[English] 日本語
Yorodumi
- PDB-6xf1: Nesprin-2G(aa1425-1649)-FHOD1(aa1-339) complex, H. sapiens -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of stress fiber assembly / nuclear lumen / nuclear outer 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 / regulation of stress fiber assembly / nuclear lumen / nuclear outer membrane / filopodium membrane / nuclear migration / intermediate filament cytoskeleton / centrosome localization / cortical actin cytoskeleton organization / lamellipodium membrane / intercalated disc / positive regulation of stress fiber assembly / sarcoplasmic reticulum membrane / Meiotic synapsis / sarcoplasmic reticulum / Z disc / : / actin filament binding / nuclear envelope / actin binding / nuclear membrane / cytoskeleton / positive regulation of cell migration / protein domain specific binding / focal adhesion / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
FHOD1, N-terminal GTPase-binding domain / Formin N-terminal GTPase-binding domain / Nuclear anchorage protein 1-like / 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 ...FHOD1, N-terminal GTPase-binding domain / Formin N-terminal GTPase-binding domain / Nuclear anchorage protein 1-like / 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 / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)

-
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 / Water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more