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- PDB-1xtj: structure of human UAP56 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 1xtj
Titlestructure of human UAP56 in complex with ADP
ComponentsProbable ATP-dependent RNA helicase p47
KeywordsGENE REGULATION / alpha-beta fold
Function / homology
Function and homology information


transcription export complex / U6 snRNP / RNA secondary structure unwinding / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / U4 snRNP ...transcription export complex / U6 snRNP / RNA secondary structure unwinding / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / U4 snRNP / RNA Polymerase II Transcription Termination / spliceosomal complex assembly / RHOBTB2 GTPase cycle / mRNA export from nucleus / U6 snRNA binding / mRNA Splicing - Major Pathway / RNA splicing / spliceosomal complex / mRNA splicing, via spliceosome / RNA helicase activity / RNA helicase / nuclear speck / mRNA binding / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 ...RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ADENOSINE-5'-DIPHOSPHATE / Spliceosome RNA helicase DDX39B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShi, H. / Cordin, O. / Minder, C.M. / Linder, P. / Xu, R.-M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of the human ATP-dependent splicing and export factor UAP56
Authors: Shi, H. / Cordin, O. / Minder, C.M. / Linder, P. / Xu, R.-M.
History
DepositionOct 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable ATP-dependent RNA helicase p47
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9524
Polymers44,4401
Non-polymers5123
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.988, 78.201, 63.192
Angle α, β, γ (deg.)90.00, 103.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase p47 / HLA-B associated transcript-1 / UAP56


Mass: 44440.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13838
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.1 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 290 K / pH: 7.5
Details: MPD Tris MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2003
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→32.7 Å / Num. obs: 9164 / % possible obs: 97 % / Observed criterion σ(I): 0
Reflection shellResolution: 2.7→2.8 Å / % possible all: 94.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XTI

1xti


Resolution: 2.7→32.7 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.3 751 RANDOM
Rwork0.21 --
obs0.21 9153 -
all-9697 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.257 Å20 Å2-5.792 Å2
2---12.097 Å20 Å2
3---12.354 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 28 89 3139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0076
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.298
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3336
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87188
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.5251.5
X-RAY DIFFRACTIONc_mcangle_it2.652
X-RAY DIFFRACTIONc_scbond_it1.9962
X-RAY DIFFRACTIONc_scangle_it3.0822.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ADP_XPLOR.PARAMADP_XPLOR.TOP
X-RAY DIFFRACTION5ACY_XPLOR.PARAMACY_XPLOR.TOP

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