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- PDB-8b46: Crystal structure of the SUN1-KASH6 9:9 complex -

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Basic information

Entry
Database: PDB / ID: 8b46
TitleCrystal structure of the SUN1-KASH6 9:9 complex
Components
  • Inositol 1,4,5-triphosphate receptor associated 2
  • SUN domain-containing protein 1
KeywordsSTRUCTURAL PROTEIN / LINC complex / nuclear structure / microtubules
Function / homology
Function and homology information


nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / vesicle targeting / meiotic nuclear membrane microtubule tethering complex / vesicle fusion / homologous chromosome pairing at meiosis / lamin binding / nuclear inner membrane ...nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic attachment of telomere to nuclear envelope / vesicle targeting / meiotic nuclear membrane microtubule tethering complex / vesicle fusion / homologous chromosome pairing at meiosis / lamin binding / nuclear inner membrane / centrosome localization / azurophil granule membrane / immune system process / nucleus organization / single fertilization / response to mechanical stimulus / protein-membrane adaptor activity / Meiotic synapsis / ossification / spindle pole / nuclear envelope / chromosome / microtubule binding / spermatogenesis / nuclear membrane / chromosome, telomeric region / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / endoplasmic reticulum membrane / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
MRVI1 / MRVI1 protein / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / SUN domain-containing protein 1-5 / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain profile. / SUN domain / Sad1 / UNC-like C-terminal
Similarity search - Domain/homology
: / SUN domain-containing protein 1 / Inositol 1,4,5-triphosphate receptor associated 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGurusaran, M. / Erlandsen, B.S. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
CitationJournal: Commun Biol / Year: 2024
Title: The crystal structure of SUN1-KASH6 reveals an asymmetric LINC complex architecture compatible with nuclear membrane insertion.
Authors: Gurusaran, M. / Erlandsen, B.S. / Davies, O.R.
History
DepositionSep 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
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

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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
D: Inositol 1,4,5-triphosphate receptor associated 2
E: Inositol 1,4,5-triphosphate receptor associated 2
F: Inositol 1,4,5-triphosphate receptor associated 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,64310
Polymers82,4916
Non-polymers1534
Water10,485582
1
A: SUN domain-containing protein 1
B: SUN domain-containing protein 1
C: SUN domain-containing protein 1
D: Inositol 1,4,5-triphosphate receptor associated 2
E: Inositol 1,4,5-triphosphate receptor associated 2
F: Inositol 1,4,5-triphosphate receptor associated 2
hetero molecules

A: SUN domain-containing protein 1
B: SUN domain-containing protein 1
C: SUN domain-containing protein 1
D: Inositol 1,4,5-triphosphate receptor associated 2
E: Inositol 1,4,5-triphosphate receptor associated 2
F: Inositol 1,4,5-triphosphate receptor associated 2
hetero molecules

A: SUN domain-containing protein 1
B: SUN domain-containing protein 1
C: SUN domain-containing protein 1
D: Inositol 1,4,5-triphosphate receptor associated 2
E: Inositol 1,4,5-triphosphate receptor associated 2
F: Inositol 1,4,5-triphosphate receptor associated 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,93030
Polymers247,47218
Non-polymers45812
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)134.094, 134.094, 106.586
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRVALA1 - 194
d_21ens_1THRVALB1 - 194
d_31ens_1THRVALC1 - 194

NCS oper:
IDCodeMatrixVector
1given(-0.169459797514, -0.498271938528, -0.850299036988), (-0.773960279246, 0.601421826967, -0.198184944425), (0.610138396739, 0.624513299557, -0.487559509702)69.8973205265, 40.7043673623, 2.44397908899
2given(-0.229817965356, -0.780805732781, 0.580969973798), (-0.398192593424, 0.620134429791, 0.675925992643), (-0.888046373418, -0.0759980042081, -0.453429092599)44.918272488, 5.44411756421, 63.5507757519

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Components

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


Mass: 22530.379 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: Protein/peptide Inositol 1,4,5-triphosphate receptor associated 2 / Lymphoid-restricted membrane protein / Protein Jaw1


