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- PDB-2gk6: Structural and Functional insights into the human Upf1 helicase core -

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Basic information

Entry
Database: PDB / ID: 2gk6
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


double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / regulation of translational termination / histone mRNA catabolic process / 3'-UTR-mediated mRNA destabilization ...double-stranded DNA helicase activity / supraspliceosomal complex / positive regulation of mRNA cis splicing, via spliceosome / exon-exon junction complex / telomere maintenance via semi-conservative replication / positive regulation of mRNA catabolic process / cell cycle phase transition / 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 / DNA duplex unwinding / 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) / helicase activity / P-body / cellular response to lipopolysaccharide / DNA helicase / DNA replication / chromosome, telomeric region / RNA helicase activity / RNA helicase / DNA repair / chromatin binding / protein-containing complex binding / chromatin / perinuclear region of cytoplasm / ATP hydrolysis activity / RNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytosol / 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 / : ...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
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Regulator of nonsense transcripts 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,2068
Polymers140,1132
Non-polymers1,0936
Water4,197233
1
A: Regulator of nonsense transcripts 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6034
Polymers70,0561
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulator of nonsense transcripts 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6034
Polymers70,0561
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.284, 67.836, 87.250
Angle α, β, γ (deg.)114.41, 90.13, 110.22
Int Tables number1
Space group name H-MP1

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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.: 2 / 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7.5
Details: 100mM Tris, 8-13% PEG3350, 140mM (NH4)3PO4, 10% EG, 10mM DTT, pH 7.5, 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: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 43423 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
ADSCdata collection
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJK

2gjk


Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.326 / SU ML: 0.26 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.308 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27193 2207 5.1 %RANDOM
Rwork0.2352 ---
obs0.23709 41163 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.418 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å21.53 Å21.21 Å2
2--3.32 Å22.56 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9496 0 66 233 9795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229738
X-RAY DIFFRACTIONr_bond_other_d0.0110.028948
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.97413186
X-RAY DIFFRACTIONr_angle_other_deg0.79320884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14551196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.21486
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021866
X-RAY DIFFRACTIONr_nbd_refined0.1840.22100
X-RAY DIFFRACTIONr_nbd_other0.2170.210552
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.25590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.2153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2430.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.55996
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92229694
X-RAY DIFFRACTIONr_scbond_it0.94433742
X-RAY DIFFRACTIONr_scangle_it1.6574.53492
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.35 115
Rwork0.27 2293
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)
10.98540.15520.01950.7354-0.37750.4305-0.0646-0.1143-0.1002-0.0060.0108-0.0560.0059-0.040.05380.07450.04180.00130.0846-0.04960.0414-6.8713-14.32122.9957
20.62730.063-0.13040.5435-0.2910.5446-0.01610.07180.077-0.02770.0106-0.0187-0.03540.00060.00550.1007-0.0304-0.00360.0865-0.01860.0517-38.6333-28.123940.6078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA293 - 3243 - 34
2X-RAY DIFFRACTION1AA325 - 41535 - 125
3X-RAY DIFFRACTION1AA416 - 699126 - 409
4X-RAY DIFFRACTION1AA700 - 911410 - 621
5X-RAY DIFFRACTION2BB293 - 3243 - 34
6X-RAY DIFFRACTION2BB325 - 41535 - 125
7X-RAY DIFFRACTION2BB416 - 699126 - 409
8X-RAY DIFFRACTION2BB700 - 911410 - 621

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