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- PDB-1t6n: Crystal structure of the N-terminal domain of human UAP56 -

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Basic information

Entry
Database: PDB / ID: 1t6n
TitleCrystal structure of the N-terminal domain of human UAP56
ComponentsProbable ATP-dependent RNA helicase
Keywordspre-mRNA processing protein / RecA-like fold
Function / homology
Function and homology information


transcription export complex / U6 snRNP / RNA secondary structure unwinding / mRNA 3'-end processing / ATP-dependent protein binding / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNP / RNA export from nucleus ...transcription export complex / U6 snRNP / RNA secondary structure unwinding / mRNA 3'-end processing / ATP-dependent protein binding / ATP-dependent activity, acting on RNA / U4 snRNA binding / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNP / RNA export from nucleus / RNA Polymerase II Transcription Termination / spliceosomal complex assembly / RHOBTB2 GTPase cycle / U6 snRNA binding / mRNA export from nucleus / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Spliceosome RNA helicase DDX39B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.94 Å
AuthorsZhao, R.
CitationJournal: Structure / Year: 2004
Title: Crystal Structure of UAP56, a DExD/H-Box Protein Involved in Pre-mRNA Splicing and mRNA Export
Authors: Zhao, R. / Shen, J. / Green, M.R. / MacMorris, M. / Blumenthal, T.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,4794
Polymers50,1012
Non-polymers3782
Water5,675315
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.453, 47.284, 87.190
Angle α, β, γ (deg.)90.00, 98.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Probable ATP-dependent RNA helicase / U2AF65 ASSOCIATED PROTEIN / UAP56


Mass: 25050.531 Da / Num. of mol.: 2 / Fragment: N-terminal domain (residues 34-251)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAT1 / Plasmid: pGEX-KG / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q13838
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, PEG MME 2000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97921, 0.97923, 0.96417
SYNCHROTRONAPS 19-BM20.97934
SYNCHROTRONAPS 14-BM-C31.0332
Detector
IDDetectorDate
1CCDOct 10, 2003
2CCDOct 10, 2003
3CCDJun 8, 2003
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979231
30.964171
40.979341
51.03321
ReflectionResolution: 1.94→30 Å / Num. all: 29757 / Num. obs: 29132 / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.5
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.4 / % possible all: 98.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.94→30 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1969 -RANDOM
Rwork0.216 ---
obs0.216 27950 93.7 %-
all-29817 --
Displacement parametersBiso mean: 24.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 26 315 3649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.08
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d2.122
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.414
X-RAY DIFFRACTIONc_mcangle_it2.164
X-RAY DIFFRACTIONc_scbond_it2.538
X-RAY DIFFRACTIONc_scangle_it3.812
LS refinement shellResolution: 1.94→2.01 Å /
RfactorNum. reflection
Rfree0.2719 197
Rwork0.3378 -

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