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- PDB-5aor: Structure of MLE RNA ADP AlF4 complex -

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Basic information

Entry
Database: PDB / ID: 5aor
TitleStructure of MLE RNA ADP AlF4 complex
Components
  • 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
  • DOSAGE COMPENSATION REGULATOR
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / HELICASE / DOSAGE COMPENSATION / MLE / DEAH / ROX
Function / homology
Function and homology information


RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulation of cytoplasmic translation / regulatory region RNA binding / sex-chromosome dosage compensation / PKR-mediated signaling / MSL complex ...RIP-mediated NFkB activation via ZBP1 / X chromosome located dosage compensation complex, transcription activating / 3'-5' DNA/RNA helicase activity / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / male courtship behavior, veined wing generated song production / regulation of cytoplasmic translation / regulatory region RNA binding / sex-chromosome dosage compensation / PKR-mediated signaling / MSL complex / dosage compensation by hyperactivation of X chromosome / positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity / polytene chromosome / 3'-5' RNA helicase activity / regulation of mRNA processing / axon extension / lncRNA binding / 3'-5' DNA helicase activity / DNA duplex unwinding / nuclear chromosome / positive regulation of heterochromatin formation / X chromosome / DNA helicase activity / helicase activity / determination of adult lifespan / double-stranded RNA binding / chromosome / double-stranded DNA binding / RNA helicase activity / RNA helicase / ribonucleoprotein complex / chromatin binding / chromatin / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / RNA binding / ATP binding / nucleus / cytosol
Similarity search - Function
DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation ...DHX9, first double-stranded RNA binding domain / DHX9, second double-stranded RNA binding domain / DHX9, DEXH-box helicase domain / : / Helicase associated domain (HA2), ratchet-like / DEAD-box helicase, OB fold / Oligonucleotide/oligosaccharide-binding (OB)-fold / Helicase-associated domain / Helicase associated domain (HA2), winged-helix / Helicase associated domain (HA2) Add an annotation / Double-stranded RNA binding motif / Double-stranded RNA binding motif / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / 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
ADENOSINE-5'-DIPHOSPHATE / TETRAFLUOROALUMINATE ION / RNA / RNA (> 10) / Dosage compensation regulator
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsPrabu, J.R. / Conti, E.
CitationJournal: Mol.Cell / Year: 2015
Title: Structure of the RNA Helicase Mle Reveals the Molecular Mechanisms for Uridine Specificity and RNA-ATP Coupling.
Authors: Prabu, J.R. / Muller, M. / Thomae, A.W. / Schussler, S. / Bonneau, F. / Becker, P.B. / Conti, E.
History
DepositionSep 11, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 / _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 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DOSAGE COMPENSATION REGULATOR
B: DOSAGE COMPENSATION REGULATOR
C: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
D: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,63613
Polymers294,3194
Non-polymers1,3179
Water10,791599
1
A: DOSAGE COMPENSATION REGULATOR
C: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8307
Polymers147,1602
Non-polymers6715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-66.2 kcal/mol
Surface area43290 Å2
MethodPISA
2
B: DOSAGE COMPENSATION REGULATOR
D: 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,8066
Polymers147,1602
Non-polymers6474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-52.6 kcal/mol
Surface area41630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.373, 154.373, 198.194
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / RNA chain , 2 types, 4 molecules ABCD

#1: Protein DOSAGE COMPENSATION REGULATOR / ATP-DEPENDENT RNA HELICASE MLE / PROTEIN MALE-LESS / PROTEIN MALELESS / PROTEIN NO ACTION POTENTIAL ...ATP-DEPENDENT RNA HELICASE MLE / PROTEIN MALE-LESS / PROTEIN MALELESS / PROTEIN NO ACTION POTENTIAL / MLE HELICASE


Mass: 143836.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24785, RNA helicase
#2: RNA chain 5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP)-3'


Mass: 3322.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 5 types, 608 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growDetails: 20 % PEG 3350 0.2 M MAGNESIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 143331 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 13.25 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.1
Reflection shellResolution: 2.08→2.2 Å / Redundancy: 13.17 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.7 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KX2

3kx2


Resolution: 2.08→48.82 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 10.622 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22071 7169 5 %RANDOM
Rwork0.19044 ---
obs0.19196 136162 99.91 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.805 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.08→48.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15855 404 79 599 16937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916701
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215996
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.95822709
X-RAY DIFFRACTIONr_angle_other_deg1.315336847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.24852001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3224.011743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.434152919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.53515129
X-RAY DIFFRACTIONr_chiral_restr0.0890.22595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02118347
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023692
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_it2.7482.5928004
X-RAY DIFFRACTIONr_mcbond_other2.7472.5928003
X-RAY DIFFRACTIONr_mcangle_it4.2213.8699993
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.623.0128696
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.079→2.133 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 519 -
Rwork0.291 9856 -
obs--98.92 %
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)
10.63930.10720.30390.3920.10920.54210.0050.0828-0.0077-0.00810.0099-0.0380.0058-0.0213-0.01490.09130.0080.01520.154-0.02390.0205192.04483.135203.726
20.60950.0292-0.04710.3073-0.00351.03470.0673-0.1086-0.0810.00080.00540.05680.129-0.1518-0.07270.1405-0.0262-0.04660.16680.05370.0538122.15791.315221.772
36.96161.27580.3076.30780.66944.2430.4875-1.038-0.12870.2178-0.2782-0.03390.447-0.6434-0.20930.2363-0.0770.01860.3360.08040.1716125.89497.851226.182
44.3211-2.04720.59121.24220.76915.1887-0.21110.260.2360.1305-0.0742-0.2167-0.20060.2330.28530.2125-0.0171-0.10990.3389-0.00310.4953190.36391.743203.384
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A145 - 1158
2X-RAY DIFFRACTION2B138 - 1158
3X-RAY DIFFRACTION3D1 - 10
4X-RAY DIFFRACTION4C1 - 11

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