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- PDB-8b5x: Crystal structure of the SUN1-KASH6 9:6 complex -

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Basic information

Entry
Database: PDB / ID: 8b5x
TitleCrystal structure of the SUN1-KASH6 9:6 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 / meiotic nuclear membrane microtubule tethering complex / vesicle targeting / homologous chromosome pairing at meiosis / lamin binding / vesicle fusion / 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 / meiotic nuclear membrane microtubule tethering complex / vesicle targeting / homologous chromosome pairing at meiosis / lamin binding / vesicle fusion / nuclear inner membrane / azurophil granule membrane / centrosome localization / nucleus organization / response to mechanical stimulus / single fertilization / protein-membrane adaptor activity / immune system process / Meiotic synapsis / ossification / spindle pole / nuclear envelope / chromosome / spermatogenesis / microtubule binding / nuclear membrane / chromosome, telomeric region / intracellular membrane-bounded organelle / centrosome / endoplasmic reticulum membrane / Neutrophil degranulation / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
MRVI1 / MRVI1 protein / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / 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 / Inositol 1,4,5-triphosphate receptor associated 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsErlandsen, B.S. / Gurusaran, M. / 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 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 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
Revision 1.2Nov 20, 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
D: Inositol 1,4,5-triphosphate receptor associated 2
E: Inositol 1,4,5-triphosphate receptor associated 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6779
Polymers77,5245
Non-polymers1534
Water5,981332
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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,03127
Polymers232,57315
Non-polymers45812
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)133.921, 133.921, 106.581
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:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: VAL / End label comp-ID: VAL / Auth seq-ID: 618 - 811 / Label seq-ID: 9 - 202

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB
d_3CC

NCS oper:
IDCodeMatrixVector
1given(0.959858490649, 0.123234466303, -0.251962188124), (-0.152114185065, -0.526018342782, -0.836759211338), (-0.235654307474, 0.841497456545, -0.486157462143)-13.8064177585, 36.1539211382, -76.8058755474
2given(0.917560415427, -0.267221554281, -0.29440707357), (0.115504078365, -0.529382464846, 0.840483797461), (-0.380449328981, -0.805199880055, -0.454875215018)2.1132488631, 86.3269337449, -14.1675236982

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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.: 2
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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M sodium acetate; 0.1 M Sodium citrate tribasic dihydrate pH 5.5 (+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: 1.98→115.98 Å / Num. obs: 43359 / % possible obs: 57.8 % / Redundancy: 21.2 % / Biso Wilson estimate: 35.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.048 / Net I/σ(I): 12.5
Reflection shellResolution: 1.984→2.221 Å / Rmerge(I) obs: 2.107 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2170 / CC1/2: 0.663 / Rpim(I) all: 0.458 / % possible all: 10.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8B46

