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- PDB-6gd1: Structure of HuR RRM3 -

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Basic information

Entry
Database: PDB / ID: 6gd1
TitleStructure of HuR RRM3
ComponentsThioredoxin 1,ELAV-like protein 1
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / DNA polymerase processivity factor activity ...HuR (ELAVL1) binds and stabilizes mRNA / negative regulation of miRNA-mediated gene silencing / post-transcriptional gene silencing / regulation of stem cell population maintenance / mRNA 3'-UTR AU-rich region binding / mRNA stabilization / lncRNA binding / miRNA binding / 3'-UTR-mediated mRNA stabilization / DNA polymerase processivity factor activity / mRNA destabilization / sarcoplasm / protein-disulfide reductase activity / positive regulation of superoxide anion generation / cell redox homeostasis / mRNA 3'-UTR binding / positive regulation of translation / P-body / protein homooligomerization / cytoplasmic stress granule / protein import into nucleus / double-stranded RNA binding / cytoplasmic vesicle / postsynapse / ribonucleoprotein complex / mRNA binding / glutamatergic synapse / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / RNA recognition motif ...HuR, RNA recognition motif 2 / Splicing factor ELAV/Hu / Paraneoplastic encephalomyelitis antigen / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Nucleotide-binding alpha-beta plait domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin 1 / ELAV-like protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsPabis, M. / Sattler, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1035 Germany
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs.
Authors: Pabis, M. / Popowicz, G.M. / Stehle, R. / Fernandez-Ramos, D. / Asami, S. / Warner, L. / Garcia-Maurino, S.M. / Schlundt, A. / Martinez-Chantar, M.L. / Diaz-Moreno, I. / Sattler, M.
History
DepositionApr 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin 1,ELAV-like protein 1
B: Thioredoxin 1,ELAV-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6426
Polymers45,5502
Non-polymers924
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-48 kcal/mol
Surface area17250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.920, 67.660, 70.140
Angle α, β, γ (deg.)90.00, 91.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thioredoxin 1,ELAV-like protein 1 / Trx-1 / Hu-antigen R / HuR


Mass: 22775.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: trxA, fipA, tsnC, b3781, JW5856, ELAVL1, HUR / Production host: Escherichia coli (E. coli) / References: UniProt: P0AA25, UniProt: Q15717
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% (w/v) PEG 2000 MME, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.042 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.042 Å / Relative weight: 1
ReflectionResolution: 2.01→8.99 Å / Num. obs: 26790 / % possible obs: 99.7 % / Redundancy: 6.73 % / Rrim(I) all: 0.1 / Net I/σ(I): 12.48
Reflection shellResolution: 2.01→2.06 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1988 / Rrim(I) all: 0.85 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TRX

2trx


Resolution: 2.01→8.98 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.878 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24417 1301 4.9 %RANDOM
Rwork0.17617 ---
obs0.17943 25205 98.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.844 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.01→8.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 4 286 3165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022987
X-RAY DIFFRACTIONr_bond_other_d0.0020.022837
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9594046
X-RAY DIFFRACTIONr_angle_other_deg1.07836593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3835384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00325.656122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.93115523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.423156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02587
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_it3.7213.7951513
X-RAY DIFFRACTIONr_mcbond_other3.7163.7911512
X-RAY DIFFRACTIONr_mcangle_it5.4165.6521886
X-RAY DIFFRACTIONr_mcangle_other5.4175.6551887
X-RAY DIFFRACTIONr_scbond_it4.1524.1671474
X-RAY DIFFRACTIONr_scbond_other4.154.171475
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2316.0792155
X-RAY DIFFRACTIONr_long_range_B_refined8.60145.853473
X-RAY DIFFRACTIONr_long_range_B_other8.5445.5033401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.059 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 78 -
Rwork0.306 1813 -
obs--99.32 %

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