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- PDB-6xf1: Nesprin-2G(aa1425-1649)-FHOD1(aa1-339) complex, H. sapiens -

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Basic information

Entry
Database: PDB / ID: 6xf1
TitleNesprin-2G(aa1425-1649)-FHOD1(aa1-339) complex, H. sapiens
Components
  • FH1/FH2 domain-containing protein 1
  • Nesprin-2
KeywordsSTRUCTURAL PROTEIN / spectrin repeat / FH3 domain / armadillo repeat / scaffold protein / nuclear positioning / transmembrane / actin-associated nuclear line
Function / homology
Function and homology information


nuclear migration along microfilament / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / regulation of cilium assembly / establishment of centrosome localization / bleb / intermediate filament cytoskeleton / regulation of stress fiber assembly / filopodium membrane ...nuclear migration along microfilament / nucleokinesis involved in cell motility in cerebral cortex radial glia guided migration / cytoskeleton-nuclear membrane anchor activity / meiotic nuclear membrane microtubule tethering complex / regulation of cilium assembly / establishment of centrosome localization / bleb / intermediate filament cytoskeleton / regulation of stress fiber assembly / filopodium membrane / nuclear lumen / cortical actin cytoskeleton organization / centrosome localization / nuclear migration / nuclear outer membrane / lamellipodium membrane / intercalated disc / positive regulation of stress fiber assembly / sarcoplasmic reticulum membrane / Meiotic synapsis / sarcoplasmic reticulum / Z disc / fibrillar center / actin filament binding / nuclear envelope / actin binding / nuclear membrane / cytoskeleton / cilium / positive regulation of cell migration / focal adhesion / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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-2 / FH1/FH2 domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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-2
B: FH1/FH2 domain-containing protein 1
C: Nesprin-2
D: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)125,0494
Polymers125,0494
Non-polymers00
Water43224
1
A: Nesprin-2
B: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)62,5242
Polymers62,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nesprin-2
D: FH1/FH2 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)62,5242
Polymers62,5242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.825, 52.443, 177.458
Angle α, β, γ (deg.)90.000, 123.268, 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 1424 through 1440 or (resid 1441...
d_2ens_1(chain "C" and (resid 1424 through 1555 or resid 1557 through 1649))
d_1ens_2(chain "B" and (resid 18 through 265 or (resid 266...
d_2ens_2(chain "D" and (resid 18 or (resid 19 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ASPPHEA5 - 78
d_12ens_1GLYGLUA81 - 136
d_13ens_1VALASPA138 - 230
d_21ens_1ASPGLUC1 - 130
d_22ens_1VALASPC134 - 226
d_11ens_2VALLEUB1 - 307
d_21ens_2VALASPD5 - 33
d_22ens_2LEUMETD36 - 81
d_23ens_2PHELYSD85 - 91
d_24ens_2LEULEUD97 - 321

NCS ensembles :
ID
ens_1
ens_2

NCS oper: (Code: givenMatrix: (0.439755513536, 0.0486806679109, -0.896797235102), (0.0720090054529, -0.99722637603, -0.018821744995), (-0.895226111912, -0.0563005108566, -0.442041243584)Vector: 136. ...NCS oper: (Code: given
Matrix: (0.439755513536, 0.0486806679109, -0.896797235102), (0.0720090054529, -0.99722637603, -0.018821744995), (-0.895226111912, -0.0563005108566, -0.442041243584)
Vector: 136.817337932, -36.176390987, 252.552566443)

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Components

#1: Protein Nesprin-2 / KASH domain-containing protein 2 / KASH2 / Nuclear envelope spectrin repeat protein 2 / Nucleus and ...KASH domain-containing protein 2 / KASH2 / Nuclear envelope spectrin repeat protein 2 / Nucleus and actin connecting element protein / Protein NUANCE / Synaptic nuclear envelope protein 2 / Syne-2


Mass: 27034.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYNE2, KIAA1011, NUA / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8WXH0
#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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.72 Å3/Da / Density % sol: 66.98 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris/HCl pH 8.5, 0.2 M potassium sodium tartrate, 21% PEG 3350

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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: Dec 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→67.3 Å / Num. obs: 50981 / % possible obs: 98.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 77.92 Å2 / CC1/2: 0.99 / Rpim(I) all: 0.071 / Net I/σ(I): 21.6
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 4500 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Blu-Icedata collection
HKL-2000data processing
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DAD

