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- PDB-2xzl: Upf1-RNA complex -

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Basic information

Entry
Database: PDB / ID: 2xzl
TitleUpf1-RNA complex
Components
  • 5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3
  • ATP-DEPENDENT HELICASE NAM7
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / NMD / RNA DEGRADATION / ALLOSTERIC REGULATION
Function / homology
Function and homology information


cytoplasmic RNA surveillance / double-stranded DNA helicase activity / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / intracellular mRNA localization / regulation of translational termination / silent mating-type cassette heterochromatin formation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit binding ...cytoplasmic RNA surveillance / double-stranded DNA helicase activity / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / intracellular mRNA localization / regulation of translational termination / silent mating-type cassette heterochromatin formation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit binding / nuclear-transcribed mRNA catabolic process / single-stranded DNA binding / DNA recombination / DNA helicase / RNA helicase activity / protein ubiquitination / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Helix Hairpins - #1240 / Elongation Factor Tu (Ef-tu); domain 3 - #230 / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-binding domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase ...Helix Hairpins - #1240 / Elongation Factor Tu (Ef-tu); domain 3 - #230 / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, Cys/His rich zinc-binding domain / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / Helix Hairpins / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / RNA / ATP-dependent helicase NAM7
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E.
CitationJournal: Mol.Cell / Year: 2011
Title: Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and its Regulation by Upf2.
Authors: Chakrabarti, S. / Jayachandran, U. / Bonneau, F. / Fiorini, F. / Basquin, C. / Domcke, S. / Le Hir, H. / Conti, E.
History
DepositionNov 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT HELICASE NAM7
B: 5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,31820
Polymers92,7082
Non-polymers3,61018
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7120 Å2
ΔGint-53.9 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.135, 114.117, 65.730
Angle α, β, γ (deg.)90.00, 110.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein ATP-DEPENDENT HELICASE NAM7 / UP FRAMESHIFT FACTOR 1 / NONSENSE-MEDIATED MRNA DECAY PROTEIN 1 / NUCLEAR ACCOMODATION OF ...UP FRAMESHIFT FACTOR 1 / NONSENSE-MEDIATED MRNA DECAY PROTEIN 1 / NUCLEAR ACCOMODATION OF MITOCHONDRIA 7 PROTEIN / UP-FRAMESHIFT SUPPRESSOR 1


Mass: 89997.070 Da / Num. of mol.: 1 / Fragment: CH DOMAIN AND HELICASE DOMAIN, RESIDUES 54-850
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) GOLD PLYSS / References: UniProt: P30771, RNA helicase
#2: RNA chain 5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3


Mass: 2710.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 6 types, 114 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.54 Å3/Da / Density % sol: 51.52 % / Description: NONE
Crystal growpH: 6
Details: 50MM MES PH 6.0, 200MM AMMONIUM ACETATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 23, 2009 / Details: LN2-COOLED DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→53.2 Å / Num. obs: 33993 / % possible obs: 98.1 % / Observed criterion σ(I): 3.2 / Redundancy: 2.2 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WJV

2wjv


Resolution: 2.4→41.882 Å / SU ML: 0.28 / σ(F): 1.33 / Phase error: 24.45 / Stereochemistry target values: ML
Details: RESIDUES 138-143, 157-159, 213-224 261-262 AND 283-291 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2431 1725 5.1 %
Rwork0.1974 --
obs0.1999 33972 97.89 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.692 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 19.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.2786 Å20 Å20.0757 Å2
2---0.175 Å20 Å2
3---0.4536 Å2
Refinement stepCycle: LAST / Resolution: 2.4→41.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5649 164 132 96 6041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026059
X-RAY DIFFRACTIONf_angle_d0.6678237
X-RAY DIFFRACTIONf_dihedral_angle_d13.72208
X-RAY DIFFRACTIONf_chiral_restr0.047970
X-RAY DIFFRACTIONf_plane_restr0.0031002
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.48580.26871630.21453241X-RAY DIFFRACTION99
2.4858-2.58530.25211520.21063233X-RAY DIFFRACTION99
2.5853-2.7030.28321600.21683257X-RAY DIFFRACTION99
2.703-2.84540.31281670.22343265X-RAY DIFFRACTION98
2.8454-3.02370.27171720.22353215X-RAY DIFFRACTION98
3.0237-3.2570.30161750.21513247X-RAY DIFFRACTION98
3.257-3.58470.24881850.20123215X-RAY DIFFRACTION98
3.5847-4.1030.21221700.1753243X-RAY DIFFRACTION98
4.103-5.16780.18232040.15663157X-RAY DIFFRACTION97
5.1678-41.88830.22751770.19843174X-RAY DIFFRACTION94

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