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

ID or keywords:

Entry

Database: PDB / ID: 3ivk

Title

Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment

Components

Fab heavy chainFragment antigen-binding
Fab light chainFragment antigen-binding
class I ligase product

Keywords

immune system / RNA /

catalytic RNA / protein RNA complex / RNA polymerase ribozyme / RNA hairpin epitope /

immune system - RNA complex

Function / homology

Immunoglobulins /

Immunoglobulin-like /

Sandwich / Mainly Beta / : /

RNA / RNA (> 10) / RNA (> 100)

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.1 Å

Authors

Koldobskaya, 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.

History

Deposition	Sep 1, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ivk.cif.gz	314.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ivk.ent.gz	254.8 KB	Display	PDB format
PDBx/mmJSON format	3ivk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iv/3ivk ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3ivk	HTTPS FTP

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Related structure data

Related structure data	3hhnC C: citing same article (ref.)
Similar structure data	3uiz-d 4pz7-d 3be6-d 1zgl-4 4mw6-d 6id4-2 5kop-1 2p8w-d 4w8w-d 2i6e-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#121 - Jan 2010 70S Ribosomes similarity (2) #130 - Oct 2010 Riboswitches similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #253 - Jan 2021 Expressome similarity (2) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase similarity (1) #15 - Mar 2001 Transfer RNA similarity (1) #10 - Oct 2000 Ribosome similarity (2) #210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (2) #245 - May 2020 Spliceosomes similarity (2) #65 - May 2005 Self-splicing RNA similarity (2) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (2) #105 - Sep 2008 Ribonuclease A similarity (1) #98 - Feb 2008 Small Interfering RNA similarity (1) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #106 - Oct 2008 Poly(A) Polymerase similarity (1) #143 - Nov 2011 Toll-like Receptors similarity (1) #230 - Feb 2019 Initiation Factor eIF4E similarity (1) #81 - Sep 2006 Elongation Factors similarity (1) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#121 - Jan 2010
70S Ribosomes
similarity (2)
#130 - Oct 2010
Riboswitches
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
similarity (1)
#157 - Jan 2013
Transfer-Messenger RNA
similarity (2)
#260 - Aug 2021
Ribonuclease P
similarity (2)
#253 - Jan 2021
Expressome
similarity (2)
#229 - Jan 2019
Fluorescent RNA Aptamers
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (2)
#249 - Sep 2020
SARS-CoV-2 RNA-dependent RNA Polymerase
similarity (1)
#15 - Mar 2001
Transfer RNA
similarity (1)
#10 - Oct 2000
Ribosome
similarity (2)
#210 - Jun 2017
Adenine Riboswitch in Action
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
similarity (2)
#245 - May 2020
Spliceosomes
similarity (2)
#65 - May 2005
Self-splicing RNA
similarity (2)
#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#105 - Sep 2008
Ribonuclease A
similarity (1)
#98 - Feb 2008
Small Interfering RNA
similarity (1)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#161 - May 2013
Ricin
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#106 - Oct 2008
Poly(A) Polymerase
similarity (1)
#143 - Nov 2011
Toll-like Receptors
similarity (1)
#230 - Feb 2019
Initiation Factor eIF4E
similarity (1)
#81 - Sep 2006
Elongation Factors
similarity (1)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#21 - Sep 2001
Antibodies
similarity (1)
#256 - Apr 2021
SARS-CoV-2 Spike and Antibodies
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

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

178 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

L: Fab light chain

H: Fab heavy chain

M: class I ligase product

hetero molecules

defined by author&software
88.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fab light chain

A: Fab heavy chain

C: class I ligase product

hetero molecules

defined by author&software
88.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	M-126- MG
2	1	C-126- MG

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	L
2	1	B
1	2	H
2	2	A
1	3	M
2	3	C
1	4	M
2	4	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	L	1 - 215
2	1	1	1	B	1 - 215
1	1	2	1	H	1 - 233
2	1	2	1	A	1 - 233
1	1	3	1	M	1 - 128
2	1	3	1	C	1 - 128
1	1	4	1	M	122 - 137
2	1	4	1	C	122 - 137

NCS ensembles :

ID
1
2
3
4

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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 / Fragment antigen-binding 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 / Fragment antigen-binding 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 / Chloride Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.13 Å³/Da / Density % sol: 70.19 %
Crystal grow	Temperature: 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 source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.127 Å / Relative weight: 1
Reflection	Resolution: 3.1→50 Å / Num. obs: 52330 / % possible obs: 98.2 % / Redundancy: 6.7 % / R_merge(I) obs: 0.155 / Net I/σ(I): 6.1
Reflection shell	Resolution: 3.1→3.15 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.585 / % possible all: 79.6

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	3.1 Å	49.8 Å
Translation	3.1 Å	49.8 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER	1.3.3	phasing
REFMAC	5.4.0073	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.1→50 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.225	2648	5.1 %	RANDOM
R_work	0.207	-	-	-
obs	0.208	52239	98.2 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 68.09 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.79 Å²	0 Å²	0 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6604	5470	37	104	12215