8b46


Resolution: 1.98→32.17 Å / SU ML: 0.2158 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.0829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2107 2257 5.21 %
Rwork0.1733 41068 -
obs0.1753 43325 57.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.5 Å2
Refinement stepCycle: LAST / Resolution: 1.98→32.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 4 332 5275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845077
X-RAY DIFFRACTIONf_angle_d1.09556898
X-RAY DIFFRACTIONf_chiral_restr0.0608734
X-RAY DIFFRACTIONf_plane_restr0.0091897
X-RAY DIFFRACTIONf_dihedral_angle_d13.76561848
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS2.56379077352
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.88113640443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.151440.281131X-RAY DIFFRACTION2.92
2.03-2.070.1456110.2393275X-RAY DIFFRACTION6.19
2.07-2.130.2132270.2507444X-RAY DIFFRACTION10.06
2.13-2.180.3213340.2295683X-RAY DIFFRACTION15.45
2.18-2.250.2641540.2421932X-RAY DIFFRACTION21.21
2.25-2.320.273580.25081222X-RAY DIFFRACTION27.48
2.32-2.40.2624780.24441702X-RAY DIFFRACTION37.99
2.4-2.50.29481080.2372125X-RAY DIFFRACTION47.93
2.5-2.610.25081360.2362754X-RAY DIFFRACTION61.94
2.61-2.750.27052230.2424031X-RAY DIFFRACTION90.92
2.75-2.920.25122670.21734431X-RAY DIFFRACTION100
2.92-3.150.24642480.18954449X-RAY DIFFRACTION100
3.15-3.460.20432200.17034466X-RAY DIFFRACTION99.96
3.47-3.970.17342370.14764467X-RAY DIFFRACTION100
3.97-4.990.17542540.13484477X-RAY DIFFRACTION99.98
4.99-32.170.20412980.15744479X-RAY DIFFRACTION99.75
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)
10.2980413952840.3013227008860.6084423629862.54094286720.2193281548411.716629713070.0156510993174-0.0490549271998-0.04725091169840.0696698425950.0366453434169-0.4145984757610.1870710481830.070245946559-0.0133112082080.131593044947-0.0536150616905-0.05995876629340.3643207965570.00331524983670.327958663643-29.794773231738.9580503584-13.9916769698
21.72021989761-1.280300130871.060578880251.74968107644-0.9551067298592.19867845730.06417979407180.045846613329-0.152637753889-0.03860774255870.0521020069810.1931132065970.156829816335-0.0986852086485-0.1546084285960.195592902933-0.0982082352527-0.01239776921460.296058545201-0.006032573545920.212090270422-42.74792656546.7879822506-10.0802053619
32.02697456809-0.146490504130.6285514373644.2697346429-0.3650840717094.88461149598-0.00256604198178-0.209449540245-0.282831205240.4641116770640.00836995204958-0.3889059918390.04140307012110.496623786836-0.04518379821670.16798422961-0.0254039613201-0.1216894531550.374415927081-0.06976028730160.237167900543-27.942754256844.4813976514-2.32136837206
42.14142659970.931193423804-0.7991992777093.193291268551.425824073221.61901426938-0.126707580747-0.0849949306562-0.3210650895870.6187907659820.126996799082-0.3072380661980.272975075990.2375496312420.04663414390480.280404842485-0.0285015843908-0.1263071672340.3748706816880.0005143410172750.228847788923-30.095180027841.1214237347-0.204135434391
51.698633974350.80163191961-0.2323333029992.48782962244-0.6983823486812.741191919980.00835245041446-0.100423812407-0.107418105836-0.0953740698646-0.0238789859434-0.2201130964910.1934293534310.334616956194-0.04301076061580.1993668679610.04099125876530.008709912698620.23842521284-0.07904133264690.235119273425-35.40267095831.771730179-28.9300351556
62.094791896410.04668720282930.1264735096151.756890210030.03087670436633.46900240194-0.0286140044197-0.0409810264183-0.1714394721680.0988862409593-0.00346285837642-0.1133144686420.267144240548-0.02341852847550.01537129107560.267978306768-0.0379168532712-0.004051877074450.139900781938-0.05198589421830.265741706807-42.343772853225.2548125224-25.7069265433
73.734128219111.303962909140.2118480924024.69016150892-0.02997006043352.457280641340.174243091330.455160840665-0.827705663667-0.1506868488870.123543217812-0.4389414553990.5478817912570.37220430117-0.292486267070.3802172574050.05383100144010.02799542910190.212103539958-0.1199604237810.42253226237-35.542112701317.4097396041-31.608430427
