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- PDB-7z8y: Crystal structure of the SUN1-KASH6 9:6 complex -

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Basic information

Entry
Database: PDB / ID: 7z8y
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: 2.29 Å
AuthorsGurusaran, 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
DepositionMar 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 / citation_author
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 1.2Oct 16, 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)74,2739
Polymers74,1205
Non-polymers1534
Water4,107228
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)222,82027
Polymers222,36115
Non-polymers45812
Water21612
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)133.762, 133.762, 106.711
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_1(chain "A" and (resid 618 through 798 or resid 802 through 811))
d_2ens_1(chain "B" and (resid 618 through 798 or resid 802 through 811))
d_3ens_1(chain "C" and (resid 618 through 798 or resid 802 through 811))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRTYRA1 - 181
d_12ens_1TYRVALA185 - 194
d_21ens_1THRTYRB1 - 181
d_22ens_1TYRVALB185 - 194
d_31ens_1THRTYRC1 - 181
d_32ens_1TYRVALC185 - 194

NCS oper:
IDCodeMatrixVector
1given(0.918997833691, -0.110984563934, 0.378319188305), (0.265145091094, -0.536184863008, -0.801376237076), (0.291789414373, 0.83677250149, -0.463325715248)-3.43904691706, 134.978999185, -19.8695442386
2given(0.91961066672, 0.171660380367, 0.353339688497), (-0.247716253122, -0.444685305618, 0.860750624111), (0.304881746902, -0.879083439032, -0.366414284146)-25.1873547534, 87.1397901653, 104.251443414

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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: 3264.669 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.: 228 / 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: 3.72 Å3/Da / Density % sol: 66.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis Tris 5.5, 0.3 M magnesium formate, 30% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.29→78.49 Å / Num. obs: 32666 / % possible obs: 67.2 % / Redundancy: 20 % / Biso Wilson estimate: 35.01 Å2 / Rpim(I) all: 0.074 / Net I/σ(I): 10.6
Reflection shellResolution: 2.29→2.52 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1635 / Rpim(I) all: 0.499

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487model building
PHENIX1.20.1_4487refinement
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R2I

