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- PDB-8edl: Cryo-EM structure of the full-length human NF1 dimer -

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Basic information

Entry
Database: PDB / ID: 8edl
TitleCryo-EM structure of the full-length human NF1 dimer
ComponentsIsoform I of Neurofibromin
KeywordsSIGNALING PROTEIN / GTPase activating protein / Ras signaling / Cancer
Function / homology
Function and homology information


positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / negative regulation of mast cell proliferation / gamma-aminobutyric acid secretion, neurotransmission ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / Schwann cell migration / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / negative regulation of mast cell proliferation / gamma-aminobutyric acid secretion, neurotransmission / mast cell apoptotic process / Schwann cell proliferation / vascular associated smooth muscle cell proliferation / mast cell proliferation / glutamate secretion, neurotransmission / negative regulation of Schwann cell proliferation / negative regulation of leukocyte migration / negative regulation of neurotransmitter secretion / negative regulation of vascular associated smooth muscle cell migration / positive regulation of adenylate cyclase activity / forebrain morphogenesis / hair follicle maturation / regulation of cell-matrix adhesion / regulation of blood vessel endothelial cell migration / smooth muscle tissue development / camera-type eye morphogenesis / cell communication / negative regulation of oligodendrocyte differentiation / peripheral nervous system development / sympathetic nervous system development / myeloid leukocyte migration / myelination in peripheral nervous system / phosphatidylcholine binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / metanephros development / negative regulation of Ras protein signal transduction / phosphatidylethanolamine binding / regulation of bone resorption / collagen fibril organization / regulation of long-term synaptic potentiation / neural tube development / endothelial cell proliferation / forebrain astrocyte development / artery morphogenesis / pigmentation / regulation of postsynapse organization / negative regulation of neuroblast proliferation / negative regulation of protein import into nucleus / adrenal gland development / regulation of synaptic transmission, GABAergic / negative regulation of cell-matrix adhesion / regulation of GTPase activity / spinal cord development / Rac protein signal transduction / negative regulation of osteoclast differentiation / negative regulation of endothelial cell proliferation / oligodendrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / negative regulation of astrocyte differentiation / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / negative regulation of MAPK cascade / regulation of angiogenesis / Schwann cell development / negative regulation of stem cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of fibroblast proliferation / negative regulation of MAP kinase activity / positive regulation of vascular associated smooth muscle cell proliferation / skeletal muscle tissue development / positive regulation of endothelial cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of ERK1 and ERK2 cascade / GTPase activator activity / extracellular matrix organization / negative regulation of angiogenesis / osteoclast differentiation / liver development / positive regulation of GTPase activity / negative regulation of cell migration / stem cell proliferation / long-term synaptic potentiation / negative regulation of protein kinase activity / wound healing / regulation of long-term neuronal synaptic plasticity / brain development / visual learning / cerebral cortex development / cognition / osteoblast differentiation / Regulation of RAS by GAPs / protein import into nucleus / positive regulation of neuron apoptotic process / MAPK cascade / heart development / presynapse / cellular response to heat / actin cytoskeleton organization / fibroblast proliferation / regulation of gene expression
Similarity search - Function
: / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain ...: / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Divergent CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Rho GTPase activation protein / PH-like domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsDarling, J.E. / Merk, A. / Grisshammer, R. / Ognjenovic, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of the full-length human NF1 dimer
Authors: Ognjenovic, J. / Merk, A.
History
DepositionSep 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform I of Neurofibromin


Theoretical massNumber of molelcules
Total (without water)317,4111
Polymers317,4111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform I of Neurofibromin / Neurofibromatosis-related protein NF-1


Mass: 317410.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NF1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P21359

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full-length human NF1 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.320 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 200
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 9.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 161208 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00229847
ELECTRON MICROSCOPYf_angle_d0.48940883
ELECTRON MICROSCOPYf_dihedral_angle_d3.9714663
ELECTRON MICROSCOPYf_chiral_restr0.0384970
ELECTRON MICROSCOPYf_plane_restr0.0035354

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