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- PDB-6xf2: Nesprin-1G (aa2070-2200)-FHOD1(aa1-339) complex, H. sapiens -

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Basic information

Entry
Database: PDB / ID: 6xf2
TitleNesprin-1G (aa2070-2200)-FHOD1(aa1-339) complex, H. sapiens
Components
  • FH1/FH2 domain-containing protein 1
  • Nesprin-1
KeywordsSTRUCTURAL PROTEIN / spectrin repeat / FH3 domain / armadillo repeat / scaffold protein / nuclear positioning / transmembrane / actin-associated / nuclear line
Function / homology
Function and homology information


nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / establishment of centrosome localization / bleb / lamin binding / regulation of stress fiber assembly / muscle cell differentiation / cortical actin cytoskeleton organization / nuclear migration ...nuclear matrix anchoring at nuclear membrane / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / establishment of centrosome localization / bleb / lamin binding / regulation of stress fiber assembly / muscle cell differentiation / cortical actin cytoskeleton organization / nuclear migration / nucleus organization / Golgi organization / nuclear outer membrane / intercalated disc / positive regulation of stress fiber assembly / Meiotic synapsis / sarcomere / P-body / actin filament binding / nuclear envelope / actin binding / spermatogenesis / nuclear membrane / postsynaptic membrane / cytoskeleton / nucleolus / enzyme binding / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
FHOD1, N-terminal GTPase-binding domain / : / : / Formin N-terminal GBD / : / FHOD1/3 FH3 domain / : / : / Nesprin-1, spectrin repeats / Nesprin-1 domain ...FHOD1, N-terminal GTPase-binding domain / : / : / Formin N-terminal GBD / : / FHOD1/3 FH3 domain / : / : / Nesprin-1, spectrin repeats / Nesprin-1 domain / KASH domain / Nuclear envelope localisation domain / KASH domain profile. / Nuclear envelope localisation domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Nesprin-1 / FH1/FH2 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 7.11 Å
AuthorsLim, S.M. / Schwartz, T.U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-AR065484 United States
CitationJournal: Structure / Year: 2021
Title: Structures of FHOD1-Nesprin1/2 complexes reveal alternate binding modes for the FH3 domain of formins.
Authors: Lim, S.M. / Cruz, V.E. / Antoku, S. / Gundersen, G.G. / Schwartz, T.U.
History
DepositionJun 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nesprin-1
B: FH1/FH2 domain-containing protein 1
C: Nesprin-1
D: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)101,4984
Polymers101,4984
Non-polymers00
Water00
1
A: Nesprin-1
B: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,7492
Polymers50,7492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nesprin-1
D: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)50,7492
Polymers50,7492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)209.367, 142.051, 58.047
Angle α, β, γ (deg.)90.000, 106.311, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 2070 through 2107 and (name N...
d_2ens_1(chain "C" and ((resid 2070 through 2082 and (name N...
d_1ens_2chain "B"
d_2ens_2chain "D"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRSERA1 - 38
d_12ens_1GLUSERA45 - 115
d_21ens_1THRSERC1 - 109
d_11ens_2SERLEUB1 - 321
d_21ens_2SERLEUD1 - 321

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.335859701739, 0.00149563432109, 0.941910836452), (0.0262725208394, -0.999624536509, -0.00778078769711), (0.941545546108, 0.0273596251148, -0.335772892767)-80.9551075548, -17.2678258491, 115.054471815
2given(0.311262054772, -0.0489289662367, 0.949063690972), (0.0130207751797, -0.998360364503, -0.0557408468022), (0.950234914467, 0.0297075554617, -0.310114605389)-81.5543634327, -17.4473440714, 114.31970569

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Components

#1: Protein 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: 15259.411 Da / Num. of mol.: 2
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
#2: Protein FH1/FH2 domain-containing protein 1 / Formin homolog overexpressed in spleen 1 / FHOS / Formin homology 2 domain-containing protein 1


Mass: 35489.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FHOD1, FHOS, FHOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y613

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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: 3.75 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES/NaOH pH 7.0, 0.2 M sodium thiocyanate, 40% 5/4 pentaerythritol propoxylate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 7.1→60.58 Å / Num. obs: 2378 / % possible obs: 98.2 % / Redundancy: 6 % / Biso Wilson estimate: 464.08 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.063 / Net I/σ(I): 15.6
Reflection shellResolution: 7.1→7.35 Å / Num. unique obs: 232 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Cootmodel building
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6XF1

6xf1


Resolution: 7.11→60.58 Å / SU ML: 1.2952 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.3238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3972 244 10.26 %
Rwork0.3396 2134 -
obs0.3457 2378 94.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 320.7 Å2
Refinement stepCycle: LAST / Resolution: 7.11→60.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6075 0 0 0 6075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00856159
X-RAY DIFFRACTIONf_angle_d1.67628427
X-RAY DIFFRACTIONf_chiral_restr0.07621048
X-RAY DIFFRACTIONf_plane_restr0.01041106
X-RAY DIFFRACTIONf_dihedral_angle_d13.1363915
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.31131715855
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.344154697576
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
7.11-8.950.461160.34121018X-RAY DIFFRACTION91.08
8.95-60.580.37991280.3391116X-RAY DIFFRACTION98

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