[English] 日本語
Yorodumi
- PDB-3l3c: Crystal structure of the Bacillus anthracis glmS ribozyme bound t... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more