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- PDB-2wjy: Crystal structure of the complex between human nonsense mediated ... -

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Basic information

Entry
Database: PDB / ID: 2wjy
TitleCrystal structure of the complex between human nonsense mediated decay factors UPF1 and UPF2 Orthorhombic form
ComponentsREGULATOR OF NONSENSE TRANSCRIPTS 1
KeywordsHYDROLASE / NONSENSE MEDIATED DECAY / ZINC-FINGER / ATP-BINDING / METAL-BINDING / UPF2 / UPF1 / HELICASE / NONSENSE-MEDIATED MRNA DECAY / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING
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 / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of telomere maintenance / DNA duplex unwinding / nuclear-transcribed mRNA catabolic process / telomeric DNA binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to interleukin-1 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mRNA export from nucleus / helicase activity / P-body / cellular response to lipopolysaccharide / DNA replication / DNA helicase / 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 / cytoplasm / cytosol
Similarity search - Function
Helix Hairpins - #1240 / Elongation Factor Tu (Ef-tu); domain 3 - #230 / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / RNA helicase UPF1, Cys/His rich zinc-binding domain / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase ...Helix Hairpins - #1240 / Elongation Factor Tu (Ef-tu); domain 3 - #230 / Upf1 cysteine-histidine-rich (CH-rich) domain profile. / RNA helicase UPF1, 1B domain / RNA helicase (UPF2 interacting domain) / RNA helicase UPF1, 1B domain / RNA helicase UPF1, Cys/His rich zinc-binding domain / : / DNA2/NAM7 helicase, helicase domain / DNA2/NAM7-like helicase / AAA domain / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Regulator of nonsense transcripts 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsClerici, M. / Mourao, A. / Gutsche, I. / Gehring, N.H. / Hentze, M.W. / Kulozik, A. / Kadlec, J. / Sattler, M. / Cusack, S.
CitationJournal: Embo J. / Year: 2009
Title: Unusual Bipartite Mode of Interaction between the Nonsense-Mediated Decay Factors, Upf1 and Upf2.
Authors: Clerici, M. / Mourao, A. / Gutsche, I. / Gehring, N.H. / Hentze, M.W. / Kulozik, A. / Kadlec, J. / Sattler, M. / Cusack, S.
History
DepositionJun 1, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 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_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_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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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

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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)90,94912
Polymers89,9841
Non-polymers96511
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.910, 129.140, 311.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein REGULATOR OF NONSENSE TRANSCRIPTS 1 / UPF1 / ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / UP-FRAMESHIFT SUPPRESSOR 1 ...UPF1 / ATP-DEPENDENT HELICASE RENT1 / NONSENSE MRNA REDUCING FACTOR 1 / UP-FRAMESHIFT SUPPRESSOR 1 HOMOLOG / NORF1 / HUPF1


Mass: 89984.242 Da / Num. of mol.: 1 / Fragment: CH-DOMAIN AND HELICASE DOMAIN, RESIDUES 115-914
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR (DE3)
References: UniProt: Q92900, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULPHATE ION (SO4): FROM CRSYTALLISATION MEDIUM

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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: 3.23 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 6
Details: 1.6M AMMONIUM SULPHATE, 100 MM MES PH 6, 10% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 45136 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 3.71 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.78 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2GK7, 2IYK

2gk7

2iyk


Resolution: 2.5→46.52 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.907 / SU B: 16.68 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2403 2266 5 %RANDOM
Rwork0.19552 ---
obs0.19777 42869 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.35 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6107 0 43 254 6404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226326
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9718570
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74724.386285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.786151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1731540
X-RAY DIFFRACTIONr_chiral_restr0.0930.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214721
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.53888
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13926293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82732438
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0834.52277
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 175 -
Rwork0.289 3120 -
obs--99.07 %
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)
15.75230.1417-4.67680.95990.28146.98060.12580.33850.1633-0.2399-0.0788-0.2218-0.24720.2875-0.0470.79490.02640.22730.78980.02060.312459.36517.63915.374
21.6565-0.8705-0.48552.33770.82361.35810.00310.20820.297-0.2684-0.01420.1064-0.1958-0.03340.01110.1683-0.0068-0.01370.18530.06950.178131.44237.5547.13
31.8390.0902-0.31170.9298-0.05951.11550.01720.11660.0994-0.02850.02230.0678-0.0984-0.0567-0.03950.0140.0154-0.0060.04710.00680.074627.8723.84661.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 279
2X-RAY DIFFRACTION2A288 - 457
3X-RAY DIFFRACTION3A458 - 913

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