3dad


Resolution: 2.8→67.27 Å / SU ML: 0.4048 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6156
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2616 1774 3.92 %
Rwork0.2176 43512 -
obs0.2193 45286 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 98.88 Å2
Refinement stepCycle: LAST / Resolution: 2.8→67.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8553 0 0 24 8577
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01278697
X-RAY DIFFRACTIONf_angle_d1.950611797
X-RAY DIFFRACTIONf_chiral_restr0.0931383
X-RAY DIFFRACTIONf_plane_restr0.01251522
X-RAY DIFFRACTIONf_dihedral_angle_d15.38561155
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.94093006452
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.62555184035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.32421300.31153265X-RAY DIFFRACTION97.75
2.88-2.960.36941370.28883333X-RAY DIFFRACTION98.8
2.96-3.060.35621360.29053361X-RAY DIFFRACTION99.57
3.06-3.170.35231340.27793307X-RAY DIFFRACTION99.22
3.17-3.290.32221390.27433374X-RAY DIFFRACTION99.43
3.29-3.440.34861330.27843263X-RAY DIFFRACTION97.84
3.44-3.620.3411360.24763320X-RAY DIFFRACTION98.38
3.62-3.850.24491370.23813364X-RAY DIFFRACTION99.21
3.85-4.150.26451360.21713322X-RAY DIFFRACTION99.03
4.15-4.560.26741360.19593318X-RAY DIFFRACTION97.02
4.56-5.220.22251390.17883403X-RAY DIFFRACTION99.44
5.22-6.580.26411400.24523428X-RAY DIFFRACTION99.33
6.58-67.270.19261410.16913454X-RAY DIFFRACTION97.21
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)
19.27150010223-5.870566581514.006902908456.21576041786-2.598541865124.178781787570.132204015951-0.10741260841-0.0845074384442-0.2052067048180.01283732392050.755166603495-0.155317062082-0.647955274798-0.0855380906240.4259058694970.02316527100560.02497168414410.440281105958-0.01729336228540.582500444649181.954620902-25.862297274460.335849954
29.7366791439-3.541199534761.444836114950.485492721099-0.84337956170.2683803353250.149499027017-0.04766556272410.500090602177-0.0929971173912-0.114855851956-0.125070550254-0.0384108462204-0.0580160391691-0.02358348293630.5028054348730.0380372924108-0.06190280083580.471089954906-0.02908889940040.822786560381229.606885197-44.871419653367.6904885886
35.97596885880.1596528640073.600984419723.74003672949-2.075383980376.86503429525-0.5892500271880.3099586704361.266906554720.005624718498770.2135253315020.650808362575-0.66429133618-1.610344133760.2013314374670.7804005218180.18462672129-0.2336772571921.387705745450.1197021715421.24313975059214.176546953-22.691714632843.3519973221
47.08696174837-2.12851942456-0.8713192790533.45639521088-0.1321924208465.536210376560.2557195285990.7987865483680.921714979925-0.431232770342-0.329629120261-0.0941690428971-0.3601727188020.1955842919260.0632746576660.445508454462-0.019729896875-0.03729783515240.4243672701250.1126536801240.66424793261242.907249656-31.099216514152.6873955891
57.08323838486-0.3052740570281.855264118055.795251423472.252884957086.256776267390.3147730582221.18965596666-0.242133590549-0.154228376358-0.401372670162-0.5082183350720.942459524141.186676670420.08506952874650.6431208607280.3063656656520.09520859964761.076703860250.04936694708140.904622036921262.620975309-45.742491802147.1914393111
64.67968087665-0.20708027778-2.116621861034.25192978729-1.266280246954.42653884898-0.170544305261-0.0438174164708-0.1506490543120.350662984415-0.240904182171-0.05908240105630.689141760453-0.3272800292190.3046930774960.813169255071-0.03273942403760.00477782988530.603044960139-0.07936639057520.612488291084161.9580688712.0525120903163.0646232004
71.404642842451.0575152413-2.328075744671.25960060932-3.273604254555.54932910858-0.2165506961840.0695663385879-0.115529588550.1334790253-0.0180497429161-0.192331582977-0.448877248677-0.1912873869970.1495572021691.107265334080.0130474002071-0.04478326260810.6224082603010.01318038996070.52475515416174.75754621323.791171006619.5906141346
84.26253671115-0.1079134222140.8279685702495.855568296481.246479948968.500682773890.0319772988515-0.000202626652684-0.332342368395-0.2216870254560.362449680468-0.3036927185581.35843144267-0.0901189565249-0.4252260052930.820349469416-0.0318990121963-0.06633420315840.369023288555-0.01891672150970.539139474587188.2041503521.1872258834946.2548427279
96.495482195671.10132342737-0.3289270652754.8151891955-2.952266195586.72560866537-0.1821353787990.30143912326-0.1158262092920.0320276293764-0.387169732465-0.6174043049970.2679219631121.129182638480.5823261310210.7242584223110.114264876366-0.04244174549280.584983721585-0.04408608728820.495952623681194.08751254410.017874480815.4774070664
102.094879942921.908573699130.2710457483124.47223074403-1.646747017994.61410009094-0.6131271192431.486451001531.3054162269-0.534487320422-0.340831182512-0.627516115344-1.183048886492.118599710440.6508371034711.16111816133-0.221420041935-0.0250358874571.66736529050.406746895331.15671536126209.09396440124.91363075471.56625470589
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1420 through 1522 )AA1420 - 15221 - 103
22chain 'A' and (resid 1523 through 1649 )AA1523 - 1649104 - 230
33chain 'B' and (resid 18 through 115 )BB18 - 1151 - 88
44chain 'B' and (resid 116 through 251 )BB116 - 25189 - 224
55chain 'B' and (resid 252 through 334 )BB252 - 334225 - 307
66chain 'C' and (resid 1424 through 1522 )CC1424 - 15221 - 97
77chain 'C' and (resid 1523 through 1649 )CC1523 - 164998 - 226
88chain 'D' and (resid 14 through 115 )DD14 - 1151 - 102
99chain 'D' and (resid 116 through 251 )DD116 - 251103 - 238
1010chain 'D' and (resid 252 through 334 )DD252 - 334239 - 321

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