Mass: 4966.522 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRAG2, JAW1, LRMP / Production host: Escherichia coli (E. coli) / References: UniProt: Q12912
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 582 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Magnesium chloride, 0.1 M MES pH 6.0, 3% w/v PEG 6000 (+25% ethylene glycol cryoprotectant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6702 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6702 Å / Relative weight: 1
ReflectionResolution: 1.665→116.129 Å / Num. obs: 70755 / % possible obs: 55.7 % / Redundancy: 21.1 % / Biso Wilson estimate: 25.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.043 / Net I/σ(I): 17.4
Reflection shellResolution: 1.665→1.889 Å / Rmerge(I) obs: 1.887 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3538 / CC1/2: 0.676 / Rpim(I) all: 0.622 / % possible all: 8.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R2I
Resolution: 1.67→43.89 Å / SU ML: 0.1671 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.8527
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1896 3445 4.87 %
Rwork0.1658 67275 -
obs0.1669 70720 55.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.52 Å2
Refinement stepCycle: LAST / Resolution: 1.67→43.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4961 0 4 582 5547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01365100
X-RAY DIFFRACTIONf_angle_d1.29596930
X-RAY DIFFRACTIONf_chiral_restr0.0761738
X-RAY DIFFRACTIONf_plane_restr0.0108901
X-RAY DIFFRACTIONf_dihedral_angle_d12.72651858
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.60819269146
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.85891325112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.690.280870.277798X-RAY DIFFRACTION2.09
1.69-1.710.3261220.2816215X-RAY DIFFRACTION4.7
1.71-1.740.3167230.2629291X-RAY DIFFRACTION6.22
1.74-1.760.198180.2868357X-RAY DIFFRACTION7.46
1.76-1.790.2545280.2803447X-RAY DIFFRACTION9.5
1.79-1.820.284250.2573562X-RAY DIFFRACTION11.52
1.82-1.860.2326330.2444640X-RAY DIFFRACTION13.42
1.86-1.890.2778340.2505882X-RAY DIFFRACTION18.01
1.89-1.930.2223450.24991050X-RAY DIFFRACTION21.78
1.93-1.970.213700.23471387X-RAY DIFFRACTION28.72
1.97-2.020.2316940.21721638X-RAY DIFFRACTION34.28
2.02-2.070.27051050.21791997X-RAY DIFFRACTION41.66
2.07-2.130.22421290.2172442X-RAY DIFFRACTION50.69
2.13-2.190.22431670.21073033X-RAY DIFFRACTION63.2
2.19-2.260.25252270.20653808X-RAY DIFFRACTION79.46
2.26-2.340.24692300.20694729X-RAY DIFFRACTION97.93
2.34-2.430.24282760.19734796X-RAY DIFFRACTION100
2.43-2.550.25442210.19074855X-RAY DIFFRACTION100
2.55-2.680.19522530.17934852X-RAY DIFFRACTION99.96
2.68-2.850.21042640.17564803X-RAY DIFFRACTION99.98
2.85-3.070.18122260.1674866X-RAY DIFFRACTION100
3.07-3.380.16072290.14864837X-RAY DIFFRACTION99.9
3.38-3.860.16142300.13844885X-RAY DIFFRACTION100
3.86-4.870.15682160.12744910X-RAY DIFFRACTION99.98
4.87-43.890.16042730.15994895X-RAY DIFFRACTION99.46
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.091236741220.8868199863320.6007517438460.459997498199-0.1814733135621.913196060490.0582582086797-0.0425543670503-0.357345049175-0.0376753469786-0.0155188575413-0.1854692549210.259871456697-0.02652068122090.04161611938470.2003036675270.09257081897210.0007585686579720.1864173451930.04958234338850.27048232868918.848646643145.376466776239.285137577
20.182074907032-0.104663334816-0.05741191391981.21192378231-0.8205548758841.90128961350.0157181770239-0.06845376063960.04387710738730.04692455273060.04624775906370.137588573697-0.0503805823682-0.205385760559-0.1057746985250.1419760502920.072887569528-0.007810709948030.256007355630.01144478504940.19542296115119.152944247560.517559643143.2365200787
33.173985290321.26444268388-0.7911907622512.02185308889-1.157127771444.958190554870.125424374929-0.335638502383-0.2621368287430.239684414588-0.0989145513995-0.03346303948690.2420174765660.06490915148370.02517192729430.2424704588380.0834705108509-0.07344164633020.2196643900470.05061506720190.21382650964124.597271281846.554719250351.0079564038
