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- PDB-6r15: Crystal structure of the SUN1-KASH1 6:6 complex -

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Basic information

Entry
Database: PDB / ID: 6r15
TitleCrystal structure of the SUN1-KASH1 6:6 complex
Components
  • Nesprin-1
  • SUN domain-containing protein 1
KeywordsSTRUCTURAL PROTEIN / SUN1 KASH1 NESPRIN-1 SYNE1 LINC complex Nucleoskeleton Cytoskeleton Nuclear envelope
Function / homology
Function and homology information


negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / 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 / postsynaptic endocytic zone / negative regulation of mesenchymal cell apoptotic process / homologous chromosome pairing at meiosis ...negative regulation of mini excitatory postsynaptic potential / regulation of nucleus organization / 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 / postsynaptic endocytic zone / negative regulation of mesenchymal cell apoptotic process / homologous chromosome pairing at meiosis / lamin binding / postsynaptic actin cytoskeleton / cardiac muscle cell differentiation / muscle cell differentiation / nuclear outer membrane / nuclear inner membrane / positive regulation of mesenchymal cell proliferation / centrosome localization / regulation of dendrite morphogenesis / dendritic spine head / regulation of postsynaptic neurotransmitter receptor internalization / nucleus organization / Golgi organization / response to light stimulus / response to mechanical stimulus / protein-membrane adaptor activity / Meiotic synapsis / ossification / sarcomere / P-body / positive regulation of receptor-mediated endocytosis / actin filament binding / nuclear envelope / actin binding / midbody / spermatogenesis / nuclear membrane / postsynaptic membrane / chromosome, telomeric region / signaling receptor binding / intracellular membrane-bounded organelle / nucleolus / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / Golgi apparatus / protein homodimerization activity / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
: / : / KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / SUN coiled coil domain 2 / SUN2 helix-turn-helix domain / SUN domain-containing protein 1, N-terminal / Mitochondrial RNA binding protein MRP ...: / : / KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / 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 / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile.
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / SUN domain-containing protein 1 / Nesprin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsGurusaran, M. / Davies, O.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/Z United Kingdom
Royal SocietyRG170118 United Kingdom
CitationJournal: Elife / Year: 2021
Title: A molecular mechanism for LINC complex branching by structurally diverse SUN-KASH 6:6 assemblies.
Authors: Gurusaran, M. / Davies, O.R.
History
DepositionMar 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Nesprin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5645
Polymers26,1362
Non-polymers4283
Water4,252236
1
A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules

A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules

A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules

A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules

A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules

A: SUN domain-containing protein 1
B: Nesprin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,38430
Polymers156,81812
Non-polymers2,56518
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Unit cell
Length a, b, c (Å)80.450, 80.450, 182.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-1127-

HOH

21A-1198-

HOH

31A-1220-

HOH

41A-1227-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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.: 1
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 Nesprin-1 / Enaptin / KASH domain-containing protein 1 / KASH1 / Myocyte nuclear envelope protein 1 / Myne-1 / ...Enaptin / KASH domain-containing protein 1 / KASH1 / Myocyte nuclear envelope protein 1 / Myne-1 / Nuclear envelope spectrin repeat protein 1 / Synaptic nuclear envelope protein 1 / Syne-1


Mass: 3606.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE1, C6orf98, KIAA0796, KIAA1262, KIAA1756, MYNE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NF91

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Non-polymers , 4 types, 239 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.26 Å3/Da / Density % sol: 62.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.09M NaF; 0.09M NaBr; 0.09M NaI; 0.1M Sodium HEPES pH 7.5; 0.1M MOPS (acid) pH 7.5; 18% PEGMME 550; 18% PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.82→65.09 Å / Num. obs: 32282 / % possible obs: 100 % / Redundancy: 20.6 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.019 / Rrim(I) all: 0.085 / Net I/σ(I): 21.5
Reflection shellResolution: 1.82→1.85 Å / Rmerge(I) obs: 2.141 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2344 / Rpim(I) all: 0.465 / Rrim(I) all: 2.192

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
xia2data reduction
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DXR

