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- PDB-6bzp: STGGYG from low-complexity domain of FUS, residues 77-82 -

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Basic information

Entry
Database: PDB / ID: 6bzp
TitleSTGGYG from low-complexity domain of FUS, residues 77-82
ComponentsRNA-binding protein FUS
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / Reversible-amyloid / low-complexity
Function / homology
Function and homology information


mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity ...mRNA stabilization / intracellular non-membrane-bounded organelle / positive regulation of double-strand break repair via homologous recombination / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / RNA splicing / mRNA 3'-UTR binding / transcription coregulator activity / protein homooligomerization / amyloid fibril formation / transcription coactivator activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. ...TAF15/EWS/TLS family / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / 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
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / RNA-binding protein FUS
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / cryo EM / 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-04182 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 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jun 30, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Mar 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

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Assembly

Deposited unit
A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,2453
Polymers1,0812
Non-polymers1641
Water543
1
A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules

A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules

A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules

A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules

A: RNA-binding protein FUS
B: RNA-binding protein FUS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,22615
Polymers5,40510
Non-polymers8215
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_575x,y+2,z1
crystal symmetry operation1_535x,y-2,z1
Unit cell
Length a, b, c (Å)13.790, 4.930, 101.900
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 RNA-binding protein FUS / / FUS / 75 kDa DNA-pairing protein / Oncogene FUS / Oncogene TLS / POMp75 / Translocated in liposarcoma protein


Mass: 540.526 Da / Num. of mol.: 2 / Fragment: UNP residues 77-82 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P35637
#2: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Fragment: residues 77-82 / Source method: obtained synthetically / Formula: C7H16O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: A fibril composed of a 6-residue segment of FUS / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
EM crystal formationInstrument: 24-well plate
Atmosphere: air, sealed chaomder, in equilibrium with reservoir solutionq
Details: 1 microliter of a 150 mg/mL peptide solution of STGGYG in water was mixed with 1 microliter of reservoir solution. The tray was incubated at room temperature and crystals grew within a week.
Lipid mixture: none / Temperature: 298 K / Time: 1 DAY
Buffer solutionpH: 4.6
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 Msodium acetateC2H3NaO21
20.15 Mammonium sulfate(NH4)2SO41
325 (w/v)PEG 2000 MME1
SpecimenConc.: 150 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: crystal
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
CrystalDensity Matthews: 1.6 Å3/Da / Density % sol: 23.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 0.15 M ammonium sulfate, 25% w/v PEG2000 MME