88.37427777652-2.461382830263.801628978045.482657954880.9995987231772.679646962130.05816163906721.26668768738-0.363638042562-1.20821564991-0.00942451037956-0.3302099071071.07665060873-0.00644361512250.00200268612080.705164860234-0.0830816318710.1179357567270.412574031228-0.1835547858870.413439272812-39.044689418518.2619355724-43.7008994543
91.9029853946-0.132744581111.651310988811.91283978538-1.493312245774.165738999450.141217601247-0.0700979639689-0.0530177131882-0.15995151021-0.0370622030023-0.2979801248320.4729974881820.39440020778-0.08295556952350.2876785817820.02667277817880.03339796618520.22579569999-0.07961243523830.367626340179-36.647550359120.6826627941-27.9971311932
100.257478145122-0.3947489862870.4099051132222.44010881584-0.04314496952652.78150960572-0.1043532493310.152222286075-0.1123579465030.01328775203880.0822572176539-0.25535427810.07748708150160.268290031525-0.005158987469620.14942458175-0.1008211359950.06445811690580.36897684618-0.01664389857380.231945932973-31.605950923850.4289869125-27.6560291042
112.38263214489-0.462547829917-0.4758588774043.15267058951-0.006820501861742.08283595986-0.072104275719-0.013275736264-0.2652386954920.1077341470740.06328102804320.2699114957890.337056942927-0.0389464852289-0.02936001993910.142337395482-0.1081282071020.02516809676960.236707423558-0.00677987730370.14441406344-42.038125916948.8434543616-33.6433314992
124.36046598398-1.16201945134-1.196976614294.454381124180.197206297763.971765026620.1315456644360.02119912423990.472131899001-0.1429238607230.00106501290291-0.196748045113-0.5997258545340.0329322610629-0.07990698891020.147237255504-0.1636612268670.03934323848150.3027020943450.010425022280.196583502658-35.237513826265.0229893889-36.2859886804
131.77300190226-1.00262965126-0.6555631747492.051377786560.0005849747324446.458799914390.0552251026539-0.0447565977332-0.433642491963-0.08464095605950.266331397325-0.2718097151030.1369063896880.0839453243646-0.1718045096170.129430234034-0.07277301337710.06776817404030.3283425844370.01703598259030.226373452619-37.818448680954.5021793443-37.9800665819
146.436501736821.87340945464-4.824106258292.55491288928-2.56279275394.24551226277-0.746563871224-1.39415600986-1.426201890690.248288352409-0.540088304431-0.9645614182621.676628318780.5731165074381.342398242080.7107408748660.00556425777460.1159528565460.8493421616390.1426585607930.891840081802-52.714039871643.0645470677-15.9038035641
153.504277102240.7652149510924.900261679946.51268831791-0.5358099252847.59990351159-0.2654258785010.348989953130.2698477628840.241934364079-0.02830342736210.0593143144743-0.6559549019590.2164390665130.1298080886530.151792537691-0.008810879418110.01116906269410.361371932999-0.07424291584930.210466168647-45.322484104357.91860958-18.3159966538
166.1602330093-7.37421597245-6.889401041779.290006830027.916786290577.96834486240.727867849051-1.453566878941.75321443210.0229320487450.2554650718490.207212620514-0.339736018131-0.325157489141-0.9565409160090.8638217719670.01852693907320.1212799954110.811440473576-0.09532273165980.982074067437-49.977112727229.1762639092-7.81830322697
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 670 )BB618 - 6701 - 53
66chain 'B' and (resid 671 through 727 )BB671 - 72754 - 110
77chain 'B' and (resid 728 through 772 )BB728 - 772111 - 155
88chain 'B' and (resid 773 through 789 )BB773 - 789156 - 172
99chain 'B' and (resid 790 through 811 )BB790 - 811173 - 194
1010chain 'C' and (resid 618 through 665 )CC618 - 6651 - 48
1111chain 'C' and (resid 666 through 738 )CC666 - 73849 - 121
1212chain 'C' and (resid 739 through 789 )CC739 - 789122 - 172
1313chain 'C' and (resid 790 through 811 )CC790 - 811173 - 194
1414chain 'D' and (resid 530 through 544 )DD530 - 5441 - 15
1515chain 'D' and (resid 545 through 555 )DD545 - 55516 - 26
1616chain 'E' and (resid 543 through 555 )EE543 - 5551 - 13

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