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- PDB-1m8v: Structure of Pyrococcus abyssii Sm Protein in Complex with a Urid... -

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Basic information

Entry
Database: PDB / ID: 1m8v
TitleStructure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer
Components
  • 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
  • PUTATIVE SNRNP SM-LIKE PROTEIN
KeywordsRNA BINDING PROTEIN/RNA / Protein-RNA complex / Sm protein / RNA BINDING PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


Sm-like protein family complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding
Similarity search - Function
snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. ...snRNP Sm-like, putative, archaea / SH3 type barrels. - #100 / Sm-like protein Lsm6/SmF / 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-5'-MONOPHOSPHATE / RNA / Putative snRNP Sm-like protein
Similarity search - Component
Biological speciesPyrococcus abyssi (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThore, S. / Mayer, C. / Sauter, C. / Weeks, S. / Suck, D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya
Authors: Thore, S. / Mayer, C. / Sauter, C. / Weeks, S. / Suck, D.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Oct 16, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / ndb_struct_na_base_pair / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
O: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
P: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
Q: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
R: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
S: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
T: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
U: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'
A: PUTATIVE SNRNP SM-LIKE PROTEIN
B: PUTATIVE SNRNP SM-LIKE PROTEIN
C: PUTATIVE SNRNP SM-LIKE PROTEIN
D: PUTATIVE SNRNP SM-LIKE PROTEIN
E: PUTATIVE SNRNP SM-LIKE PROTEIN
F: PUTATIVE SNRNP SM-LIKE PROTEIN
G: PUTATIVE SNRNP SM-LIKE PROTEIN
H: PUTATIVE SNRNP SM-LIKE PROTEIN
I: PUTATIVE SNRNP SM-LIKE PROTEIN
J: PUTATIVE SNRNP SM-LIKE PROTEIN
K: PUTATIVE SNRNP SM-LIKE PROTEIN
L: PUTATIVE SNRNP SM-LIKE PROTEIN
M: PUTATIVE SNRNP SM-LIKE PROTEIN
N: PUTATIVE SNRNP SM-LIKE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,32742
Polymers135,50821
Non-polymers4,81921
Water3,693205
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.000, 68.000, 84.800
Angle α, β, γ (deg.)105.00, 108.80, 100.00
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 2098.203 Da / Num. of mol.: 7 / Source method: obtained synthetically
#2: Protein
PUTATIVE SNRNP SM-LIKE PROTEIN / Sm protein PA-Sm1


Mass: 8630.029 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi (archaea) / Organelle (production host): PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q9V0Y8
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C9H13N2O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, Imidazole pH8.0, Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 4.0K
Components of the solutionsName: PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.915 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.915 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 40961 / Num. obs: 37089 / % possible obs: 90.5 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 29.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1H64

1h64


Resolution: 2.6→30 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1862 4.5 %RANDOM
Rwork0.212 ---
all-40961 --
obs-37042 90.5 %-
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.93 Å2-6.55 Å2-8.6 Å2
2--0.49 Å2-8.58 Å2
3----8.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7915 827 301 205 9248
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.65
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_dihedral_angle_d25.11
X-RAY DIFFRACTIONc_improper_angle_d1.26

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