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- PDB-6bzm: GFGNFGTS from low-complexity/FG repeat domain of Nup98, residues ... -

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Basic information

Entry
Database: PDB / ID: 6bzm
TitleGFGNFGTS from low-complexity/FG repeat domain of Nup98, residues 116-123
ComponentsNuclear pore complex protein Nup98-Nup96
KeywordsPROTEIN FIBRIL / Amyloid / LARKS / Reversible-amyloid / low-complexity / FG repeat
Function / homology
Function and homology information


nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus ...nuclear pore outer ring / telomere tethering at nuclear periphery / nuclear pore complex assembly / nuclear pore organization / nuclear pore cytoplasmic filaments / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / Rev-mediated nuclear export of HIV RNA / structural constituent of nuclear pore / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / Transport of Mature mRNA derived from an Intron-Containing Transcript / tRNA processing in the nucleus / RNA export from nucleus / Postmitotic nuclear pore complex (NPC) reformation / nucleocytoplasmic transport / positive regulation of mRNA splicing, via spliceosome / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / Regulation of HSF1-mediated heat shock response / mRNA transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / nuclear pore / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / molecular condensate scaffold activity / HCMV Late Events / promoter-specific chromatin binding / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol
Similarity search - Function
Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin autopeptidase / NUP C-terminal domain profile. / Nucleoporin peptidase S59-like
Similarity search - Domain/homology
Nuclear pore complex protein Nup98-Nup96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / AB INITIO PHASING / cryo EM / Resolution: 0.9 Å
AuthorsHughes, M.P. / Rodriguez, J.A. / Sawaya, M.R. / Cascio, D. / Chong, L. / 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 24, 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: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96


Theoretical massNumber of molelcules
Total (without water)1,5722
Polymers1,5722
Non-polymers00
Water362
1
A: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96

A: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96

A: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96

A: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96

A: Nuclear pore complex protein Nup98-Nup96
B: Nuclear pore complex protein Nup98-Nup96


Theoretical massNumber of molelcules
Total (without water)7,85810
Polymers7,85810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_755x+2,y,z1
crystal symmetry operation1_355x-2,y,z1
Unit cell
Length a, b, c (Å)4.790, 18.240, 26.440
Angle α, β, γ (deg.)93.140, 92.730, 97.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide Nuclear pore complex protein Nup98-Nup96


Mass: 785.803 Da / Num. of mol.: 2 / Fragment: UNP residues 116-123 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P52948
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / 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 crystal containing protofilaments of an 8-residue segment of Nup98
Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
EM crystal formationInstrument: hanging drop vapor diffusion / Atmosphere: air
Details: The peptide was solubilized by adding nano-pure H2O with 20% DMSO to achieve a concentration of 12 mg/mL. The peptide solution was immediately used for crystallization. Crystals grew at room ...Details: The peptide was solubilized by adding nano-pure H2O with 20% DMSO to achieve a concentration of 12 mg/mL. The peptide solution was immediately used for crystallization. Crystals grew at room temperature by hanging drop vapor diffusion.
Lipid mixture: none / Temperature: 298 K
Buffer solutionpH: 9.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.1 MCHESC8H17NO3S1
210 percent (v/v)ethanolC2H6O1
SpecimenConc.: 12 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: 1.45 Å3/Da / Density % sol: 15.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 0.1 M CHES, pH 9.5, 10% ethanol

