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- PDB-3l3c: Crystal structure of the Bacillus anthracis glmS ribozyme bound t... -

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Basic information

Entry
Database: PDB / ID: 3l3c
TitleCrystal structure of the Bacillus anthracis glmS ribozyme bound to Glc6P
Components
  • GLMS RIBOZYME
  • RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
KeywordsRNA binding protein/RNA / catalytic RNA / RNA binding 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
6-O-phosphono-alpha-D-glucopyranose / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsStrobel, S.A. / Cochrane, J.C. / Lipchock, S.V. / Smith, K.D.
CitationJournal: Biochemistry / Year: 2009
Title: Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme
Authors: Cochrane, J.C. / Lipchock, S.V. / Smith, K.D. / Strobel, S.A.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: RCSB
SupersessionDec 29, 2009ID: 3G95
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: 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 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
E: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: GLMS RIBOZYME
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: GLMS RIBOZYME
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: GLMS RIBOZYME
D: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
H: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)242,44432
Polymers241,01512
Non-polymers1,42920
Water68538
1
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
E: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6118
Polymers60,2543
Non-polymers3575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
F: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6118
Polymers60,2543
Non-polymers3575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
G: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6118
Polymers60,2543
Non-polymers3575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
H: RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: GLMS RIBOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,6118
Polymers60,2543
Non-polymers3575
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.882, 234.947, 104.540
Angle α, β, γ (deg.)90.000, 90.550, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a ternary complex and there are four biological units in the asymmetric unit (chains a,e&p, chains b,f&q, chains c,g&r, and chains d,h&s

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Components

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RNA chain , 2 types, 8 molecules EFGHPQRS

#2: RNA chain
RNA (5'-R(*AP*(A2M)*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')


Mass: 4177.608 Da / Num. of mol.: 4 / Mutation: 2'-OH at A-1 / Source method: obtained synthetically / Details: synthesized at Dharmacon
#3: RNA chain
GLMS RIBOZYME


Mass: 45624.859 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: in vitro transcribed from a DNA template

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A


Mass: 10451.204 Da / Num. of mol.: 4 / Fragment: RNA BINDING DOMAIN / 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) / Strain (production host): BL21 / References: UniProt: P09012
#5: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 54 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 49.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 11% PEG 8000, 9% DMSO, 0.02M SODIUM CACODYLATE, 0.02M MAGNESIUM CHLORIDE, 0.15M POTASSIUM CHLORIDE, pH 6.8, vapor diffusion, sitting drops, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 52648 / Num. obs: 52648 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Χ2: 1.029 / Net I/σ(I): 14.4
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.832 / Num. unique all: 4552 / Χ2: 1.026 / % possible all: 85.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
REFMAC5.5.0102phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→46.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.037 / SU ML: 0.447 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.303 2665 5.1 %RANDOM
Rwork0.263 ---
all0.265 52648 --
obs0.265 52533 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 162.32 Å2 / Biso mean: 83.982 Å2 / Biso min: 33.08 Å2
Baniso -1Baniso -2Baniso -3
1-4.1 Å20 Å2-0.87 Å2
2---4.09 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.85→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2864 13081 80 38 16063
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02117603
X-RAY DIFFRACTIONr_angle_refined_deg1.0912.84726753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7185356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.64223.636132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.91515544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg161520
X-RAY DIFFRACTIONr_chiral_restr0.0640.23511
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028423
X-RAY DIFFRACTIONr_mcbond_it0.1651.51796
X-RAY DIFFRACTIONr_mcangle_it0.322892
X-RAY DIFFRACTIONr_scbond_it0.604315807
X-RAY DIFFRACTIONr_scangle_it1.0744.523861
LS refinement shellResolution: 2.847→2.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.56 159 -
Rwork0.508 2998 -
all-3157 -
obs--79.96 %

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