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- PDB-6q6r: Recognition of different base tetrads by RHAU: X-ray crystal stru... -

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Basic information

Entry
Database: PDB / ID: 6q6r
TitleRecognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex
Components
  • ATP-dependent DNA/RNA helicase DHX36
  • Parallel stranded DNA G-quadruplex
KeywordsDNA BINDING PROTEIN / G-quadruplex / X-ray crystallography / RHAU helicase / DHX36 / G4R1 / Mle1 / DEAH-box family.
Function / homology
Function and homology information


positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / pre-miRNA binding / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of myeloid dendritic cell cytokine production ...positive regulation of intracellular mRNA localization / positive regulation of hematopoietic progenitor cell differentiation / catalytic activity, acting on a nucleic acid / positive regulation of cardioblast differentiation / telomerase RNA stabilization / pre-miRNA binding / positive regulation of mRNA 3'-end processing / positive regulation of telomere maintenance via telomere lengthening / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / positive regulation of myeloid dendritic cell cytokine production / 3'-UTR-mediated mRNA destabilization / regulation of transcription by RNA polymerase III / G-quadruplex DNA binding / positive regulation of dendritic spine morphogenesis / mRNA 3'-UTR AU-rich region binding / cellular response to arsenite ion / positive regulation of cytoplasmic translation / telomerase RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / response to exogenous dsRNA / positive regulation of telomere maintenance / positive regulation of interferon-alpha production / regulation of embryonic development / positive regulation of transcription initiation by RNA polymerase II / ATP-dependent activity, acting on DNA / regulation of mRNA stability / DNA helicase activity / ossification / mRNA 3'-UTR binding / mRNA 5'-UTR binding / histone deacetylase binding / cytoplasmic stress granule / cellular response to UV / single-stranded DNA binding / double-stranded RNA binding / cellular response to heat / spermatogenesis / perikaryon / G-quadruplex RNA binding / defense response to virus / DNA helicase / cell differentiation / chromosome, telomeric region / RNA helicase activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / negative regulation of translation / nuclear speck / RNA helicase / RNA polymerase II cis-regulatory region sequence-specific DNA binding / axon / innate immune response / dendrite / positive regulation of gene expression / magnesium ion binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain ...: / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase associated domain (HA2), winged-helix / Helicase-associated domain / Helicase associated domain (HA2) Add an annotation / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / DNA (> 10) / ATP-dependent DNA/RNA helicase DHX36
Similarity search - Component
Biological speciesunidentified (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHeddi, B. / Cheong, V.V. / Schmitt, E. / Mechulam, Y. / Phan, A.T.
Funding support Singapore, 2items
OrganizationGrant numberCountry
National Research Foundation (Singapore)NRF-NRFI2017-09 Singapore
Ministry of Education (Singapore)MOE2012-T3-1-001 Singapore
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex.
Authors: Heddi, B. / Cheong, V.V. / Schmitt, E. / Mechulam, Y. / Phan, A.T.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3Jul 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _audit_author.name / _database_2.pdbx_DOI ..._audit_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parallel stranded DNA G-quadruplex
B: Parallel stranded DNA G-quadruplex
C: Parallel stranded DNA G-quadruplex
D: Parallel stranded DNA G-quadruplex
E: ATP-dependent DNA/RNA helicase DHX36
F: ATP-dependent DNA/RNA helicase DHX36
G: ATP-dependent DNA/RNA helicase DHX36
H: ATP-dependent DNA/RNA helicase DHX36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,65618
Polymers34,2658
Non-polymers39110
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint30 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.390, 42.250, 61.404
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain
Parallel stranded DNA G-quadruplex


Mass: 5122.284 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others)
#2: Protein/peptide
ATP-dependent DNA/RNA helicase DHX36 / DEAD/H box polypeptide 36 / DEAH-box protein 36 / G4-resolvase-1 / G4R1 / MLE-like protein 1 / RNA ...DEAD/H box polypeptide 36 / DEAH-box protein 36 / G4-resolvase-1 / G4R1 / MLE-like protein 1 / RNA helicase associated with AU-rich element protein


Mass: 3443.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHX36, DDX36, KIAA1488, MLEL1, RHAU / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2U1, DNA helicase, RNA helicase
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 55% methylpentanediol, 40 mM sodium cacodylate (pH 6.0), 80 mM potassium chloride and 12 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→60.6 Å / Num. obs: 45681 / % possible obs: 99.35 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.827 % / CC1/2: 0.998 / Rsym value: 0.079 / Net I/σ(I): 8.68
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 3.62 % / Mean I/σ(I) obs: 1.62 / Num. unique obs: 7212 / CC1/2: 0.816 / Rsym value: 0.763 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2LK7

2lk7


Resolution: 1.5→60.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.057 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.085 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24481 2308 5.1 %RANDOM
Rwork0.1853 ---
obs0.18832 43297 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å2-0.4 Å2
2---0.47 Å20 Å2
3----0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.5→60.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms564 1364 10 265 2203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132149
X-RAY DIFFRACTIONr_bond_other_d0.0030.021309
X-RAY DIFFRACTIONr_angle_refined_deg1.9471.3213202
X-RAY DIFFRACTIONr_angle_other_deg1.71233073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.104566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.90120.425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26815114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.038154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.021455
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02449
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_it5.4192.491270
X-RAY DIFFRACTIONr_mcbond_other5.3512.478269
X-RAY DIFFRACTIONr_mcangle_it6.5963.715331
X-RAY DIFFRACTIONr_mcangle_other6.5873.727332
X-RAY DIFFRACTIONr_scbond_it4.852.4641879
X-RAY DIFFRACTIONr_scbond_other4.8492.4661880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9753.6552871
X-RAY DIFFRACTIONr_long_range_B_refined6.71322.8863458
X-RAY DIFFRACTIONr_long_range_B_other6.41122.2863396
X-RAY DIFFRACTIONr_rigid_bond_restr5.41233458
X-RAY DIFFRACTIONr_sphericity_free45.9315143
X-RAY DIFFRACTIONr_sphericity_bonded20.31153394
LS refinement shellResolution: 1.501→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 153 -
Rwork0.346 3082 -
obs--96.25 %

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