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- PDB-2gk7: Structural and Functional insights into the human Upf1 helicase core -

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Basic information

Entry
Database: PDB / ID: 2gk7
TitleStructural and Functional insights into the human Upf1 helicase core
ComponentsRegulator of nonsense transcripts 1
KeywordsHYDROLASE / Upf1 / helicase / NMD
Function / homology
Function and homology information


positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / cell cycle phase transition / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization ...positive regulation of mRNA cis splicing, via spliceosome / supraspliceosomal complex / double-stranded DNA helicase activity / exon-exon junction complex / cell cycle phase transition / positive regulation of mRNA catabolic process / telomere maintenance via semi-conservative replication / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / telomeric DNA binding / nuclear-transcribed mRNA catabolic process / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / mRNA export from nucleus / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / P-body / helicase activity / cellular response to lipopolysaccharide / DNA helicase / chromosome, telomeric region / DNA replication / RNA helicase activity / RNA helicase / DNA repair / chromatin binding / chromatin / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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 / : / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / 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 / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, SAD / Resolution: 2.8 Å
AuthorsCheng, Z. / Muhlrad, D. / Parker, R. / Song, H.
CitationJournal: Embo J. / Year: 2007
Title: Structural and functional insights into the human Upf1 helicase core
Authors: Cheng, Z. / Muhlrad, D. / Lim, M.K. / Parker, R. / Song, H.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 9, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 2023Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of nonsense transcripts 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1512
Polymers70,0561
Non-polymers951
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)195.189, 195.189, 45.458
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Regulator of nonsense transcripts 1 / ATP-dependent helicase RENT1 / Nonsense mRNA reducing factor 1 / NORF1 / Up-frameshift suppressor 1 ...ATP-dependent helicase RENT1 / Nonsense mRNA reducing factor 1 / NORF1 / Up-frameshift suppressor 1 homolog / hUpf1


Mass: 70056.422 Da / Num. of mol.: 1 / Fragment: helicase core domain(residues 295-914)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 STAR
References: UniProt: Q92900, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.8
Details: 100mM Na/K Phosphate, 6-8% PEG3350, 10mM DTT, pH 5.8, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2005
RadiationMonochromator: GRAPHATE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 24896 / % possible obs: 100 %
Reflection shellResolution: 2.8→2.87 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, SAD
Starting model: 2GJK

2gjk


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.889 / SU B: 43.334 / SU ML: 0.394 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.133 / ESU R Free: 0.404
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29833 1138 5.1 %RANDOM
Rwork0.25784 ---
obs0.25993 21121 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.622 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2--1.8 Å20 Å2
3----3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 5 58 4782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224808
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9696499
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39324.292219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.70215868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241532
X-RAY DIFFRACTIONr_chiral_restr0.090.2728
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.22342
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23276
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4621.53031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8224794
X-RAY DIFFRACTIONr_scbond_it1.02631977
X-RAY DIFFRACTIONr_scangle_it1.7634.51705
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.448 74 -
Rwork0.385 1529 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 75.007 Å / Origin y: 33.975 Å / Origin z: 6.8122 Å
111213212223313233
T0.022 Å20.4696 Å2-0.3481 Å2--0.2115 Å2-0.1176 Å2---0.1408 Å2
L2.5339 °2-0.1277 °2-0.169 °2-1.8021 °20.0242 °2--1.4307 °2
S-0.579 Å °-0.1715 Å °0.503 Å °0.0953 Å °0.3034 Å °0.1484 Å °-0.294 Å °-0.4489 Å °0.2755 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA295 - 3245 - 34
2X-RAY DIFFRACTION1AA325 - 41535 - 125
3X-RAY DIFFRACTION1AA416 - 699126 - 409
4X-RAY DIFFRACTION1AA700 - 908410 - 618

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