42.79219444329-0.292087991020.979373547751.475041307661.321239259791.623689204580.201407090521-0.49931570628-0.3710519990120.334253984864-0.2486031617240.0923601700620.380479379835-0.2022807233720.07573146522790.2599295841250.0289872294742-0.04293094405620.3191673995120.08962083180660.19825586135620.556788469146.715967919253.1100812256
52.8264731337-0.6752276891580.1790993029852.05256663926-0.3886820760442.54365719819-0.03686851847590.251140612723-0.351900846458-0.13298793884-0.00684897169404-0.2474059933960.7152034903190.2605863996470.1203170916980.3196515655850.1096513946810.003080081807770.220167686923-0.08633477652020.28861448922518.053718967742.07903786318.9869539153
62.13487228493-0.0308896346815-1.708596834620.732681169187-0.5807145346542.761101559540.02024577917890.09557600279540.1269998418550.167638164931-0.0321247821033-0.19474644350.0714724134030.0485524635471-0.01542313843460.1798917569880.0261562471836-0.05162328642050.362688959142-0.01374941046530.297255998664-7.1574099155156.46961753835.7337532159
73.13623859460.0067159878231-0.3907284295182.504925405580.08657743200094.62389467260.200634276695-0.4822359418520.6575126840810.416368253029-0.0374228777005-0.206230582411-0.505194517954-0.374705923565-0.09834530051780.2910432703990.0120429664309-0.001372340253170.466182822911-0.07166976911830.351350305829-5.2306049454161.539583730239.5030464973
81.914633264030.1760163615460.3139897245091.53982773038-0.229875549253.267791820330.08947168128390.0287859643957-0.224568048513-0.04249982574290.001364479477780.06864786660920.270927128268-0.0319503060188-0.07809418654030.143209164588-0.00796963107947-0.03217237817320.200715718481-0.04297138367630.2288719863242.3020258548246.359616115624.5378591957
98.443114208930.550538107151-0.2116673726564.93226569572-1.010968463433.666074252070.131866743575-1.77481868877-0.8268095630510.554290574386-0.1421594198910.2844485464020.439933431058-0.164613358115-0.07100003085590.272711477879-0.0631130582967-0.01244215078170.4293174833640.1119442134840.3755865919410.42748997761637.162580951736.4340781231
104.71619961036-0.8753779109260.5044308912784.03323297457-1.63657350492.551999034360.1222135947240.659872557743-0.104324707615-0.5926982645240.06979165675160.9995590821260.430597024596-0.560056522954-0.2225357021380.258962588098-0.0631517353246-0.08366358583870.492657670731-0.07633783059530.433996704077-9.4273035447647.108456307213.926429198
114.62931968074-0.08609606856311.718950643042.64092131333-0.5816322375454.92044119874-0.01013797638660.229803181791-0.9016046439-0.2777489468580.08719599603910.07250375132531.02741873434-0.115098684069-0.1853464622660.39390297656-0.0807789760124-0.04434642965820.174120748342-0.1078173515670.4279271319471.2456141046734.792682499121.0620218923
123.414318092090.08344954941121.463352442065.41582878358-1.22945754820.88146208759-0.07279590751061.18362850355-0.578382945989-1.4062002250.3163097950290.2944221827680.942154953092-0.825611157563-0.01480138247270.558870643751-0.143011666827-0.1358123584280.574427654813-0.138902659650.413609597031-3.5672209932243.20493355929.38089107071
133.064642979330.518721817694-1.117626249552.61835142283-2.184825297883.471426155280.02506242416250.0829541766177-0.219157554245-0.1435799883140.06534702086870.1166372898160.410182024628-0.332176428647-0.04486345145880.180354841125-0.0345744296095-0.06654993794770.184388222763-0.05157673818870.247241138221-0.41174605224242.261315421325.361837075
141.117328664780.8268366025220.1532966313511.33250550594-0.06848159792222.812252722090.08501126444810.0450991275229-0.249897535794-0.0147256576429-0.0499645300022-0.03463837573930.3328976160920.0688337141975-0.04700214640.1811040291480.128258244620.005067455418730.253616872188-0.03115611824380.22821376213927.872056043152.67733490825.7344905013
