MER)
H: Fab HAVx Heavy Chain
L: Fab HAVx Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0024
Polymers72,6143
Non-polymers3891
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-42 kcal/mol
Surface area28650 Å2
MethodPISA
2
B: Self-alkylating ribozyme (58-MER)
C: Fab HAVx Heavy Chain
D: Fab HAVx Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0024
Polymers72,6143
Non-polymers3891
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-43 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.962, 99.832, 90.636
Angle α, β, γ (deg.)90.000, 97.200, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
12chain C
22chain H
13chain D
23chain L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 58
211chain BB1 - 58
112chain CC1 - 229
212chain HH1 - 229
113chain DD1 - 214
213chain LL1 - 214

NCS ensembles :
ID
1
2
3

-
Components

#1: RNA chain Self-alkylating ribozyme (58-MER)


Mass: 18674.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Aeropyrum pernix (archaea)
#2: Antibody Fab HAVx Heavy Chain


Mass: 27588.012 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)
#3: Antibody Fab HAVx Light Chain


Mass: 26351.588 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)
#4: Chemical ChemComp-V4J / 2-{[(4R)-4-hydroxyhexyl]oxy}ethyl 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoate


Mass: 388.522 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H32N2O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 835 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M ammonium fluoride, 10% PEG3350, pH 6.2

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2018
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.708→83.3 Å / Num. obs: 159200 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/av σ(I): 11.2 / Net I/σ(I): 11.2
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.848 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7389 / CC1/2: 0.235 / Rpim(I) all: 1.16 / Rrim(I) all: 2.187 / % possible all: 93.3

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MWN

6mwn


Resolution: 1.708→83.3 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1819 1.26 %
Rwork0.1891 142234 -
obs0.1894 144053 89.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.01 Å2 / Biso mean: 45.5685 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 1.708→83.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6738 2474 52 835 10099
Biso mean--86.87 42.94 -
Num. residues----999
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1386X-RAY DIFFRACTION8.642TORSIONAL
12B1386X-RAY DIFFRACTION8.642TORSIONAL
21C2044X-RAY DIFFRACTION8.642TORSIONAL
22H2044X-RAY DIFFRACTION8.642TORSIONAL
31D2052X-RAY DIFFRACTION8.642TORSIONAL
32L2052X-RAY DIFFRACTION8.642TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7083-1.75440.4151060.3686809567
1.7544-1.80610.33121260.3312905775
1.8061-1.86440.33311270.3028969480
1.8644-1.9310.30991290.26021023484
1.931-2.00830.27331220.23911083589
2.0083-2.09970.26921420.22181107791
2.0997-2.21050.24431520.20951149194
2.2105-2.3490.23311420.2071159196
2.349-2.53030.20271520.20271179297
2.5303-2.7850.20861510.20861195498
2.785-3.1880.2351600.19791199298
3.188-4.01650.20521520.16481217099
4.0165-100.15251580.13951225299
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)
11.0229-0.0421-0.11760.63060.08660.2375-0.0813-0.6730.12230.56650.18550.12-0.2598-0.0632-0.0430.69790.12580.05480.5877-0.04290.3011-4.511316.995110.1184
20.672-0.1981-0.52861.49330.43820.5751-0.14660.89060.125-1.15820.2788-0.0745-0.61930.1074-0.04771.0613-0.2844-0.01771.00050.10280.3829-34.703221.2838-53.8967
30.65010.4526-0.19130.9387-0.36780.5018-0.0084-0.0757-0.00520.1330.0217-0.0114-0.00670.0202-0.01780.25040.0105-0.030.1825-0.00050.2546-55.27512.2044-3.8761
41.37720.7146-0.51270.7554-0.35140.4195-0.07830.0505-0.273-0.08870.0102-0.06610.0642-0.02810.08080.23890.0298-0.0330.1464-0.00790.2736-51.2421-3.6269-10.2515
50.2948-0.3357-0.30910.79730.45721.1297-0.01410.0839-0.0404-0.16130.067-0.01070.04370.0411-0.05910.2517-0.0311-0.01890.2039-0.01090.24617.935513.9814-40.1861
60.7614-0.5661-0.61840.75420.40690.7304-0.0862-0.0243-0.15090.03510.04540.05250.07990.09630.04910.3085-0.0427-0.04510.2445-0.01210.277815.162-2.9333-36.0288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA1 - 58
2X-RAY DIFFRACTION2Chain BB1 - 58
3X-RAY DIFFRACTION3Chain CC1 - 229
4X-RAY DIFFRACTION4Chain DD1 - 214
5X-RAY DIFFRACTION5Chain HH1 - 230
6X-RAY DIFFRACTION6Chain LL1 - 214

+
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