[English] 日本語
Yorodumi
- PDB-1i5l: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i5l
TitleCRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA
Components
  • 5'-R(*UP*UP*U)-3'
  • PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
KeywordsRNA BINDING PROTEIN/RNA / SNRNP / SM / CORE SNRNP DOMAIN / RNA BINDING PROTEIN / SINGLE-STRANDED RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / Sm-like protein Lsm7/SmG / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / Sm-like protein Lsm7/SmG / SH3 type barrels. - #100 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
URIDINE / RNA / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsToro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D.
CitationJournal: EMBO J. / Year: 2001
Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.
Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D.
History
DepositionFeb 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine / struct_biol / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
U: 5'-R(*UP*UP*U)-3'
Y: 5'-R(*UP*UP*U)-3'
A: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
B: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
C: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
D: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
E: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
F: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
G: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
H: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
I: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
J: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
K: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
L: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
M: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
N: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,20820
Polymers119,23116
Non-polymers9774
Water1,02757
1
U: 5'-R(*UP*UP*U)-3'
A: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
B: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
C: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
D: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
E: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
F: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
G: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,34811
Polymers59,6168
Non-polymers7333
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: 5'-R(*UP*UP*U)-3'
H: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
I: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
J: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
K: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
L: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
M: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
N: PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8609
Polymers59,6168
Non-polymers2441
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.858, 130.438, 70.047
Angle α, β, γ (deg.)90, 115.36, 90
Int Tables number4
Space group name H-MP1211
Details: The 14 monomers are organized in two ring-shaped heptamers.

-
Components

#1: RNA chain 5'-R(*UP*UP*U)-3'


Mass: 873.540 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN AF-SM1 / AF-SM1


Mass: 8391.709 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0875 / Plasmid: MODIFIED PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29386
#3: Chemical
ChemComp-URI / URIDINE / Uridine


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: PEG6000, sodium citrate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG600011
2sodium citrate11
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
111 mg/mlprotein1drop
212 %PEG60001reservoir
3100 mMsodium citrate1reservoirpH4.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 27, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.75→25 Å / Num. all: 28746 / Num. obs: 28746 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 82.323 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique all: 4203 / Rsym value: 0.354 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 70211 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 97.5 %

-
Processing

Software
NameVersionClassification
MOLREPphasing
CNS1refinement
MAR345data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I4K

1i4k


Resolution: 2.75→25 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1469 -random
Rwork0.225 ---
all0.229 28722 --
obs0.229 28722 97.5 %-
Displacement parametersBiso mean: 82.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å20 Å219.2 Å2
2---17.03 Å20 Å2
3---9.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7797 114 68 57 8036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.458 242 -
Rwork0.392 --
obs--97.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.225 / Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 82.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.26
LS refinement shell
*PLUS
Rfactor Rfree: 0.458 / Rfactor Rwork: 0.392

+
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