PDB-3hhn: Crystal structure of class I ligase ribozyme self-ligation produc...

ID or keywords:

Entry

Database: PDB / ID: 3hhn

Title

Crystal structure of class I ligase ribozyme self-ligation product, in complex with U1A RBD

Components

Class I ligase ribozyme, self-ligation product
U1 small nuclear ribonucleoprotein A

Keywords

LIGASE/RNA / Ligase Ribozyme / Ribozyme / Catalytic RNA / Protein-RNA complex / Ribonucleoprotein / RNA-binding / LIGASE-RNA COMPLEX

Function / homology

Function and homology information

U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.987 Å

Authors

Shechner, D.M. / Grant, R.A. / Bagby, S.C. / Bartel, D.P.

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	May 15, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 24, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Oct 13, 2021	Group: Database references / Derived calculations Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3hhn.cif.gz	214.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3hhn_validation.pdf.gz	480.8 KB	Display	wwPDB validaton report
Full document	3hhn_full_validation.pdf.gz	498.7 KB	Display
Data in XML	3hhn_validation.xml.gz	25.2 KB	Display
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/3hhn ftp://data.pdbj.org/pub/pdb/validation_reports/hh/3hhn	HTTPS FTP

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Related structure data

Related structure data	3ivkC C: citing same article (ref.)
Similar structure data	3r1l-d 3r1h-d 2wmn-1 1slq-4 11607 2onl-d 2wmo-1 5ukl-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (6) #121 - Jan 2010 70S Ribosomes similarity (2) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1) #157 - Jan 2013 Transfer-Messenger RNA similarity (2) #253 - Jan 2021 Expressome similarity (2) #260 - Aug 2021 Ribonuclease P similarity (2) #181 - Jan 2015 Cascade and CRISPR similarity (1) #229 - Jan 2019 Fluorescent RNA Aptamers similarity (1) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (2) #65 - May 2005 Self-splicing RNA similarity (7) #15 - Mar 2001 Transfer RNA similarity (1) #249 - Sep 2020 SARS-CoV-2 RNA-dependent RNA Polymerase 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) #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) #161 - May 2013 Ricin similarity (2) #227 - Nov 2018 Telomerase similarity (2) #266 - Feb 2022 Oligosaccharyltransferase similarity (2) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #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) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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PDBj /

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Related items in Molecule of the Month

#130 - Oct 2010
Riboswitches
similarity (6)
#121 - Jan 2010
70S Ribosomes
similarity (2)
#16 - Apr 2001
Aminoacyl-tRNA Synthetases
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#157 - Jan 2013
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#253 - Jan 2021
Expressome
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#146 - Feb 2012
Aminoglycoside Antibiotics
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#65 - May 2005
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#15 - Mar 2001
Transfer RNA
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#249 - Sep 2020
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similarity (1)
#10 - Oct 2000
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Zinc Fingers
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#226 - Oct 2018
Aminoglycoside Antibiotics and Resistance
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#245 - May 2020
Spliceosomes
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#262 - Oct 2021
Fifty Years of Open Access to PDB Structures
similarity (2)
#105 - Sep 2008
Ribonuclease A
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#98 - Feb 2008
Small Interfering RNA
similarity (1)
#161 - May 2013
Ricin
similarity (2)
#227 - Nov 2018
Telomerase
similarity (2)
#266 - Feb 2022
Oligosaccharyltransferase
similarity (2)
#104 - Aug 2008
Selenocysteine Synthase
similarity (1)
#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)
#89 - May 2007
Aconitase and Iron Regulatory Protein 1
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

B: U1 small nuclear ribonucleoprotein A

C: Class I ligase ribozyme, self-ligation product

D: U1 small nuclear ribonucleoprotein A

E: Class I ligase ribozyme, self-ligation product

hetero molecules

112 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	59.561, 70.412, 70.906
Angle α, β, γ (deg.)	100.29, 99.61, 103.89
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.997674, -0.02015, -0.06512), (0.054503, 0.337955, -0.939583), (0.04094, -0.940947, -0.33607)	44.2229, 4.07716, 6.07216
2	given	(-0.996547, 0.082889, 0.004858), (0.014281, 0.228743, -0.973382), (-0.081794, -0.969952, -0.229137)	43.9515, 4.13934, 13.7552
3	given	(-0.99696, 0.076586, 0.014306), (0.004375, 0.238361, -0.971167), (-0.077788, -0.968152, -0.237971)	44.2542, 4.76111, 13.2276
4	given	(-0.989498, 0.083346, -0.118099), (0.070917, -0.432026, -0.899069), (-0.125955, -0.898002, 0.421578)	37.141102, 2.3111, 45.9007

Details

THIS CRYSTAL STRUCTURE IS NOT A BIOLOGICAL ASSEMBLY. IN SOLUTION, THE RNA-U1A COMPLEX IS EXPECTED TO HAVE ONE COPY OF EACH MOLECULE.

