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- PDB-6xjy: Crystal structure of a self-alkylating ribozyme - short time incu... -

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Basic information

Entry
Database: PDB / ID: 6xjy
TitleCrystal structure of a self-alkylating ribozyme - short time incubation with the 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 / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
Aeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.156 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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)145,2276
Polymers145,2276
Non-polymers00
Water4,900272
1
A: Self-alkylating ribozyme (58-MER)
H: Fab HAVx Heavy Chain
L: Fab HAVx Light Chain


Theoretical massNumber of molelcules
Total (without water)72,6143
Polymers72,6143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-42 kcal/mol
Surface area28340 Å2
MethodPISA
2
B: Self-alkylating ribozyme (58-MER)
C: Fab HAVx Heavy Chain
D: Fab HAVx Light Chain


Theoretical massNumber of molelcules
Total (without water)72,6143
Polymers72,6143
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-44 kcal/mol
Surface area28330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.603, 79.382, 106.067
Angle α, β, γ (deg.)90.000, 111.520, 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 - 228
212chain HH1 - 228
113chain DD1 - 214
213chain LL1 - 214

NCS ensembles :
ID
1
2
3

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 0.1 M ammonium fluoride, 10% PEG3350, pH 6.2

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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: Feb 13, 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: 2.156→79.38 Å / Num. obs: 69519 / % possible obs: 97.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 44.31 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.072 / Rrim(I) all: 0.153 / Net I/av σ(I): 7.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.16→2.2 Å / Redundancy: 4 % / Rmerge(I) obs: 1.867 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 4237 / CC1/2: 0.295 / Rpim(I) all: 1.046 / Rrim(I) all: 2.148 / % possible all: 91.5

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MWN

6mwn


Resolution: 2.156→61.851 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2851 2006 2.91 %
Rwork0.2271 66912 -
obs0.2288 68918 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.71 Å2 / Biso mean: 47.6681 Å2 / Biso min: 26.67 Å2
Refinement stepCycle: final / Resolution: 2.156→61.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 2474 0 272 9454
Biso mean---45.48 -
Num. residues----994
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1386X-RAY DIFFRACTION8.958TORSIONAL
12B1386X-RAY DIFFRACTION8.958TORSIONAL
21C2025X-RAY DIFFRACTION8.958TORSIONAL
22H2025X-RAY DIFFRACTION8.958TORSIONAL
31D2026X-RAY DIFFRACTION8.958TORSIONAL
32L2026X-RAY DIFFRACTION8.958TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.156-2.20950.41191270.3555413683
2.2095-2.26930.39851390.32472996
2.2693-2.3360.32981460.3001481697
2.336-2.41140.30831500.287479397
2.4114-2.49760.36951340.2907479597
2.4976-2.59760.3861420.2773477396
2.5976-2.71590.32061440.276483198
2.7159-2.8590.31941540.2621486998
2.859-3.03820.31941390.2578485198
3.0382-3.27270.31431440.2475487598
3.2727-3.6020.3441510.2234479697
3.602-4.12320.25131390.2047480497
4.1232-5.19440.2041460.1777494399
5.1944-61.8510.23391510.1884490196

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