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- PDB-5zgl: hnRNP A1 segment GGGYGGS (residues 234-240) -

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Basic information

Entry
Database: PDB / ID: 5zgl
TitlehnRNP A1 segment GGGYGGS (residues 234-240)
Components7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1
KeywordsRNA BINDING PROTEIN / phase separation / reversibility
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 / cellular response to glucose starvation / localization / 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 / Resolution: 0.95 Å
AuthorsXie, M. / Luo, F. / Gui, X. / Zhao, M. / He, J. / Li, D. / Liu, C.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis for reversible amyloids of hnRNPA1 elucidates their role in stress granule assembly.
Authors: Xinrui Gui / Feng Luo / Yichen Li / Heng Zhou / Zhenheng Qin / Zhenying Liu / Jinge Gu / Muyun Xie / Kun Zhao / Bin Dai / Woo Shik Shin / Jianhua He / Lin He / Lin Jiang / Minglei Zhao / Bo ...Authors: Xinrui Gui / Feng Luo / Yichen Li / Heng Zhou / Zhenheng Qin / Zhenying Liu / Jinge Gu / Muyun Xie / Kun Zhao / Bin Dai / Woo Shik Shin / Jianhua He / Lin He / Lin Jiang / Minglei Zhao / Bo Sun / Xueming Li / Cong Liu / Dan Li /
Abstract: Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of ...Subcellular membrane-less organelles consist of proteins with low complexity domains. Many of them, such as hnRNPA1, can assemble into both a polydisperse liquid phase and an ordered solid phase of amyloid fibril. The former mirrors biological granule assembly, while the latter is usually associated with neurodegenerative disease. Here, we observe a reversible amyloid formation of hnRNPA1 that synchronizes with liquid-liquid phase separation, regulates the fluidity and mobility of the liquid-like droplets, and facilitates the recruitment of hnRNPA1 into stress granules. We identify the reversible amyloid-forming cores of hnRNPA1 (named hnRACs). The atomic structures of hnRACs reveal a distinct feature of stacking Asp residues, which contributes to fibril reversibility and explains the irreversible pathological fibril formation caused by the Asp mutations identified in familial ALS. Our work characterizes the structural diversity and heterogeneity of reversible amyloid fibrils and illuminates the biological function of reversible amyloid formation in protein phase separation.
History
DepositionMar 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Mar 4, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1
B: 7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)1,1072
Polymers1,1072
Non-polymers00
Water724
1
A: 7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1


  • defined by author
  • Evidence: microscopy
  • 554 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5541
Polymers5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1


  • defined by author
  • 554 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)5541
Polymers5541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)11.957, 10.141, 21.372
Angle α, β, γ (deg.)90.000, 100.110, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide 7-mer peptide from Heterogeneous nuclear ribonucleoprotein A1 / hnRNP A1 / Helix-destabilizing protein / Single-strand RNA-binding protein / hnRNP core protein A1


Mass: 553.526 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P09651
#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

Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium sulfate, 30% PEG 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 0.95→11.771 Å / Num. obs: 5179 / Redundancy: 3.267 % / Biso Wilson estimate: 6.903 Å2 / Net I/σ(I): 13.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
0.95-0.983.0170.1796.641780.9620.21836.2
0.98-13.1890.1158.632060.9840.13946.4
1-1.033.2720.1238.483560.9910.14781.1
1.03-1.063.3040.1099.463590.990.1384.9
1.06-1.13.4160.09410.243390.9950.11185.4
1.1-1.143.3670.07412.723760.9940.08888.7
1.14-1.183.3660.0712.763520.9970.08391.2
1.18-1.233.3040.07612.853160.9980.09191.3
1.23-1.283.3880.07214.063200.9930.08689.1
1.28-1.353.3150.07913.72980.9870.09489.5
1.35-1.423.2440.07214.153160.9880.08697.8
1.42-1.53.2560.06415.712700.9920.07687.7
1.5-1.613.2490.06116.682770.9920.074100
1.61-1.743.1920.05917.072600.9940.07290.9
1.74-1.93.310.05618.262260.9940.06798.7
1.9-2.133.1580.05818.432090.9910.06993.3
2.13-2.463.0770.05418.841940.9920.06696.5
2.46-3.013.1060.05419.141600.9940.06698.2
3.01-4.253.0360.05918.751120.9920.07388.2
4.25-11.7743.1450.05419.24550.9970.06478.6

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XSCALEdata scaling
HKL-2000data collection
SHELXDphasing
SHELXTmodel building
SHELXLmodel building
RefinementResolution: 0.95→11.771 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 14.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1211 518 10.04 %
Rwork0.0998 4642 -
obs0.102 5160 82.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.26 Å2 / Biso mean: 7.4997 Å2 / Biso min: 3.51 Å2
Refinement stepCycle: final / Resolution: 0.95→11.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms78 0 0 4 82
Biso mean---30.63 -
Num. residues----14
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01278
X-RAY DIFFRACTIONf_angle_d1.193100
X-RAY DIFFRACTIONf_chiral_restr0.0954
X-RAY DIFFRACTIONf_plane_restr0.01416
X-RAY DIFFRACTIONf_dihedral_angle_d15.12722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-1.04560.1871900.128582591558
1.0456-1.19670.1171340.09531206134087
1.1967-1.50730.09981430.09471281142491
1.5073-11.77220.12371510.09921330148195

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