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- PDB-3ivk: Crystal Structure of the Catalytic Core of an RNA Polymerase Ribo... -

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Basic information

Entry
Database: PDB / ID: 3ivk
TitleCrystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment
Components
  • Fab heavy chain
  • Fab light chain
  • class I ligase product
Keywordsimmune system / RNA / catalytic RNA / protein RNA complex / RNA polymerase ribozyme / RNA hairpin epitope / immune system - RNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsKoldobskaya, Y. / Duguid, E.M. / Shechner, D.M. / Koide, S. / Kossiakoff, A.A. / Bartel, D.P. / Piccirilli, J.A.
Citation
Journal: Science / Year: 2009
Title: Crystal structure of the catalytic core of an RNA-polymerase ribozyme.
Authors: Shechner, D.M. / Grant, R.A. / Bagby, S.C. / Koldobskaya, Y. / Piccirilli, J.A. / Bartel, D.P.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2010
Title: A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination.
Authors: Koldobskaya, Y. / Duguid, E.M. / Shechner, D.M. / Suslov, N.B. / Ye, J. / Sidhu, S.S. / Bartel, D.P. / Koide, S. / Kossiakoff, A.A. / Piccirilli, J.A.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab light chain
H: Fab heavy chain
B: Fab light chain
A: Fab heavy chain
M: class I ligase product
C: class I ligase product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,52143
Polymers176,4246
Non-polymers1,09837
Water1,874104
1
L: Fab light chain
H: Fab heavy chain
M: class I ligase product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,77322
Polymers88,2123
Non-polymers56119
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-142 kcal/mol
Surface area38220 Å2
MethodPISA
2
B: Fab light chain
A: Fab heavy chain
C: class I ligase product
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,74921
Polymers88,2123
Non-polymers53718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-143 kcal/mol
Surface area38220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.499, 206.452, 135.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11M-126-

MG

21C-126-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A
13M
23C
14M
24C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111L1 - 215
2111B1 - 215
1121H1 - 233
2121A1 - 233
1131M1 - 128
2131C1 - 128
1141M122 - 137
2141C122 - 137

NCS ensembles :
ID
1
2
3
4

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Components

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RNA chain , 1 types, 2 molecules MC

#3: RNA chain class I ligase product


Mass: 41299.711 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: syn

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Antibody , 2 types, 4 molecules LBHA

#1: Antibody Fab light chain


Mass: 23162.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: man / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab heavy chain


Mass: 23749.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: man / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 141 molecules

#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 277 K / pH: 6
Details: Fab-RNA: 10 mM Tris pH 7.6, 20.1 mM MgCl2, 0.1 mM EDTA, 150 mM NaCl. Screen solution: 50 mM cacodylate pH 6.0, 20 mM NaCl, 1 mM CdCl2, 32% MPD. Cryo: Paratone-N, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 52330 / % possible obs: 98.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 6.1
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.585 / % possible all: 79.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.1 Å49.8 Å
Translation3.1 Å49.8 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMAC5.4.0073refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 35.104 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.659 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2648 5.1 %RANDOM
Rwork0.207 ---
obs0.208 52239 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6604 5470 37 104 12215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02113092
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3232.49819152
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.765870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65323.672256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.239151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0731532
X-RAY DIFFRACTIONr_chiral_restr0.0580.22328
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1911.54348
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.4127026
X-RAY DIFFRACTIONr_scbond_it0.71638744
X-RAY DIFFRACTIONr_scangle_it1.254.512126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11L1629tight positional0.020.05
12B1629tight positional0.020.05
21H1673tight positional0.010.05
22A1673tight positional0.010.05
31M2777tight positional0.050.05
32C2777tight positional0.050.05
41M68tight positional0.030.05
42C68tight positional0.030.05
11L1629tight thermal0.020.5
12B1629tight thermal0.020.5
21H1673tight thermal0.020.5
22A1673tight thermal0.020.5
31M2777tight thermal0.020.5
32C2777tight thermal0.020.5
41M68tight thermal0.050.5
42C68tight thermal0.050.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 157 -
Rwork0.317 3126 -
obs--84.24 %
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)
12.11971.5972-0.4524.5663-0.59113.0859-0.2023-0.065-0.1673-0.0205-0.2294-0.2272-0.07510.29530.4318-0.34840.01760.1485-0.19570.0384-0.248322.71153.229-43.802
25.54571.55930.05982.05120.41253.1099-0.2174-0.05890.2493-0.0048-0.18630.1417-0.2980.03350.4038-0.23080.0067-0.036-0.3494-0.1306-0.262853.27822.5799.852
35.2078-0.45543.672.3496-0.88235.76760.1862-0.4541-0.16270.4155-0.3569-0.33140.08880.07270.1706-0.1732-0.1575-0.0067-0.10310.1775-0.16747.47571.422-26.999
42.13380.00510.96034.9209-3.42365.9343-0.43440.38940.2828-0.48950.29680.2258-0.1472-0.13130.1375-0.1195-0.1548-0.1832-0.1480.0043-0.158971.70247.148-6.972
52.72472.79951.13663.95621.5543.65420.2049-0.4189-0.4530.4997-0.3113-0.3139-0.04650.04460.1065-0.2194-0.02440.1358-0.14950.1767-0.109419.542.452-25.641
63.6322.8078-1.80593.2593-1.08613.3712-0.28530.51540.303-0.49510.19740.47810.01410.00760.088-0.1584-0.0323-0.176-0.1777-0.1414-0.110842.47819.474-8.319
72.57491.2166-0.14386.0993-1.20532.92040.3757-0.81080.10590.9815-0.34940.2024-0.3766-0.3494-0.0262-0.0041-0.13690.01120.21930.0495-0.25836.83174.302-15.662
86.41211.07821.80492.88280.4252.7033-0.28750.956-0.1549-0.77050.31490.01010.21340.3276-0.02750.1722-0.1354-0.05620.0064-0.001-0.264874.47936.509-18.319
91.50030.80230.77270.46820.20641.487-0.30540.386-0.3269-0.24030.1369-0.05760.1907-0.08440.16840.0886-0.08060.3687-0.079-0.16760.09098.46529.096-67.421
100.46960.8063-0.07191.6427-0.74091.48710.1608-0.23210.060.4296-0.32160.33990.1021-0.18140.1609-0.0886-0.07820.18970.075-0.36210.106529.0898.45133.435
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2B1 - 108
3X-RAY DIFFRACTION3L109 - 213
4X-RAY DIFFRACTION4B109 - 213
5X-RAY DIFFRACTION5H3 - 125
6X-RAY DIFFRACTION6A3 - 125
7X-RAY DIFFRACTION7H126 - 226
8X-RAY DIFFRACTION8A126 - 226
9X-RAY DIFFRACTION9M1 - 121
10X-RAY DIFFRACTION10C1 - 121

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