#1: Protein	U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A Mass: 11209.120 Da / Num. of mol.: 2 / Fragment: RNA binding domain: UNP residues 1-100 / Mutation: Y31H, Q31R Source method: isolated from a genetically manipulated source Details: Overexpressed in E. coli from a pET11a derivative bearing the the "double" mutant U1A RBD (1-98) Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: Modified pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09012
#2: RNA chain	Class I ligase ribozyme, self-ligation product Mass: 44168.270 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic construct transcribed in vitro using T7 RNA polymerase off of a linearized plasmid pUC307HP
#3: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.49 Å³/Da / Density % sol: 50.58 %

Crystal grow

Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50mM Sodium cacodylate pH 6.0, 40mM Magnesium acetate, 26% 2-methyl-2,4-pentane diol (MPD), 1mM Spermine HCl. Diffraction-quality crystals grown by microseeding., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Components of the solutions

ID	Name	Crystal-ID	Sol-ID
1	Sodium cacodylate	1	1
2	Magnesium acetate	1	1
3	MPD	1	1
4	Spermine HCl	1	1
5	Sodium cacodylate	1	2
6	Magnesium acetate	1	2
7	MPD	1	2
8	Spermine HCl	1	2

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 8-BM / Wavelength: 0.9792 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2004

Radiation

Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9792 Å / Relative weight: 1

Reflection

Resolution: 2.987→50 Å / Num. obs: 21075 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / R_merge(I) obs: 0.069 / Χ²: 2.471 / Net I/σ(I): 28.185

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
2.987-3.11	3.2	0.311	2069	1.977	93.9
3.11-3.23	3.6	0.231	2120	2.108	98.2
3.23-3.38	3.8	0.187	2147	2.169	98.8
3.38-3.56	3.7	0.172	2066	3.301	95.3
3.56-3.78	3.7	0.133	2091	3.513	96.7
3.78-4.07	3.7	0.105	2041	2.913	94.6
4.07-4.48	3.9	0.067	2176	2.146	99.1
4.48-5.13	3.8	0.055	2134	2.173	99
5.13-6.46	3.8	0.044	2179	2.193	99.4
6.46-50	3.7	0.033	2052	2.257	95

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
SHELXD		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.987→40.121 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.773 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.234	1078	5.12 %	Random
R_work	0.202	-	-	-
obs	0.202	21046	96.7 %	-

Solvent computation

B_sol: 29.083 Å² / k_sol: 0.249 e/Å³

Displacement parameters

B_iso max: 174.15 Å² / B_iso mean: 77.482 Å² / B_iso min: 30.91 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.445 Å²	0.804 Å²	4.474 Å²
2-	-	-1.81 Å²	-9.248 Å²
3-	-	-	-0.635 Å²

Refine analyze

Luzzati coordinate error obs: 0.33 Å

Refinement step

Cycle: LAST / Resolution: 2.987→40.121 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1475	5844	34	192	7545

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.797	1
X-RAY DIFFRACTION	f_bond_d	0.002	1
X-RAY DIFFRACTION	f_chiral_restr	0.032	1
X-RAY DIFFRACTION	f_dihedral_angle_d	19.955	1
X-RAY DIFFRACTION	f_plane_restr	0.002	1
X-RAY DIFFRACTION	f_nbd_refined	4.084	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.987-3.013	0.31	434	X-RAY DIFFRACTION	40	78
3.013-3.039	0.292	482	X-RAY DIFFRACTION	40	89
3.039-3.066	0.277	500	X-RAY DIFFRACTION	40	93
3.066-3.094	0.271	509	X-RAY DIFFRACTION	40	90
3.094-3.123	0.266	494	X-RAY DIFFRACTION	40	92
3.123-3.154	0.273	491	X-RAY DIFFRACTION	40	94
3.154-3.185	0.257	519	X-RAY DIFFRACTION	40	94
3.185-3.218	0.24	520	X-RAY DIFFRACTION	40	94
3.218-3.252	0.225	509	X-RAY DIFFRACTION	40	93
3.252-3.288	0.231	491	X-RAY DIFFRACTION	40	94
3.288-3.325	0.236	528	X-RAY DIFFRACTION	40	93
3.325-3.365	0.257	519	X-RAY DIFFRACTION	40	95
3.365-3.405	0.247	480	X-RAY DIFFRACTION	40	93
3.405-3.449	0.341	429	X-RAY DIFFRACTION	40	83
3.449-3.494	0.246	534	X-RAY DIFFRACTION	40	91
3.494-3.542	0.248	509	X-RAY DIFFRACTION	40	95
3.542-3.592	0.235	486	X-RAY DIFFRACTION	40	94
3.592-3.646	0.244	505	X-RAY DIFFRACTION	40	89
3.646-3.703	0.28	478	X-RAY DIFFRACTION	40	88
3.703-3.763	0.196	507	X-RAY DIFFRACTION	40	94
3.763-3.828	0.215	496	X-RAY DIFFRACTION	40	92
3.828-3.898	0.28	454	X-RAY DIFFRACTION	40	85
3.898-3.973	0.229	485	X-RAY DIFFRACTION	40	87
3.973-4.054	0.178	493	X-RAY DIFFRACTION	40	93
4.054-4.142	0.182	525	X-RAY DIFFRACTION	40	94
4.142-4.238	0.186	517	X-RAY DIFFRACTION	40	93
4.238-4.344	0.192	507	X-RAY DIFFRACTION	40	95
4.344-4.461	0.175	517	X-RAY DIFFRACTION	40	95
4.461-4.592	0.174	508	X-RAY DIFFRACTION	40	95
4.592-4.74	0.169	533	X-RAY DIFFRACTION	40	95
4.74-4.91	0.186	502	X-RAY DIFFRACTION	40	95
4.91-5.106	0.184	494	X-RAY DIFFRACTION	40	91
5.106-5.338	0.172	526	X-RAY DIFFRACTION	40	94
5.338-5.618	0.166	507	X-RAY DIFFRACTION	40	96
5.618-5.969	0.172	516	X-RAY DIFFRACTION	40	93
5.969-6.429	0.172	514	X-RAY DIFFRACTION	40	94
6.429-7.072	0.184	510	X-RAY DIFFRACTION	40	95
7.072-8.088	0.164	501	X-RAY DIFFRACTION	40	93
8.088-10.163	0.158	518	X-RAY DIFFRACTION	40	93
10.163-40.125	0.139	421	X-RAY DIFFRACTION	40	79

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