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- PDB-1u6b: CRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS -

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Entry
Database: PDB / ID: 1u6b
TitleCRYSTAL STRUCTURE OF A SELF-SPLICING GROUP I INTRON WITH BOTH EXONS
Components
  • 197-MER
  • 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP *GP*CP*C)-3'
  • 5'-R(*CP*AP*(5MU))-3'
  • U1 small nuclear ribonucleoprotein A
KeywordsSTRUCTURAL PROTEIN/RNA / INTRON / EXON / RIBOZYME / GROUP I / U1A / RNA / STRUCTURAL PROTEIN-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 ...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 / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsAdams, P.L. / Stahley, M.R. / Kosek, A.B. / Wang, J. / Strobel, S.A.
Citation
Journal: Nature / Year: 2004
Title: Crystal Structure of a Self-Splicing Group I Intron with Both Exons.
Authors: Adams, P.L. / Stahley, M.R. / Kosek, A.B. / Wang, J. / Strobel, S.A.
#1: Journal: To be published
Title: Crystal Structure of a Group I Intron Splicing Intermediate
Authors: Adams, P.L. / Stahely, M.R. / Gill, M.L. / Berman, C. / Kosek, A.B. / Wang, J. / Strobel, S.A.
#2: Journal: To be published
Title: RNA Kink Turns to the Left and to the Right
Authors: Strobel, S.A. / Adams, P.L. / Stahley, M.R. / Wang, J.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1981
Title: In Vitro Splicing of the Ribosomal RNA Precursor of Tetrahymena: Involvement of a Guanosine Nucleotide in the Excision of Intervening Sequence
Authors: Cech, T.R. / Zaug, A.J. / Grabowaski, P.J.
#4: Journal: Nature / Year: 1992
Title: Self-Splicing Intron in tRNA Genes of Widely Divergent Bacteria
Authors: Reinhold-Hurek, B. / Shub, D.A.
History
DepositionJul 29, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionAug 10, 2004ID: 1T42
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE NUCLEOTIDES 1001B TO 1014B BELONG TO AN ENGINEERED U1A LOOP AND ARE INSERTED BETWEEN GUA- ...SEQUENCE NUCLEOTIDES 1001B TO 1014B BELONG TO AN ENGINEERED U1A LOOP AND ARE INSERTED BETWEEN GUA-107B AND CYT-112B. THERE ARE NO NUCLEOTIDES BETWEEN GUA-1B AND GUA-5B DUE TO A CLONING DESIGN. O2' OF DEOXY MODIFICATION OF RNA NUCLEOTIDES ARE INCLUDED WITH Q=0.00 AND B=0.00. THEY ARE AT GUA-206C, CYT-1C, CYT-205C, AND THY-1D. CHAINS B AND C ARE TWO PARTS OF THE ORIGINAL ONE INTRON SEQUENCE BECAUSE OF AN EXPERIMENTAL DESIGN. THE U1A PROTEIN USED IN THIS STUDY WAS A DOUBLE MUTANT IN WHICH TYR-31/GLN-36 WAS REPLACED WITH HIS-31/ARG-36. THE FIRST THREE RESIDUES IN U1A PROTEIN WERE MISSING IN THE STRUCTURE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: 197-MER
C: 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP *GP*CP*C)-3'
D: 5'-R(*CP*AP*(5MU))-3'
A: U1 small nuclear ribonucleoprotein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,86422
Polymers83,3524
Non-polymers51118
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.541, 108.541, 249.158
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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RNA chain , 3 types, 3 molecules BCD

#1: RNA chain 197-MER


Mass: 64057.023 Da / Num. of mol.: 1 / Fragment: GROUP I INTRON / Source method: obtained synthetically / Details: RNA WAS IS TRANSCRIBED BY T7 RNA POLYMERASE.
#2: RNA chain 5'-R(*AP*AP*GP*CP*CP*AP*CP*AP*CP*AP*AP*AP*CP*CP*AP*GP*AP*CP*GP *GP*CP*C)-3'


Mass: 7045.354 Da / Num. of mol.: 1 / Fragment: GROUP I EXON / Source method: obtained synthetically
#3: RNA chain 5'-R(*CP*AP*(5MU))-3'


Mass: 909.623 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Protein , 1 types, 1 molecules A

#4: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 11340.315 Da / Num. of mol.: 1 / Mutation: Y31H,Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: PET11 / Production host: Escherichia coli (E. coli) / References: UniProt: P09012

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Non-polymers , 3 types, 72 molecules

#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 4.4 Å3/Da / Density % sol: 72.06 %
Crystal growpH: 6.8 / Details: pH 6.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 24640

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.1→48.22 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.872 / SU B: 22.65 / SU ML: 0.382 / Cross valid method: THROUGHOUT / ESU R: 1.805 / ESU R Free: 0.444 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 1086 4.4 %RANDOM
Rwork0.24572 ---
obs0.24712 23553 89.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 80.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--0.6 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms775 4768 18 54 5615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216118
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3332.8839357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.257594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.21000
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022899
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.1583.5476
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1364771
X-RAY DIFFRACTIONr_scbond_it2.42555642
X-RAY DIFFRACTIONr_scangle_it4.2888586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.267 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.375 131
Rwork0.32 2660
Refinement TLS params.Method: refined / Origin x: 42.8243 Å / Origin y: 86.5701 Å / Origin z: 61.9647 Å
111213212223313233
T0.3316 Å2-0.1263 Å20.2437 Å2-0.1048 Å2-0.0604 Å2--0.2601 Å2
L0.7126 °2-0.1026 °20.1122 °2--0.0291 °2-0.0227 °2--0.1295 °2
S-0.1133 Å °0.0084 Å °-0.3508 Å °-0.0406 Å °0.0706 Å °-0.0343 Å °-0.0699 Å °0.0939 Å °0.0426 Å °

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