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- PDB-6xjz: Crystal structure of a self-alkylating ribozyme - apo form -

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Basic information

Entry
Database: PDB / ID: 6xjz
TitleCrystal structure of a self-alkylating ribozyme - apo form
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: 2.488 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

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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
Water2,738152
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 area5510 Å2
ΔGint-42 kcal/mol
Surface area28890 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 area5470 Å2
ΔGint-45 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.505, 82.419, 105.213
Angle α, β, γ (deg.)90.000, 111.000, 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 - 227
212chain HH1 - 227
113chain DD1 - 212
213chain LL1 - 212

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 / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.57 %
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-C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 9, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.46→162.73 Å / Num. obs: 47938 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 60.3 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.076 / Rrim(I) all: 0.141 / Net I/av σ(I): 6 / Net I/σ(I): 6
Reflection shellResolution: 2.46→2.5 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 0.5 / Num. unique obs: 4672 / CC1/2: 0.347 / Rpim(I) all: 1.519 / Rrim(I) all: 2.711 / % possible all: 95.5

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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: 2.488→81.695 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2638 2008 4.19 %
Rwork0.2001 45900 -
obs0.2029 47908 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 204.23 Å2 / Biso mean: 75.7485 Å2 / Biso min: 27.87 Å2
Refinement stepCycle: final / Resolution: 2.488→81.695 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6664 2474 0 152 9290
Biso mean---59.54 -
Num. residues----988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1386X-RAY DIFFRACTION9.309TORSIONAL
12B1386X-RAY DIFFRACTION9.309TORSIONAL
21C2001X-RAY DIFFRACTION9.309TORSIONAL
22H2001X-RAY DIFFRACTION9.309TORSIONAL
31D1982X-RAY DIFFRACTION9.309TORSIONAL
32L1982X-RAY DIFFRACTION9.309TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.488-2.55020.4261120.3423252376
2.5502-2.61920.40381350.3417333799
2.6192-2.69630.39331420.3509330399
2.6963-2.78330.41991600.3025329699
2.7833-2.88280.30061300.2594334199
2.8828-2.99820.31671600.2507331899
2.9982-3.13470.31161450.2288333899
3.1347-3.29990.3071370.2289326697
3.2999-3.50670.30421440.204335299
3.5067-3.77740.27361480.20153349100
3.7774-4.15760.25691510.19293373100
4.1576-4.75910.21711410.1564331098
4.7591-5.99570.22921500.1646337599
5.9957-81.6950.19941530.1617341999
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)
10.5125-0.1611-1.34631.14423.27845.74420.2179-0.74190.4846-0.08320.2804-0.0902-0.66510.5219-0.48060.95410.0260.04741.1489-0.27780.7469-20.2685.9950.83
20.7779-1.229-1.06461.13832.20653.0012-0.31620.4707-0.33070.03740.4443-0.06020.90191.1792-0.03611.00840.23640.16421.3614-0.17720.7998-6.849-55.007-33.739
33.66021.5864-0.85491.1878-0.60950.7797-0.11320.1917-0.0231-0.22310.16870.1140.1493-0.3747-0.04970.528-0.0192-0.04060.50410.01960.3639-56.415-46.507-18.814
42.90461.4513-1.05121.4525-0.82841.3834-0.00840.1283-0.16-0.20050.07830.03950.3375-0.1532-0.06290.56210.0027-0.06530.33670.06450.4047-51.741-57.429-5.577
50.845-0.70761.5521.002-1.62222.874-0.07050.0828-0.05540.1290.19850.215-0.1079-0.3095-0.13680.4747-0.00190.06990.53140.0270.5835-47.054-1.559-43.52
61.0018-0.45731.09651.3029-1.41653.054-0.0434-0.0510.16160.08720.03840.1844-0.0978-0.2390.02360.3546-0.04320.00440.3285-0.02010.4687-34.6179.313-50.197
70.18160.0782-0.0676-0.2867-0.08420.4148-0.0323-0.05050.00620.03120.04440.12490.00120.0385-0.01560.44710.00690.01870.29480.00930.3065-35.443-22.244-21.691
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:58 )A1 - 58
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:58 )B1 - 58
3X-RAY DIFFRACTION3( CHAIN C AND RESID 4:227 )C4 - 227
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1:212 )D1 - 212
5X-RAY DIFFRACTION5( CHAIN H AND RESID 4:227 )H4 - 227
6X-RAY DIFFRACTION6( CHAIN L AND RESID 1:212 )L1 - 212
7X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )A101 - 126
8X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )C301 - 338
9X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )B101 - 110
10X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )D301 - 326
11X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )H301 - 322
12X-RAY DIFFRACTION7( CHAIN A AND RESID 101:126 ) OR ( CHAIN C AND RESID 301:338 ) OR ( CHAIN B AND RESID 101:110 ) OR ( CHAIN D AND RESID 301:326 ) OR ( CHAIN H AND RESID 301:322 ) OR ( CHAIN L AND RESID 301:330 )L301 - 330

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