151.65144654050.80813954506-0.3631834918112.27703649590.4118362048211.610062885130.05583322218360.002148200428740.07875846931320.0404653135111-0.05302147424750.2358146086010.0847550131043-0.228968353465-0.04685464320130.1089825592710.08868252520896.62695274803E-50.249110662321-0.02211030970110.1591325365521.303373327160.938055665519.6967297593
163.944144804771.641558771830.2406281416043.567620517240.8902849741914.34263134064-0.06244231740120.1044130241310.0760336690132-0.1761161654340.144157846471-0.117269188526-0.2647690845890.219033829855-0.03224077192810.1127684128830.1266630651220.01485396940180.237740408009-0.03213545523670.12787638168736.626548462462.111273126215.3699885866
173.321308782480.339489528412-0.8632550143082.768744813791.597469264694.912897157-0.3209817887980.1636165494140.09007801419250.04060232266150.196180873045-0.591131609856-0.7604441000111.72395670191-0.2485914636490.1341714973640.04326455194060.0270388192450.604227117018-0.02063112438740.24732859716143.016077613565.318069536520.6725637269
180.7249557022870.125988938487-0.7013982507572.361711620030.476845469623.133736052090.01467643849390.0724749447588-0.1255472937180.01190570487960.1023977103030.045751127792-0.0803762948484-0.110205782346-0.08851519618520.1380858808030.09214780009280.02635629345880.229158647347-0.02628741481590.15896998990728.298141700560.086139397515.3060531317
199.2074183804-1.63132784707-5.4524737597.59687851372.457335924343.52192662168-0.579256510562-0.520352618192-1.58739725611.72088447823-0.1681092711651.169248163131.3922845304-1.521179293660.7715044846150.841869669726-0.08995004757260.2089850113970.7559275035860.002063226319270.75049993989810.873879790867.286723333337.3105096299
207.87125552185-1.410227277142.673130001556.95377020708-4.591651760527.360860721650.1349261511370.260325105530.501743531766-0.020096526723-0.549949639449-0.324944577821-0.1447079726110.5338077498410.4206055359620.1570969949690.0799741815988-0.0158578611320.195955926848-0.04030268075330.15936818372327.472446986568.360590844734.9478145888
213.39730759917-3.867430172320.3552972070465.07577598401-0.1219740679532.58405232977-0.635921883581-0.7237946841491.492601820632.934910101120.532500690201-1.61314357034-0.993234736685-0.109096038315-0.03506302929251.17916381347-0.100855647439-0.1702008650661.05377010466-0.199927358991.037527913460.12349485111858.089342887245.3762933773
222.674484341-2.23516823088-1.029188470753.749897295612.16735161221.466556276970.3537511625670.5905040432310.246515184540.305418559534-0.2987487724721.61809288478-0.510538583064-0.941668715638-0.007644853374520.2963813765530.04496604289050.07323738982520.6831666204980.05918395894690.41648646813313.731182967159.106726976713.0110858897
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 618 through 666 )AA618 - 6661 - 49
22chain 'A' and (resid 667 through 712 )AA667 - 71250 - 95
33chain 'A' and (resid 713 through 772 )AA713 - 77296 - 155
44chain 'A' and (resid 773 through 811 )AA773 - 811156 - 194
55chain 'B' and (resid 618 through 654 )BB618 - 6541 - 37
66chain 'B' and (resid 655 through 670 )BB655 - 67038 - 53
77chain 'B' and (resid 671 through 681 )BB671 - 68154 - 64
88chain 'B' and (resid 682 through 727 )BB682 - 72765 - 110
99chain 'B' and (resid 728 through 738 )BB728 - 738111 - 121
1010chain 'B' and (resid 739 through 753 )BB739 - 753122 - 136
1111chain 'B' and (resid 754 through 772 )BB754 - 772137 - 155
1212chain 'B' and (resid 773 through 789 )BB773 - 789156 - 172
1313chain 'B' and (resid 790 through 811 )BB790 - 811173 - 194
1414chain 'C' and (resid 618 through 665 )CC618 - 6651 - 48
1515chain 'C' and (resid 666 through 738 )CC666 - 73849 - 121
1616chain 'C' and (resid 739 through 772 )CC739 - 772122 - 155
1717chain 'C' and (resid 773 through 789 )CC773 - 789156 - 172
1818chain 'C' and (resid 790 through 811 )CC790 - 811173 - 194
1919chain 'D' and (resid 530 through 544 )DD530 - 5441 - 15
2020chain 'D' and (resid 545 through 555 )DD545 - 55516 - 26
2121chain 'E' and (resid 543 through 555 )EE543 - 5551 - 13
2222chain 'F' and (resid 553 through 555 )FF553 - 5551 - 3

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