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- PDB-8e20: Cryo-EM structure of the full-length human NF1 dimer -

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Basic information

Entry
Database: PDB / ID: 8.0E+20
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 / negative regulation of Schwann cell migration / Schwann cell migration / amygdala development / vascular associated smooth muscle cell migration / Schwann cell proliferation / negative regulation of mast cell proliferation ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / Schwann cell migration / amygdala development / vascular associated smooth muscle cell migration / Schwann cell proliferation / negative regulation of mast cell proliferation / mast cell apoptotic process / gamma-aminobutyric acid secretion, neurotransmission / vascular associated smooth muscle cell proliferation / glutamate secretion, neurotransmission / negative regulation of Schwann cell proliferation / negative regulation of leukocyte migration / mast cell proliferation / forebrain morphogenesis / regulation of cell-matrix adhesion / hair follicle maturation / regulation of blood vessel endothelial cell migration / cell communication / camera-type eye morphogenesis / smooth muscle tissue development / negative regulation of neurotransmitter secretion / negative regulation of oligodendrocyte differentiation / sympathetic nervous system development / myeloid leukocyte migration / peripheral nervous system development / myelination in peripheral nervous system / phosphatidylcholine binding / negative regulation of Ras protein signal transduction / metanephros development / phosphatidylethanolamine binding / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of long-term synaptic potentiation / collagen fibril organization / regulation of postsynapse organization / endothelial cell proliferation / regulation of bone resorption / artery morphogenesis / neural tube development / adrenal gland development / negative regulation of neuroblast proliferation / forebrain astrocyte development / negative regulation of protein import into nucleus / regulation of synaptic transmission, GABAergic / pigmentation / spinal cord development / negative regulation of astrocyte differentiation / negative regulation of vascular associated smooth muscle cell migration / negative regulation of endothelial cell proliferation / negative regulation of osteoclast differentiation / Rac protein signal transduction / oligodendrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of GTPase activity / negative regulation of cell-matrix adhesion / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / negative regulation of fibroblast proliferation / skeletal muscle tissue development / negative regulation of stem cell proliferation / positive regulation of vascular associated smooth muscle cell proliferation / negative regulation of MAPK cascade / positive regulation of endothelial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / extracellular matrix organization / GTPase activator activity / osteoclast differentiation / negative regulation of cell migration / negative regulation of angiogenesis / stem cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / liver development / regulation of long-term neuronal synaptic plasticity / brain development / cerebral cortex development / visual learning / cognition / long-term synaptic potentiation / Regulation of RAS by GAPs / protein import into nucleus / osteoblast differentiation / positive regulation of neuron apoptotic process / presynapse / MAPK cascade / cellular response to heat / heart development / regulation of gene expression / actin cytoskeleton organization / fibroblast proliferation / neuron apoptotic process / angiogenesis / Ras protein signal transduction / response to hypoxia
Similarity search - Function
: / PH domain-like / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain 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 (rasGAP) domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins (rasGAP) domain 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: 3.6 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: Proc Natl Acad Sci U S A / Year: 2023
Title: Destabilizing NF1 variants act in a dominant negative manner through neurofibromin dimerization.
Authors: Lucy C Young / Ruby Goldstein de Salazar / Sae-Won Han / Zi Yi Stephanie Huang / Alan Merk / Matthew Drew / Joseph Darling / Vanessa Wall / Reinhard Grisshammer / Alice Cheng / Madeline R ...Authors: Lucy C Young / Ruby Goldstein de Salazar / Sae-Won Han / Zi Yi Stephanie Huang / Alan Merk / Matthew Drew / Joseph Darling / Vanessa Wall / Reinhard Grisshammer / Alice Cheng / Madeline R Allison / Matthew J Sale / Dwight V Nissley / Dominic Esposito / Jana Ognjenovic / Frank McCormick /
Abstract: The majority of pathogenic mutations in the neurofibromatosis type I () gene reduce total neurofibromin protein expression through premature truncation or microdeletion, but it is less well ...The majority of pathogenic mutations in the neurofibromatosis type I () gene reduce total neurofibromin protein expression through premature truncation or microdeletion, but it is less well understood how loss-of-function missense variants drive NF1 disease. We have found that patient variants in codons 844 to 848, which correlate with a severe phenotype, cause protein instability and exert an additional dominant-negative action whereby wild-type neurofibromin also becomes destabilized through protein dimerization. We have used our neurofibromin cryogenic electron microscopy structure to predict and validate other patient variants that act through a similar mechanism. This provides a foundation for understanding genotype-phenotype correlations and has important implications for patient counseling, disease management, and therapeutics.
History
DepositionAug 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform I of Neurofibromin
B: Isoform I of Neurofibromin


Theoretical massNumber of molelcules
Total (without water)634,8222
Polymers634,8222
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.: 2
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
Has protein modificationN

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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: 320 kDa/nm / 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
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 692875 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00429816
ELECTRON MICROSCOPYf_angle_d0.57840838
ELECTRON MICROSCOPYf_dihedral_angle_d4.9644660
ELECTRON MICROSCOPYf_chiral_restr0.0414964
ELECTRON MICROSCOPYf_plane_restr0.0045349

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