6r2i


Resolution: 2.29→48.46 Å / SU ML: 0.2519 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.3037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1732 5.3 %
Rwork0.1847 30920 -
obs0.1865 32652 67.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.62 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 4 228 5176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365100
X-RAY DIFFRACTIONf_angle_d0.73056933
X-RAY DIFFRACTIONf_chiral_restr0.0478740
X-RAY DIFFRACTIONf_plane_restr0.0051901
X-RAY DIFFRACTIONf_dihedral_angle_d11.65441858
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.80069211602
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS3.58736597378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.3343150.2708224X-RAY DIFFRACTION5.92
2.36-2.440.3021280.23534X-RAY DIFFRACTION14.04
2.44-2.520.3027500.2516798X-RAY DIFFRACTION20.93
2.52-2.630.2872930.2681250X-RAY DIFFRACTION33.33
2.63-2.740.29511010.25032020X-RAY DIFFRACTION52.66
2.75-2.890.30531700.2492995X-RAY DIFFRACTION78.38
2.89-3.070.26342360.22853782X-RAY DIFFRACTION99.48
3.07-3.310.23982200.20023822X-RAY DIFFRACTION100
3.31-3.640.19661850.17943874X-RAY DIFFRACTION100
3.64-4.170.2032130.15983842X-RAY DIFFRACTION100
4.17-5.250.1812010.1453865X-RAY DIFFRACTION100
5.25-48.460.19092200.17893914X-RAY DIFFRACTION99.76
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)
10.877670269360.545726917597-0.4037977910832.77648217494-0.1697266482143.00383143788-0.112688768485-0.1883057182050.0658621598677-0.1026362474070.0811616237449-0.22358723766-0.1577728238710.2218549238340.04051396957630.2160509766970.0638370686902-0.07221407920260.387207481484-0.01673846919690.24291106229735.403910324665.447246365440.1014040883
21.73376916940.3425088379690.6788745231242.38738560728-0.339705353922.33603137851-0.07402437873740.05496620696660.267276570083-0.09918540777620.05642404279640.134238832838-0.336634008322-0.0799124868901-0.02059743189240.2222349127860.0812766041223-0.02147132766080.319481274219-0.01053614984320.2046406184424.923592246667.047102413346.1670538388
34.453737155661.374631613681.501249661964.311986034170.09673457219615.177864324370.0680416636354-0.1844036678-0.5337917990340.02348291960520.0400924845931-0.2735994611370.485355497369-0.0749980722893-0.09416207137360.2133662306150.137207308434-0.0207060418350.3568298960650.01012019229050.27315729381431.778458404650.861142107248.8499479704
41.045485933311.331751166680.7396268130432.888798617920.6237975148935.65416549010.29746686481-0.1218626005990.126419374518-0.07791547928290.0334764604284-0.0482586999424-0.391586461897-0.0662430325355-0.06618813872750.1159095753430.0674912005196-0.06753251355180.335584479870.02969336458860.23263508356529.01102602861.699759357250.5270552106
50.3795492090920.00180762919263-0.4626608639881.58200232138-0.08115269671671.6610166889-0.01755197860670.06202155461030.0866239210268-0.09912594652180.0743701607737-0.213049329164-0.05393475839410.122854701969-0.0752467276240.2016628411320.07974732197560.02624833841180.324172002975-0.02171562400550.26028464425632.412745062271.919390037123.8470961231
63.359139963480.193250811263-0.588228498026.5150947719-0.1655238694384.41499475306-0.01767429531260.2957666435590.365018040564-0.653577671674-0.00891850291797-0.219868714406-0.3220762455070.2430097847940.09728581980140.2721570565060.01480831685670.06631028497150.391343333295-0.006875080459950.26802361198437.684139076774.655264228211.6764530861
72.857304142360.178774822501-0.3227342518291.98853043078-0.6606788015222.11448895494-0.0344989016396-0.378900039544-0.06321891600790.2798719908630.061719185913-0.345946679586-0.1314486581060.57897014792-0.01592823469970.24806665687-0.00224607685763-0.09477386996210.345313428179-0.06184124096030.3005005673138.024790600280.462393172446.8022425962
87.44228480256-0.4691268798616.826953765876.33566050922-4.663652860319.07329737778-0.546408972120.0362028422310.0818035864175-0.377766254076-0.186607213817-0.488701523971-1.18272948929-0.8164745382350.8904156465640.3708881745130.02303324522340.1052480393450.455856670587-0.009651436568290.41238981770917.134109595395.545907234228.8506000808
93.20136929213-1.380028582570.07032133346072.30703570802-1.725856686681.6005292894-0.1232776599390.246364630106-0.362028327918-0.4151583855370.05899486770590.1328106112730.079926223218-0.241057003167-0.0702238659560.4274897834310.079122054132-0.02310481853250.331743181667-0.1036734142550.30550732346413.374095521488.514326025529.1232166652
101.897383902210.0960025142824-1.081330270391.46280063808-0.01652345780263.52478341803-0.02064912815080.001673716625140.299396609876-0.08460181312160.0195850651575-0.152928820604-0.2550044199540.236965929109-0.03309245288740.3077603021170.0272103877306-0.03521171322310.197587593825-0.04800414025110.3525324568128.75801800591.324782984941.4504669617
114.26985917275-0.704405790397-1.256536971044.072803786060.2746983748724.038223922780.0941903845122-0.2402727086690.5365682014260.2058639576760.0140401226843-0.360205006383-0.5563760585370.199177073962-0.2323093746920.406129377505-0.00969965063575-0.05537409540780.227092966135-0.06478049955350.41838289143431.542412078898.515075602744.1620118009
127.693666694562.38261274784-2.861637938224.976325555480.08096381502971.302992181570.253421248621-1.637095247990.2772536613691.03891110137-0.260927050192-0.120926552331-0.7927292428230.1456393030990.1943789327120.6988926195450.0162884211656-0.05341482887740.519696739698-0.1716594801060.48947695055227.888986132397.652988741856.521419437
132.68750072589-0.306069273336-1.104702046562.609043592160.4400784838534.76616556875-0.229235119632-0.1363547719010.3669903097680.06949217109590.0672712268403-0.36447366756-0.5816279798120.05763674938330.1613202151990.2441883231980.00609307485698-0.06066168260080.211775459646-0.06807870496390.35931310657930.267943709895.143443306740.1505811882
145.989320781791.32939470661-4.561168611228.23863572166-2.924707921948.115444579780.1039757143850.7758683864410.746822883987-0.3331879198160.201469765943-0.187073148478-1.626362902430.408218233129-0.3606622489580.794100469929-0.0270469593578-0.1579982940760.5798075426270.05255337768660.73662487862314.211030456273.16059342727.9531998334
154.74516201459-3.99554515164-6.546962054416.518346370114.689674288339.73364025-0.310313382007-0.258795635656-0.5339833604060.157780658498-0.8544957915870.8107765244520.448542008442-0.8039804894440.6837909063970.2852665626380.0411908363083-0.07887134822720.431692545792-0.05648396712470.30135478963521.61303080457.993262061630.8328274685
166.863616106026.234394759080.3773263087085.639165799720.4437400404650.445576108145-0.7253619254392.01443991313-1.00302330096-0.8536147198070.4567688352790.5408577201890.266714409071-0.5422026913870.03189341302071.05723992576-0.0155979545981-0.04718958402671.26457879873-0.2834985699271.0242074660417.019996388187.031296476220.2410664853
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 665 )AA618 - 6651 - 48
22chain 'A' and (resid 666 through 738 )AA666 - 73849 - 121
33chain 'A' and (resid 739 through 789 )AA739 - 789122 - 172
44chain 'A' and (resid 790 through 811 )AA790 - 811173 - 194
55chain 'B' and (resid 618 through 738 )BB618 - 7381 - 121
66chain 'B' and (resid 739 through 811 )BB739 - 811122 - 194
77chain 'C' and (resid 618 through 656 )CC618 - 6561 - 39
88chain 'C' and (resid 657 through 667 )CC657 - 66740 - 50
99chain 'C' and (resid 668 through 686 )CC668 - 68651 - 69
1010chain 'C' and (resid 687 through 727 )CC687 - 72770 - 110
1111chain 'C' and (resid 728 through 772 )CC728 - 772111 - 155
1212chain 'C' and (resid 773 through 789 )CC773 - 789156 - 172
1313chain 'C' and (resid 790 through 811 )CC790 - 811173 - 194
1414chain 'D' and (resid 529 through 544 )DD529 - 5441 - 16
1515chain 'D' and (resid 545 through 555 )DD545 - 55517 - 27
1616chain 'E' and (resid 543 through 555 )EE543 - 5551 - 13

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