[English] 日本語
Yorodumi
- PDB-4w92: Crystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w92
TitleCrystal structure of Bacillus subtilis cyclic-di-AMP riboswitch ydaO
Components
  • C-di-AMP ribsoswitch
  • U1 small nuclear ribonucleoprotein A
Keywordsrna binding protein/rna / riboswitch / cyclic-di-AMP / protein-RNA complex / 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-2BA / : / RNA / RNA (> 10) / RNA (> 100) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Bacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.209 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
CitationJournal: Embo J. / Year: 2014
Title: Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA.
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / refine_hist
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: U1 small nuclear ribonucleoprotein A
C: C-di-AMP ribsoswitch
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53211
Polymers48,9932
Non-polymers1,5409
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-58 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.281, 83.062, 233.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

-
Protein / RNA chain , 2 types, 2 molecules BC

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 10692.992 Da / Num. of mol.: 1 / Fragment: unp residues 6-96 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pIDTBlue / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: RNA chain C-di-AMP ribsoswitch


Mass: 38299.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)

-
Non-polymers , 4 types, 9 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 / Details: PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2014
RadiationMonochromator: Double crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 9964 / % possible obs: 99.2 % / Redundancy: 12.2 % / Biso Wilson estimate: 86.47 Å2 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.056 / Rrim(I) all: 0.165 / Χ2: 1.611 / Net I/av σ(I): 18.267 / Net I/σ(I): 5.1 / Num. measured all: 122045
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.266.84380.5130.4911.08891.1
3.26-3.318.94770.5850.4261.10695.2
3.31-3.389.64690.5690.4431.13598.9
3.38-3.4510.15060.590.411.21199.8
3.45-3.5211.64820.8520.2911.27999.80.962
3.52-3.611.84990.840.281.2021000.9310.973
3.6-3.6912.34810.8780.251.3221000.8450.882
3.69-3.7912.85050.9270.2111.2551000.7290.76
3.79-3.91134820.950.181.2331000.6280.653
3.91-4.0313.45110.9590.1561.2991000.5520.574
4.03-4.1813.54880.9710.1321.2331000.4690.488
4.18-4.3413.75010.9860.1051.3631000.3730.388
4.34-4.5413.95060.9840.0921.3991000.330.343
4.54-4.7813.64930.9870.0671.5381000.2390.248
4.78-5.0813.85080.9990.0611.5381000.2130.222
5.08-5.4713.55040.9940.0461.6981000.1630.17
5.47-6.0213.15180.9970.041.7661000.1390.145
6.02-6.8912.75110.9960.0352.05899.40.120.125
6.89-8.6713.65240.9950.0272.5561000.0950.099
8.67-5012.256110.0183.91599.30.0590.062

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementResolution: 3.209→48.787 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.01 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 1807 9.93 %Random selection
Rwork0.2517 16383 --
obs0.2553 8069 98.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 211.66 Å2 / Biso mean: 100.4238 Å2 / Biso min: 31.58 Å2
Refinement stepCycle: final / Resolution: 3.209→48.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 2033 98 0 2789
Biso mean--54.75 --
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033044
X-RAY DIFFRACTIONf_angle_d0.7284599
X-RAY DIFFRACTIONf_chiral_restr0.027596
X-RAY DIFFRACTIONf_plane_restr0.002215
X-RAY DIFFRACTIONf_dihedral_angle_d14.7531399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2094-3.29620.42041100.36841008111881
3.2962-3.39310.3711430.33571278142197
3.3931-3.50260.36811440.31491269141399
3.5026-3.62780.33051390.298212531392100
3.6278-3.7730.30611450.282413211466100
3.773-3.94460.33281400.252512821422100
3.9446-4.15250.25241390.236812791418100
4.1525-4.41250.27271420.235912741416100
4.4125-4.75290.2481390.222912751414100
4.7529-5.23070.27561390.208912961435100
5.2307-5.98650.24211490.214612881437100
5.9865-7.53780.25791460.24512791425100
7.5378-48.79270.29551320.24941281141399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.35240.06150.10970.0350.00640.03880.29280.0493-0.0660.21930.03710.02290.0478-0.09530.15581.6375-0.0885-0.11461.01330.19890.320940.6191-153.6712761.2609
20.11960.148-0.02370.21140.05250.28610.11310.1188-0.17720.2978-0.0073-0.1534-0.1006-0.064-0.00180.9646-0.2246-0.23491.1274-0.20020.391842.0671-156.7037751.529
30.09390.02550.19990.06160.10150.4392-0.5817-0.4298-0.8025-0.2099-0.1138-0.0995-0.22260.2676-0.03280.56630.06360.03711.28020.11941.478742.3941-160.2353738.1968
40.101-0.10730.02330.1083-0.02840.0574-0.30510.120.5288-0.0649-0.3469-0.41030.5209-0.2137-0.00080.5328-0.005-0.07540.5896-0.15970.900331.7124-156.4511744.7798
50.01160.0112-0.00490.0045-0.01170.0283-0.3122-0.02620.4368-0.03820.43370.2939-0.2574-0.135600.8237-0.16360.12910.7703-0.17990.858834.212-149.7389748.5748
6-0.00070.0020.0028-0.0031-0.00350.01990.1436-0.4390.20580.1575-0.1514-0.2241-0.08650.20780.14670.2376-0.1356-0.57290.709-0.13812.199347.735-153.6299741.488
70.0007-0.0232-0.01620.76410.50860.33720.0080.1327-0.0862-0.3612-0.0129-0.1121-0.04230.0789-0.4890.769-0.1652-0.05290.4765-0.41830.271436.1333-151.64752.7831
80.1593-0.14830.15150.4666-0.04350.18010.17490.0652-0.1714-0.0874-0.01780.0276-0.0721-0.04680.62080.8561-0.063-0.04460.9745-0.00430.139432.9802-159.9406757.4525
90.1718-0.52920.1682.0975-1.08770.8872-1.11930.4721-0.0511.02430.1184-0.7037-0.24380.2474-0.01950.6225-0.0682-0.13051.1105-0.01841.520637.6691-166.1625745.1451
100.16610.38530.10951.54320.4670.13360.2075-0.55650.07630.5088-0.09690.0076-0.20340.47750.06980.9658-0.0982-0.24251.1078-0.04070.548842.5954-155.232755.972
110.0422-0.01940.11880.18650.03830.378-0.0115-0.07750.00390.01760.00290.0247-0.0162-0.07340.00911.1457-0.1441-0.60771.36970.45160.642939.6864-141.0731756.5213
122.82151.1766-0.92731.83230.66280.9908-0.25370.35410.3026-0.46860.15940.4643-0.1921-0.5839-0.00560.8264-0.0866-0.37981.01940.17341.459765.6915-146.0327723.8217
130.2013-0.14490.23470.246-0.07170.2679-0.5088-0.97721.33380.58780.08120.9739-0.1022-0.05950.00010.9320.03810.18161.2013-0.14861.548783.7583-146.7647738.8935
140.1148-0.3513-0.15581.8913-0.41071.4443-0.21580.0550.577-0.24910.18850.7734-0.099-0.4259-0.00010.7796-0.1147-0.10790.9828-0.09021.329574.2971-142.9455724.4702
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 10 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 11 through 15 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 16 through 22 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 23 through 37 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 45 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 46 through 54 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 61 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 62 through 72 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 82 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 83 through 91 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 96 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 65 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 66 through 82 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 83 through 119 )C0

+
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