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- PDB-4pj3: Structural insight into the function and evolution of the spliceo... -

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Basic information

Entry
Database: PDB / ID: 4pj3
TitleStructural insight into the function and evolution of the spliceosomal helicase Aquarius, Structure of Aquarius in complex with AMPPNP
ComponentsIntron-binding protein aquarius
KeywordsRNA BINDING PROTEIN / RNA helicase / pre-mRNA splicing
Function / homology
Function and homology information


3'-5' RNA helicase activity / U2-type catalytic step 2 spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded RNA binding ...3'-5' RNA helicase activity / U2-type catalytic step 2 spliceosome / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / mRNA splicing, via spliceosome / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / single-stranded RNA binding / RNA helicase / mRNA binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
: / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / DNA2/NAM7 helicase, helicase domain / AAA domain / : ...: / : / Intron-binding protein aquarius, beta-barrel / Intron-binding protein aquarius insert domain / CWF11 family / Intron-binding protein aquarius, N-terminal / Intron-binding protein aquarius N-terminal / DNA2/NAM7 helicase, helicase domain / AAA domain / : / DNA2/NAM7-like helicase / DNA2/NAM7 helicase-like, C-terminal / AAA domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / RNA helicase aquarius
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.3 Å
AuthorsDe, I. / Bessonov, S. / Hofele, R. / dos Santos, K.F. / Will, C.L. / Urlaub, H. / Luhrmann, R. / Pena, V.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The RNA helicase Aquarius exhibits structural adaptations mediating its recruitment to spliceosomes.
Authors: De, I. / Bessonov, S. / Hofele, R. / Dos Santos, K. / Will, C.L. / Urlaub, H. / Luhrmann, R. / Pena, V.
History
DepositionMay 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3Jun 1, 2016Group: Data collection
Revision 1.4Nov 22, 2017Group: Advisory / Derived calculations / Refinement description
Category: pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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
Revision 1.6Oct 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: Intron-binding protein aquarius
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,1104
Polymers172,5551
Non-polymers5553
Water9,998555
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.986, 140.444, 144.761
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Intron-binding protein aquarius / Intron-binding protein of 160 kDa / IBP160


Mass: 172555.375 Da / Num. of mol.: 1 / Fragment: UNP residues 19-1485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AQR, KIAA0560 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60306
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: MES, PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979 Å
DetectorType: CUSTOM-MADE / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20004 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.84 % / Biso Wilson estimate: 29.02 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.093 / Rrim(I) all: 0.099 / Χ2: 1.216 / Net I/σ(I): 18.65 / Num. measured all: 1310360
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.3-2.40.9080.5434.2315599620005200040.581100
2.4-2.50.9410.4215.4413249116949169490.45100
2.5-2.60.9590.3526.4311264914389143890.376100
2.6-2.70.9720.2817.989688212372123710.301100
2.7-2.80.9830.2259.698413110725107240.24100
2.8-2.90.9880.18211.7672451922692260.195100
2.9-30.9910.1514.0163012801580150.16100
3-40.9980.07324.8834284243519435170.078100
4-60.9990.04540.3717640422362223620.048100
6-80.9990.04241.3943004544254420.045100
8-100.9990.03253.2115250192719270.034100
100.9990.03153.5615248203720200.03499.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
SHELXphasing
PDB_EXTRACT3.14data extraction
Cootmodel building
XSCALEdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.493 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 4118 4.9 %
Rwork0.1907 --
obs0.1925 84028 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→47.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10971 0 33 555 11559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311319
X-RAY DIFFRACTIONf_angle_d0.73915347
X-RAY DIFFRACTIONf_dihedral_angle_d13.4214284
X-RAY DIFFRACTIONf_chiral_restr0.0291674
X-RAY DIFFRACTIONf_plane_restr0.0031981
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32710.29511350.23352534X-RAY DIFFRACTION91
2.3271-2.35540.28681300.22442567X-RAY DIFFRACTION92
2.3554-2.38530.27791500.22252600X-RAY DIFFRACTION92
2.3853-2.41660.24431520.21792597X-RAY DIFFRACTION94
2.4166-2.44980.24441360.21622646X-RAY DIFFRACTION94
2.4498-2.48470.28221450.20882628X-RAY DIFFRACTION95
2.4847-2.52180.27791400.21442683X-RAY DIFFRACTION95
2.5218-2.56120.24561240.20732703X-RAY DIFFRACTION95
2.5612-2.60320.24531470.20372638X-RAY DIFFRACTION95
2.6032-2.64810.25991440.19692715X-RAY DIFFRACTION96
2.6481-2.69630.25851250.20432715X-RAY DIFFRACTION96
2.6963-2.74810.25451410.20272738X-RAY DIFFRACTION97
2.7481-2.80420.26311300.21322716X-RAY DIFFRACTION97
2.8042-2.86520.28721240.21432763X-RAY DIFFRACTION97
2.8652-2.93180.26371420.21132757X-RAY DIFFRACTION98
2.9318-3.00510.24631340.21222778X-RAY DIFFRACTION98
3.0051-3.08640.23651490.21152786X-RAY DIFFRACTION98
3.0864-3.17720.24121480.21072782X-RAY DIFFRACTION99
3.1772-3.27970.25181540.20712804X-RAY DIFFRACTION99
3.2797-3.39690.22531280.2042824X-RAY DIFFRACTION99
3.3969-3.53280.2371550.20172834X-RAY DIFFRACTION99
3.5328-3.69360.21771490.19022806X-RAY DIFFRACTION99
3.6936-3.88820.21641410.1812825X-RAY DIFFRACTION100
3.8882-4.13170.22361550.17032878X-RAY DIFFRACTION100
4.1317-4.45050.18171390.15182841X-RAY DIFFRACTION100
4.4505-4.89790.15861480.14842863X-RAY DIFFRACTION100
4.8979-5.60570.19831590.16642900X-RAY DIFFRACTION100
5.6057-7.05890.21791520.18812918X-RAY DIFFRACTION100
7.0589-47.50310.17451420.1743071X-RAY DIFFRACTION100

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