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- PDB-8au0: Crystal structure of the a1 luminal coiled-coil domain of SUN1 -

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Basic information

Entry
Database: PDB / ID: 8au0
TitleCrystal structure of the a1 luminal coiled-coil domain of SUN1
ComponentsSUN domain-containing protein 1
KeywordsSTRUCTURAL PROTEIN / LINC complex / nuclear structure / microtubules
Function / homology
Function and homology information


nuclear matrix anchoring at nuclear membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / homologous chromosome pairing at meiosis / lamin binding / nuclear inner membrane / centrosome localization / response to mechanical stimulus ...nuclear matrix anchoring at nuclear membrane / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / meiotic nuclear membrane microtubule tethering complex / homologous chromosome pairing at meiosis / lamin binding / nuclear inner membrane / centrosome localization / response to mechanical stimulus / protein-membrane adaptor activity / Meiotic synapsis / ossification / nuclear envelope / spermatogenesis / nuclear membrane / chromosome, telomeric region / intracellular membrane-bounded organelle / identical protein binding / cytoplasm
Similarity search - Function
SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / SUN domain-containing protein 1-5 / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal
Similarity search - Domain/homology
SUN domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsGurusaran, M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
CitationJournal: Front Cell Dev Biol / Year: 2023
Title: Molecular insights into LINC complex architecture through the crystal structure of a luminal trimeric coiled-coil domain of SUN1.
Authors: Gurusaran, M. / Biemans, J.J. / Wood, C.W. / Davies, O.R.
History
DepositionAug 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUN domain-containing protein 1
B: SUN domain-containing protein 1
C: SUN domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)13,9603
Polymers13,9603
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-54 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.313, 35.986, 46.095
Angle α, β, γ (deg.)90.000, 104.540, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide SUN domain-containing protein 1 / Protein unc-84 homolog A / Sad1/unc-84 protein-like 1


Mass: 4653.197 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUN1, KIAA0810, UNC84A / Production host: Escherichia coli (E. coli) / References: UniProt: O94901
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 1.8 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.09M Sodium nitrate, 0.09M Disodium phosphate, 0.09M Ammonium sulfate, 0.1M Imidazole pH 6.5, 0.1M MES (acid), 37.5% MPD (racemic), 37.5% PEG 1K, 37.5% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.069→30.31 Å / Num. obs: 5986 / % possible obs: 96.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.84 Å2 / Rpim(I) all: 0.043 / Net I/σ(I): 8.6
Reflection shellResolution: 2.069→2.105 Å / Num. unique obs: 294 / Rpim(I) all: 0.287

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
Arcimboldophasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ideal helices

Resolution: 2.07→30.31 Å / SU ML: 0.2168 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.8264
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2551 286 5.52 %
Rwork0.2438 4897 -
obs0.2444 5183 84.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.98 Å2
Refinement stepCycle: LAST / Resolution: 2.07→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 0 55 1008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058960
X-RAY DIFFRACTIONf_angle_d0.78791285
X-RAY DIFFRACTIONf_chiral_restr0.0319147
X-RAY DIFFRACTIONf_plane_restr0.0029171
X-RAY DIFFRACTIONf_dihedral_angle_d15.7305364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.610.27511130.27412098X-RAY DIFFRACTION72.71
2.61-30.310.24641730.22892799X-RAY DIFFRACTION95.59
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

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)
13.48057629253-0.0745064808622-2.507904791090.576844532776-0.06371925962922.68529118638-0.0187585827590.0693514972186-0.05654932944-0.112256697615-0.0984939778356-0.06904834804570.1201587747630.03720315797930.108883285030.122117512680.01839381474780.01265974118310.0886991616564-0.02589432383090.122739187083-2.176711163711.585413136329.04635989753
23.401890541910.872350890513-3.734778765211.05327673101-0.9954200813145.592826677450.006529301315470.0214958633971-0.0228172159675-0.1171173080610.0673285870357-0.117366809306-0.05941963656130.239247529499-0.03745184288480.0796907068795-0.0154421176576-0.03456976197270.1273086527520.002267954229470.09259871969621.77424052048.1207640511413.4247923766
30.00139564260409-0.000669761433920.00108083573379-0.000584511027134-0.0002489151368650.00114050127013-0.01091966241590.01435517857830.002655155506760.001920318599140.004670738858090.0014806188622-0.005368312673110.00635078320131-0.01368801341270.01494500802610.02886769396920.01422187770750.008305199456380.01093934371750.0014782120612-4.9782393428610.39192130967.97164778887
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 361 through 400 )AA361 - 4001 - 40
22chain 'B' and (resid 361 through 401 )BB361 - 4011 - 41
33chain 'C' and (resid 361 through 401 )CC361 - 4011 - 41

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