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.021	13092
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.323	2.498	19152
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.76	5	870
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.653	23.672	256
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.239	15	1072
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.073	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	2328
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	7802
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.191	1.5	4348
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.41	2	7026
X-RAY DIFFRACTION	r_scbond_it	0.716	3	8744
X-RAY DIFFRACTION	r_scangle_it	1.25	4.5	12126
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	L	1629	tight positional	0.02	0.05
1	2	B	1629	tight positional	0.02	0.05
2	1	H	1673	tight positional	0.01	0.05
2	2	A	1673	tight positional	0.01	0.05
3	1	M	2777	tight positional	0.05	0.05
3	2	C	2777	tight positional	0.05	0.05
4	1	M	68	tight positional	0.03	0.05
4	2	C	68	tight positional	0.03	0.05
1	1	L	1629	tight thermal	0.02	0.5
1	2	B	1629	tight thermal	0.02	0.5
2	1	H	1673	tight thermal	0.02	0.5
2	2	A	1673	tight thermal	0.02	0.5
3	1	M	2777	tight thermal	0.02	0.5
3	2	C	2777	tight thermal	0.02	0.5
4	1	M	68	tight thermal	0.05	0.5
4	2	C	68	tight thermal	0.05	0.5

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.347	157	-
R_work	0.317	3126	-
obs	-	-	84.24 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.1197	1.5972	-0.452	4.5663	-0.5911	3.0859	-0.2023	-0.065	-0.1673	-0.0205	-0.2294	-0.2272	-0.0751	0.2953	0.4318	-0.3484	0.0176	0.1485	-0.1957	0.0384	-0.2483	22.711	53.229	-43.802
2	5.5457	1.5593	0.0598	2.0512	0.4125	3.1099	-0.2174	-0.0589	0.2493	-0.0048	-0.1863	0.1417	-0.298	0.0335	0.4038	-0.2308	0.0067	-0.036	-0.3494	-0.1306	-0.2628	53.278	22.579	9.852
3	5.2078	-0.4554	3.67	2.3496	-0.8823	5.7676	0.1862	-0.4541	-0.1627	0.4155	-0.3569	-0.3314	0.0888	0.0727	0.1706	-0.1732	-0.1575	-0.0067	-0.1031	0.1775	-0.167	47.475	71.422	-26.999
4	2.1338	0.0051	0.9603	4.9209	-3.4236	5.9343	-0.4344	0.3894	0.2828	-0.4895	0.2968	0.2258	-0.1472	-0.1313	0.1375	-0.1195	-0.1548	-0.1832	-0.148	0.0043	-0.1589	71.702	47.148	-6.972
5	2.7247	2.7995	1.1366	3.9562	1.554	3.6542	0.2049	-0.4189	-0.453	0.4997	-0.3113	-0.3139	-0.0465	0.0446	0.1065	-0.2194	-0.0244	0.1358	-0.1495	0.1767	-0.1094	19.5	42.452	-25.641
6	3.632	2.8078	-1.8059	3.2593	-1.0861	3.3712	-0.2853	0.5154	0.303	-0.4951	0.1974	0.4781	0.0141	0.0076	0.088	-0.1584	-0.0323	-0.176	-0.1777	-0.1414	-0.1108	42.478	19.474	-8.319
7	2.5749	1.2166	-0.1438	6.0993	-1.2053	2.9204	0.3757	-0.8108	0.1059	0.9815	-0.3494	0.2024	-0.3766	-0.3494	-0.0262	-0.0041	-0.1369	0.0112	0.2193	0.0495	-0.258	36.831	74.302	-15.662
8	6.4121	1.0782	1.8049	2.8828	0.425	2.7033	-0.2875	0.956	-0.1549	-0.7705	0.3149	0.0101	0.2134	0.3276	-0.0275	0.1722	-0.1354	-0.0562	0.0064	-0.001	-0.2648	74.479	36.509	-18.319
9	1.5003	0.8023	0.7727	0.4682	0.2064	1.487	-0.3054	0.386	-0.3269	-0.2403	0.1369	-0.0576	0.1907	-0.0844	0.1684	0.0886	-0.0806	0.3687	-0.079	-0.1676	0.0909	8.465	29.096	-67.421
10	0.4696	0.8063	-0.0719	1.6427	-0.7409	1.4871	0.1608	-0.2321	0.06	0.4296	-0.3216	0.3399	0.1021	-0.1814	0.1609	-0.0886	-0.0782	0.1897	0.075	-0.3621	0.1065	29.089	8.451	33.435

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	L	1 - 108
2	X-RAY DIFFRACTION	2	B	1 - 108
3	X-RAY DIFFRACTION	3	L	109 - 213
4	X-RAY DIFFRACTION	4	B	109 - 213
5	X-RAY DIFFRACTION	5	H	3 - 125
6	X-RAY DIFFRACTION	6	A	3 - 125
7	X-RAY DIFFRACTION	7	H	126 - 226
8	X-RAY DIFFRACTION	8	A	126 - 226
9	X-RAY DIFFRACTION	9	M	1 - 121
10	X-RAY DIFFRACTION	10	C	1 - 121

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Yorodumi