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Data collection

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 2 sec. / Electron dose: 0.01 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Num. of grids imaged: 2
Details: The detector was operated in rolling shutter with 2x2 pixel binning.
Image scansSampling size: 15.6 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 1350 mm
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
1.3861-12.7781199.28.3174237.98
1.1004-1.38612191.65.9147632.15
EM diffraction statsDetails: Phase statistics are not applicable. No imaging was used. THe phases were obtained by a crystalloghraphic direct methods program, SHELXD.
Fourier space coverage: 0.955 % / High resolution: 1.1 Å / Num. of intensities measured: 23271 / Num. of structure factors: 3220 / Phase error: 35.3 ° / Phase residual: 0.1 ° / Phase error rejection criteria: 0 / Rmerge: 0.266 / Rsym: 0.25
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Aug 18, 2015
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 1.1→13.31 Å / Num. obs: 3220 / % possible obs: 95.5 % / Redundancy: 7.227 % / Biso Wilson estimate: 6.25 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.25 / Rrim(I) all: 0.266 / Χ2: 0.754 / Net I/σ(I): 4.15 / Num. measured all: 23271 / Scaling rejects: 17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.1-1.133.9390.5531.467762631970.7290.62974.9
1.13-1.164.3660.5741.558952242050.8070.64491.5
1.16-1.194.6740.5341.7610332382210.8790.59692.9
1.19-1.237.1750.5522.3716362422280.6590.5994.2
1.23-1.276.5190.5622.2812321951890.7510.60596.9
1.27-1.3170.5092.7612181841740.8040.54494.6
1.31-1.367.4270.4962.7413741881850.7690.52998.4
1.36-1.427.8780.4843.0915441991960.7350.51998.5
1.42-1.488.6360.4583.5715891851840.5750.48699.5
1.48-1.568.6850.443.8717111971970.8990.467100
1.56-1.649.3510.3735.1317861911910.9180.393100
1.64-1.747.6760.3564.8411131461450.8390.3899.3
1.74-1.868.1520.3256.1911821451450.9050.344100
1.86-2.018.1520.326.5411821451450.7980.34100
2.01-2.28.7190.267.5612121391390.9410.277100
2.2-2.469.5670.2758.2314351521500.9310.29198.7
2.46-2.847.010.2447.03694101990.9740.26598
2.84-3.487.5580.28.3571896950.9590.21399
3.48-4.928.7660.1439.482497940.9850.15196.9
4.92-13.312.8540.1354.7511745410.9880.16291.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
EM software
IDNameVersionCategoryDetails
1EM-Menuimage acquisition
6Coot0.8.2model fitting
12SHELXD2013/23D reconstructiondirect methods
13BUSTER2.10.3model refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 13.79 Å / B: 4.93 Å / C: 101.9 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 1.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: Density map was obtained using measured diffration intensities and phases acquired from a crystallographic direct methods program, SHELXD.
Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 8.09 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum liklihood
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.1→13.31 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.051 / SU Rfree Cruickshank DPI: 0.048
RfactorNum. reflection% reflectionSelection details
Rfree0.255 322 10.01 %RANDOM
Rwork0.219 ---
obs0.223 3218 95.6 %-
Displacement parametersBiso max: 36.56 Å2 / Biso mean: 8.09 Å2 / Biso min: 4.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.9157 Å20 Å20 Å2
2---0.1121 Å20 Å2
3----0.8036 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.1→13.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms76 0 11 3 90
Biso mean--13.07 20.29 -
Num. residues----12
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
ELECTRON CRYSTALLOGRAPHYt_dihedral_angle_d30SINUSOIDAL2
ELECTRON CRYSTALLOGRAPHYt_trig_c_planes2HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_gen_planes22HARMONIC5
ELECTRON CRYSTALLOGRAPHYt_it144HARMONIC20
ELECTRON CRYSTALLOGRAPHYt_nbd
ELECTRON CRYSTALLOGRAPHYt_improper_torsion
ELECTRON CRYSTALLOGRAPHYt_pseud_angle
ELECTRON CRYSTALLOGRAPHYt_chiral_improper_torsion8SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_sum_occupancies
ELECTRON CRYSTALLOGRAPHYt_utility_distance
ELECTRON CRYSTALLOGRAPHYt_utility_angle
ELECTRON CRYSTALLOGRAPHYt_utility_torsion
ELECTRON CRYSTALLOGRAPHYt_ideal_dist_contact114SEMIHARMONIC4
ELECTRON CRYSTALLOGRAPHYt_bond_d144HARMONIC20.013
ELECTRON CRYSTALLOGRAPHYt_angle_deg237HARMONIC21.06
ELECTRON CRYSTALLOGRAPHYt_omega_torsion3.42
ELECTRON CRYSTALLOGRAPHYt_other_torsion8.81
LS refinement shellResolution: 1.1→1.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2545 85 10 %
Rwork0.2114 765 -
all0.2159 850 -
obs--88 %
Refinement TLS params.

Method: refined / Refine-ID: ELECTRON CRYSTALLOGRAPHY

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
100.14590.13950.5190.0060.06070.0031-0.006-0.0195-0.0255-0.0111-0.0134-0.0103-0.00130.0080.06110.00390.0011-0.0363-0.0042-0.03092.5784.1254.5859
20.0954-0.17420.14030.23260.15470.00140.0020.02410.00550.04620.0006-0.01040.0076-0.019-0.00260.086-0.01810.0034-0.0710.0036-0.0180.97360.213815.5476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1ELECTRON CRYSTALLOGRAPHY1{A|1 - 6}A1 - 6
2ELECTRON CRYSTALLOGRAPHY2{B|1 - 6}B1 - 6

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