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- PDB-6bxx: GYNGFG from low-complexity domain of hnRNPA1, residues 243-248 -

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Entry
Database: PDB / ID: 6bxx
TitleGYNGFG from low-complexity domain of hnRNPA1, residues 243-248
ComponentshnRNPA1
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / Reversible-amyloid / low-complexity
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 / 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
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.1 Å
AuthorsHughes, M.P. / Rodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Gonen, T. / Eisenberg, D.S.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/Office of the DirectorAG-04812 United States
National Science Foundation (NSF, United States)MCB-0958111 United States
CitationJournal: Science / Year: 2018
Title: Atomic structures of low-complexity protein segments reveal kinked β sheets that assemble networks.
Authors: Michael P Hughes / Michael R Sawaya / David R Boyer / Lukasz Goldschmidt / Jose A Rodriguez / Duilio Cascio / Lisa Chong / Tamir Gonen / David S Eisenberg /
Abstract: Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. ...Subcellular membraneless assemblies are a reinvigorated area of study in biology, with spirited scientific discussions on the forces between the low-complexity protein domains within these assemblies. To illuminate these forces, we determined the atomic structures of five segments from protein low-complexity domains associated with membraneless assemblies. Their common structural feature is the stacking of segments into kinked β sheets that pair into protofilaments. Unlike steric zippers of amyloid fibrils, the kinked sheets interact weakly through polar atoms and aromatic side chains. By computationally threading the human proteome on our kinked structures, we identified hundreds of low-complexity segments potentially capable of forming such interactions. These segments are found in proteins as diverse as RNA binders, nuclear pore proteins, and keratins, which are known to form networks and localize to membraneless assemblies.
History
DepositionDec 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hnRNPA1


Theoretical massNumber of molelcules
Total (without water)6141
Polymers6141
Non-polymers00
Water724
1
A: hnRNPA1
x 10


Theoretical massNumber of molelcules
Total (without water)6,13610
Polymers6,13610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
crystal symmetry operation3_545-x,y-1/2,-z+1/21
crystal symmetry operation3_535-x,y-3/2,-z+1/21
crystal symmetry operation3_565-x,y+3/2,-z+1/21
crystal symmetry operation3_575-x,y+5/2,-z+1/21
Unit cell
Length a, b, c (Å)16.606, 4.769, 40.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide hnRNPA1 /


Mass: 613.621 Da / Num. of mol.: 1 / Fragment: residues 243-248 / Source method: obtained synthetically
Details: Synthetic peptide GYNGFG corresponding tosegment 243-248 of hnRNPA1
Source: (synth.) Homo sapiens (human) / References: UniProt: P09651*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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

CrystalMosaicity: 0.8 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M sodium cacodylate pH 6.5, 30% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→100 Å / Num. obs: 1269 / % possible obs: 78.9 % / Redundancy: 25.7 % / Biso Wilson estimate: 3.1 Å2 / Rmerge(I) obs: 0.13 / Χ2: 1.091 / Net I/σ(I): 8.4 / Num. measured all: 32560
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.1-1.144.70.248410.948126.8
1.14-1.1810.70.271621.082138.5
1.18-1.2416.90.197791.2154.1
1.24-1.322.70.2011181.264183.7
1.3-1.3926.60.21541.028196.9
1.39-1.4931.40.1821531.22199.4
1.49-1.6428.50.1611480.951187.6
1.64-1.8832.80.1421431.049196
1.88-2.3728.40.1131791.097197.8
2.37-10024.90.11921.05199

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
DENZOdata reduction
SHELXDphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→20.486 Å / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 1.56 / Phase error: 6.83
RfactorNum. reflection% reflection
Rfree0.0865 123 9.87 %
Rwork0.0613 --
obs0.0638 1246 79.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 33.87 Å2 / Biso mean: 1.9357 Å2 / Biso min: 0.53 Å2
Refinement stepCycle: final / Resolution: 1.1→20.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms44 0 0 4 48
Biso mean---11.68 -
Num. residues----6
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01845
X-RAY DIFFRACTIONf_angle_d2.2259
X-RAY DIFFRACTIONf_chiral_restr0.1693
X-RAY DIFFRACTIONf_plane_restr0.0119
X-RAY DIFFRACTIONf_dihedral_angle_d7.06813
LS refinement shellResolution: 1.1003→20.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.0865 123 -
Rwork0.0613 1123 -
all-1246 -
obs--79 %

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