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Data collection

MicroscopyModel: FEI TECNAI 20
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-F415 (4k x 4k) / Num. of diffraction images: 398 / Num. of grids imaged: 2
Details: The detector was operated in rolling shutter mode with 2x2 pixel binning.
Image scansSampling size: 15.6 µm / Width: 4096 / Height: 4096
EM diffractionCamera length: 730 mm
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
1.4289-18.06781193.86.2155141.61
1.1342-1.42892194.36.4152548.66
0.9909-1.13423193.95.5154436.54
0.9003-0.94170.33.2117943.94
EM diffraction statsDetails: Phase statistics are not applicable. No imaging was used. The phases wwere obtained by a crystallographic direct methods program, SHELXD.
Fourier space coverage: 88 % / High resolution: 0.9 Å / Num. of intensities measured: 31674 / Num. of structure factors: 5800 / Phase error: 42.6 ° / Phase residual: 42.6 ° / Phase error rejection criteria: 0 / Rmerge: 0.289 / Rsym: 0.289
DiffractionMean temperature: 100 K
Diffraction sourceSource: ELECTRON MICROSCOPE / Type: TECNAI F20 TEM / Wavelength: 0.0251 Å
DetectorType: TVIPS F416 CMOS CAMERA / Detector: CMOS / Date: Mar 23, 2017
Radiation wavelengthWavelength: 0.0251 Å / Relative weight: 1
ReflectionResolution: 0.9→26.36 Å / Num. obs: 5800 / % possible obs: 88 % / Redundancy: 5.461 % / Biso Wilson estimate: 3.45 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.289 / Rrim(I) all: 0.313 / Χ2: 0.739 / Net I/σ(I): 3.51 / Num. measured all: 31674 / Scaling rejects: 21
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
0.9-0.922.7980.5881.126915172470.5460.71747.8
0.92-0.952.7640.4171.310565183820.8510.50773.7
0.95-0.983.5620.5911.313114403680.7210.68583.6
0.98-1.013.920.6531.3914664123740.5950.75190.8
1.01-1.045.140.5492.0120204233930.7820.60592.9
1.04-1.085.5060.4732.5821974223990.8860.51894.5
1.08-1.125.9640.4712.7922964083850.8350.51194.4
1.12-1.166.9640.4713.1527164103900.8620.50695.1
1.16-1.216.7490.4123.625514013780.8890.44794.3
1.21-1.275.8250.4053.6217303212970.8660.44192.5
1.27-1.345.9770.3853.8218413223080.9530.41795.7
1.34-1.426.430.4253.8619423163020.8280.45995.6
1.42-1.526.8360.325.0321743323180.9120.34595.8
1.52-1.646.7210.2615.7118822952800.9630.28194.9
1.64-1.85.1550.2885.2310982272130.8810.31793.8
1.8-2.015.8650.2496.1712612332150.9460.27292.3
2.01-2.327.0330.2317.3614842262110.9740.24993.4
2.32-2.855.4860.2116.847791551420.9440.23191.6
2.85-4.035.60.2167.457561421350.9660.23595.1
4.03-26.366.7140.2558.1342372630.9720.2787.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
EM software
IDNameVersionCategory
1EM-Menuimage acquisition
6Cootmodel fitting
12SHELXD2013/23D reconstruction
13BUSTER2.10.3model refinement
EM 3D crystal entity∠α: 93.14 ° / ∠β: 92.73 ° / ∠γ: 97.15 ° / A: 4.79 Å / B: 18.24 Å / C: 26.44 Å / Space group name: P1 / Space group num: 1
CTF correctionType: NONE
3D reconstructionResolution: 0.9 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES
Details: Density map was obtained using measured diffraction intensities and the phases acquired from a crystallographic direct methods program, SHELXD.
Symmetry type: 3D CRYSTAL
Atomic model buildingB value: 8 / Protocol: OTHER / Space: RECIPROCAL / Target criteria: maximum likelihood
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.9→26.36 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.895 / SU R Cruickshank DPI: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.03 / SU Rfree Blow DPI: 0.033 / SU Rfree Cruickshank DPI: 0.035
RfactorNum. reflection% reflectionSelection details
Rfree0.264 580 10 %RANDOM
Rwork0.226 ---
obs0.23 5799 87.9 %-
Displacement parametersBiso max: 59.41 Å2 / Biso mean: 8.02 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-1.2892 Å2-0.6176 Å2-0.3092 Å2
2--0.6422 Å2-0.3355 Å2
3----1.9314 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: final / Resolution: 0.9→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms112 0 0 3 115
Biso mean---14.39 -
Num. residues----16
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
ELECTRON CRYSTALLOGRAPHYt_dihedral_angle_d32SINUSOIDAL2
ELECTRON CRYSTALLOGRAPHYt_trig_c_planes4HARMONIC2
ELECTRON CRYSTALLOGRAPHYt_gen_planes34HARMONIC5
ELECTRON CRYSTALLOGRAPHYt_it202HARMONIC20
ELECTRON CRYSTALLOGRAPHYt_nbd
ELECTRON CRYSTALLOGRAPHYt_improper_torsion
ELECTRON CRYSTALLOGRAPHYt_pseud_angle
ELECTRON CRYSTALLOGRAPHYt_chiral_improper_torsion12SEMIHARMONIC5
ELECTRON CRYSTALLOGRAPHYt_sum_occupancies
ELECTRON CRYSTALLOGRAPHYt_utility_distance
ELECTRON CRYSTALLOGRAPHYt_utility_angle
ELECTRON CRYSTALLOGRAPHYt_utility_torsion
ELECTRON CRYSTALLOGRAPHYt_ideal_dist_contact237SEMIHARMONIC4
ELECTRON CRYSTALLOGRAPHYt_bond_d202HARMONIC20.014
ELECTRON CRYSTALLOGRAPHYt_angle_deg346HARMONIC21.16
ELECTRON CRYSTALLOGRAPHYt_omega_torsion3.45
ELECTRON CRYSTALLOGRAPHYt_other_torsion13.01
LS refinement shellResolution: 0.9→1.01 Å / Rfactor Rfree error: 0 / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2473 136 9.96 %
Rwork0.22 1229 -
all0.2228 1365 -
obs--72.26 %
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)
1-0.01390.04830.01030.01180.02730.00460.00060.0051-0.0047-0.00220.00060.0006-0.0003-0.0011-0.0012-0.02330.00420.0072-0.00930.0010.00141.46949.460917.6099
2-0.00330.0251-0.0290.00470.0126-0.00140.0004-0.0091-0.00280.004-0.0006-0.0004-0.00140.00320.0003-0.03380.0040.0023-0.01350-0.0033-0.272110.043629.4641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1ELECTRON CRYSTALLOGRAPHY1{ A|* }A1 - 8
2ELECTRON CRYSTALLOGRAPHY2{ B|* }B1 - 8

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