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- PDB-1l3k: UP1, THE TWO RNA-RECOGNITION MOTIF DOMAIN OF HNRNP A1 -

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Basic information

Entry
Database: PDB / ID: 1l3k
TitleUP1, THE TWO RNA-RECOGNITION MOTIF DOMAIN OF HNRNP A1
ComponentsHETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1
KeywordsRNA BINDING PROTEIN / NUCLEAR PROTEIN HNRNP A1 / RNA-RECOGNITION MOTIF / RNA-BINDING / UP1
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / localization / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsVitali, J. / Ding, J. / Jiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.-M.
CitationJournal: Nucleic Acids Res. / Year: 2002
Title: Correlated alternative side chain conformations in the RNA-recognition motif of heterogeneous nuclear ribonucleoprotein A1.
Authors: Vitali, J. / Ding, J. / Jiang, J. / Zhang, Y. / Krainer, A.R. / Xu, R.M.
History
DepositionFeb 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1


Theoretical massNumber of molelcules
Total (without water)22,3031
Polymers22,3031
Non-polymers00
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.710, 43.450, 55.060
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 / HNRNP A1 / UP1 / Helix-destabilizing protein / Single-strand binding protein / hnRNP core protein A1


Mass: 22303.082 Da / Num. of mol.: 1 / Fragment: RNA-RECOGNITION MOTIF DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09651
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: Jokhan, L., (1997) Acta Crystallogr., D53, 615. / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
2300 mM1dropNaCl
320 mMMES1droppH6.0
41 mMEDTA1drop
50.1 %beta-mercaptoethanol1drop
625 %PEG40001reservoir
720 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jan 1, 1998 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 60334 / % possible obs: 83.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 11
Reflection shellResolution: 1.1→1.14 Å / Rmerge(I) obs: 0.236 / % possible all: 52
Reflection
*PLUS
Highest resolution: 1.1 Å / Lowest resolution: 50 Å / Num. measured all: 180601 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 52 % / Rmerge(I) obs: 0.236

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementStarting model: 1UP1

1up1


Resolution: 1.1→25.78 Å / Num. parameters: 14156 / Num. restraintsaints: 9703 / Cross valid method: FREE R / σ(F): 0
Details: RESIDUES PHE 17, VAL 44 AND PHE 59 SHOW CORRELATED DISORDER IN THE SIDE CHAIN CONFORMATIONS AND THIS BEHAVIOR WAS TAKEN INTO CONSIDERATION IN REFINEMENT. THE RESIDUES WERE SPLIT IN FIVE ...Details: RESIDUES PHE 17, VAL 44 AND PHE 59 SHOW CORRELATED DISORDER IN THE SIDE CHAIN CONFORMATIONS AND THIS BEHAVIOR WAS TAKEN INTO CONSIDERATION IN REFINEMENT. THE RESIDUES WERE SPLIT IN FIVE PARTS -- B, C, D, K, L, CORRESPONDING TO THE FIVE PERMISSIBLE COMBINATIONS OF CONFORMATIONS OF PHE 17, PHE 59, AND VAL 44. THE CONFORMERS OF THE THREE RESIDUES IN EACH COMBINATION HAD COMMON OCCUPANCY VALUES AND THESE WERE REFINED AS FREE VARIABLES WITH THEIR SUM CONSTRAINED TO BE ONE USING THE FVAR AND SUMP COMMANDS. POSITIONS and THERMAL MOTIONS OF IDENTICAL CONFORMATIONS CORRESPONDING TO DIFFERENT PARTS WERE CORRELATED USING EXYZ AND EADP COMMANDS. THUS, FOR PHE 17, PARTS BCDL CORRESPOND TO THE SAME SIDE CHAIN CONFORMATION AND SIDE CHAIN ATOMS FOR PARTS BCDL HAVE SAME COORDINATES AND B FACTORS. THE OCCUPANCY FOR THIS CONFORMATION IS 0.65 WHICH IS THE SUM OF OCCUPANCIES OF B,C,D,L. PART K CORRESPONDS TO AN ALTERNATE CONFORMATION WITH OCCUPANCY 0.35. FOR PHE 59, PARTS BCD CORRESPOND TO ONE CONFORMATION WITH OCCUPANCY 0.57, THE SUM OF OCCUPANCIES OF B,C,D, and PARTS LK CORRESPOND TO AN ALTERNATE CONFORMATION WITH OCCUPANCY 0.43, THE SUM OF OCCUPANCIES OF L AND K. FOR VAL 44, PARTS LKD CORRESPOND TO ONE CONFORMATION WITH OCCUPANCY 0.61, THE SUM OF OCCUPANCIES OF L,K,D, AND PARTS B AND C CORRESPOND TO ALTERNATE CONFORMATIONS WITH OCCUPANCIES 0.19 AND 0.20.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3025 5.3 %RANDOM
Rwork0.155 ---
all0.156 57309 --
obs0.156 57309 79.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1274 / Occupancy sum non hydrogen: 1542
Refinement stepCycle: LAST / Resolution: 1.1→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1397 0 0 227 1624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0306
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.031
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.011
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.009
X-RAY DIFFRACTIONs_approx_iso_adps0.099
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.155 / Rfactor obs: 0.146 / Rfactor Rfree: 0.185 / Rfactor Rwork: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.4
X-RAY DIFFRACTIONs_chiral_restr0.039

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