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- PDB-3g8t: Crystal structure of the G33A mutant Bacillus anthracis glmS ribo... -

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Basic information

Entry
Database: PDB / ID: 3g8t
TitleCrystal structure of the G33A mutant Bacillus anthracis glmS ribozyme bound to GlcN6P
Components
  • RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
  • U1 small nuclear ribonucleoprotein A
  • glmS glucosamine-6-phosphate activated ribozyme
KeywordsRNA binding protein/RNA / catalytic RNA / mRNA processing / mRNA splicing / Nucleus / Phosphoprotein / Ribonucleoprotein / RNA-binding / Spliceosome / 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
Chem-GLP / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
syntetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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
DepositionFeb 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Apr 4, 2018Group: Data collection / Database references / Category: diffrn_source / struct_ref_seq
Item: _diffrn_source.type / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Apr 11, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_beamline / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.7Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: glmS glucosamine-6-phosphate activated ribozyme
B: U1 small nuclear ribonucleoprotein A
F: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: glmS glucosamine-6-phosphate activated ribozyme
C: U1 small nuclear ribonucleoprotein A
G: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: glmS glucosamine-6-phosphate activated ribozyme
D: U1 small nuclear ribonucleoprotein A
H: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: glmS glucosamine-6-phosphate activated ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,78726
Polymers244,50712
Non-polymers1,28014
Water1,47782
1
A: U1 small nuclear ribonucleoprotein A
E: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
P: glmS glucosamine-6-phosphate activated ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4356
Polymers61,1273
Non-polymers3083
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: U1 small nuclear ribonucleoprotein A
F: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
Q: glmS glucosamine-6-phosphate activated ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5079
Polymers61,1273
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: U1 small nuclear ribonucleoprotein A
G: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
R: glmS glucosamine-6-phosphate activated ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4597
Polymers61,1273
Non-polymers3324
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: U1 small nuclear ribonucleoprotein A
H: RNA (5'-R(*AP*(A2M)P*GP*CP*GP*CP*CP*AP*GP*AP*AP*CP*U)-3')
S: glmS glucosamine-6-phosphate activated ribozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3864
Polymers61,1273
Non-polymers2591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.389, 232.671, 106.576
Angle α, β, γ (deg.)90.00, 92.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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RNA chain , 2 types, 8 molecules EFGHPQRS

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


Mass: 4177.608 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthesized at Dharmacon / Source: (synth.) syntetic construct (others)
#3: RNA chain
glmS glucosamine-6-phosphate activated ribozyme


Mass: 45608.859 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: in vitro transcribed from a DNA template / Source: (synth.) syntetic construct (others)

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Protein / Sugars , 2 types, 8 molecules ABCD

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


Mass: 11340.315 Da / Num. of mol.: 4 / Fragment: RNA BINDING DOMAIN (UNP residues 1 to 98) / 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
#4: Sugar
ChemComp-GLP / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucopyranose / GLUCOSAMINE 6-PHOSPHATE / 6-O-phosphono-alpha-D-glucosamine / 2-amino-2-deoxy-6-O-phosphono-alpha-D-glucose / 2-amino-2-deoxy-6-O-phosphono-D-glucose / 2-amino-2-deoxy-6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 259.151 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14NO8P
IdentifierTypeProgram
a-D-GlcpN6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 2 types, 92 molecules

#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
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: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Si(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3→28.23 Å / Num. obs: 46457 / % possible obs: 97.6 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.12 / Χ2: 1.029 / Net I/σ(I): 9.863
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3-3.11444921.041194.6
3.11-3.23445361.045194.60.521
3.23-3.38445101.033196.30.35
3.38-3.56445491.046195.50.341
3.56-3.78446761.0361980.249
3.78-4.07447041.029199.10.181
4.07-4.484.147291.012199.80.137
4.48-5.134.247401.02511000.098
5.13-6.464.247731.00711000.072
6.46-504.147481.025198.20.046

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→28.23 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.835 / Occupancy max: 1 / Occupancy min: 1 / SU B: 25.212 / SU ML: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.318 2333 5.1 %RANDOM
Rwork0.25 ---
obs0.253 45861 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 116.03 Å2 / Biso mean: 61.196 Å2 / Biso min: 8.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-1.67 Å2
2---0.52 Å2-0 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 3→28.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 13172 74 82 16182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.02117726
X-RAY DIFFRACTIONr_bond_other_d00.027858
X-RAY DIFFRACTIONr_angle_refined_deg0.8922.8526953
X-RAY DIFFRACTIONr_angle_other_deg1.696319720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4585346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.58423.185135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.96415582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.371524
X-RAY DIFFRACTIONr_chiral_restr0.0410.23514
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.029542
X-RAY DIFFRACTIONr_gen_planes_other00.022010
X-RAY DIFFRACTIONr_mcbond_it0.1791.51754
X-RAY DIFFRACTIONr_mcbond_other0.0161.5720
X-RAY DIFFRACTIONr_mcangle_it0.33322838
X-RAY DIFFRACTIONr_scbond_it0.503315972
X-RAY DIFFRACTIONr_scangle_it0.914.524115
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 174 -
Rwork0.334 3078 -
all-3252 -
obs--95.06 %

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