4dxr


Resolution: 1.82→65.09 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0.18 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1817 2976 5.02 %
Rwork0.1587 --
obs0.1598 32230 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 1.82→65.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 26 236 2059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131926
X-RAY DIFFRACTIONf_angle_d0.9952620
X-RAY DIFFRACTIONf_dihedral_angle_d15.643726
X-RAY DIFFRACTIONf_chiral_restr0.068272
X-RAY DIFFRACTIONf_plane_restr0.007343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8201-1.84990.3451340.30552684X-RAY DIFFRACTION100
1.8499-1.88180.26921540.28812726X-RAY DIFFRACTION100
1.8818-1.9160.29541700.27562650X-RAY DIFFRACTION100
1.916-1.95290.24221390.25412634X-RAY DIFFRACTION100
1.9529-1.99270.28241450.23512688X-RAY DIFFRACTION100
1.9927-2.03610.24241400.21052658X-RAY DIFFRACTION100
2.0361-2.08340.25781500.20342696X-RAY DIFFRACTION100
2.0834-2.13550.19811210.1852695X-RAY DIFFRACTION100
2.1355-2.19330.22521420.18542683X-RAY DIFFRACTION100
2.1933-2.25780.19891350.17252676X-RAY DIFFRACTION100
2.2578-2.33070.17591310.16312690X-RAY DIFFRACTION100
2.3307-2.4140.19651880.15832658X-RAY DIFFRACTION100
2.414-2.51070.17121590.15492658X-RAY DIFFRACTION100
2.5107-2.62490.22341450.15212671X-RAY DIFFRACTION100
2.6249-2.76330.18021410.15892707X-RAY DIFFRACTION100
2.7633-2.93650.16331220.1562680X-RAY DIFFRACTION100
2.9365-3.16320.16841470.1572685X-RAY DIFFRACTION100
3.1632-3.48150.15731010.14942722X-RAY DIFFRACTION100
3.4815-3.98520.16131370.1342687X-RAY DIFFRACTION100
3.9852-5.02070.14121440.1192684X-RAY DIFFRACTION100
5.0207-65.13370.1761310.16172701X-RAY DIFFRACTION100
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)
10.9453-0.36631.39031.138-1.28394.25360.02970.1047-0.00820.0197-0.0490.0524-0.0298-0.010.01620.26470.01620.02880.2846-0.00920.31429.700224.366282.1059
25.4869-4.8081-5.67256.51185.41696.10650.06321.69350.45470.1474-0.10390.11810.397-1.42850.18510.63390.03540.00360.83120.1030.43843.337937.762954.2833
33.2204-0.04470.03431.55630.25451.33610.02170.05290.1521-0.0481-0.10280.0868-0.1147-0.10740.0980.28120.0318-0.01240.2636-0.00050.273922.951634.912574.0994
43.90561.11590.93053.76360.36442.28150.0839-0.04310.10150.0449-0.12420.49470.0473-0.3387-0.0260.24010.03170.02110.2965-0.0390.267318.783133.559374.7753
52-2.323-6.36468.941-0.15514.32172.0625-2.4547-0.3234.6262-0.5537-2.8911.44753.1771-1.39241.670.0785-0.45932.0631-0.28931.08999.530546.121258.9434
63.8405-3.75482.29423.8136-1.93328.35610.62870.76110.2446-0.5018-0.99030.7520.1472-0.86270.30190.50710.0206-0.12030.5801-0.02750.509318.107737.00757.3898
77.53425.3994-4.29234.8747-3.95753.29360.01270.76990.4458-0.52950.40240.4333-0.8969-0.7438-0.3820.68290.0626-0.01110.55060.05180.331227.343231.341455.5288
85.8279-4.42132.88214.6242-4.98137.57970.69080.5032-1.4307-1.20470.43962.1030.8735-1.2678-1.13350.5158-0.0478-0.17650.6045-0.05650.660220.924816.78863.6841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 615:661)
2X-RAY DIFFRACTION2(chain A and resid 662:678)
3X-RAY DIFFRACTION3(chain A and resid 679:774)
4X-RAY DIFFRACTION4(chain A and resid 775:812)
5X-RAY DIFFRACTION5(chain B and resid 8769:8773)
6X-RAY DIFFRACTION6(chain B and resid 8774:8781)
7X-RAY DIFFRACTION7(chain B and resid 8782:8788)
8X-RAY DIFFRACTION8(chain B and resid 8789:8797)

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