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- EMDB-28038: Cryo-EM structure of the full-length human NF1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-28038
TitleCryo-EM structure of the full-length human NF1 dimer
Map dataCryo-EM structure of the full-length human NF1 dimer
Sample
  • Complex: Full-length human NF1
    • Protein or peptide: Neurofibromin
KeywordsGTPase activating protein / Ras signaling / Cancer / SIGNALING PROTEIN
Function / homology
Function and homology information


positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / Schwann cell migration / regulation of glial cell differentiation / myeloid leukocyte migration / observational learning / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / glutamate secretion, neurotransmission ...positive regulation of mast cell apoptotic process / negative regulation of Rac protein signal transduction / Schwann cell migration / regulation of glial cell differentiation / myeloid leukocyte migration / observational learning / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / glutamate secretion, neurotransmission / mast cell apoptotic process / vascular associated smooth muscle cell proliferation / negative regulation of mast cell proliferation / regulation of cell-matrix adhesion / Schwann cell proliferation / gamma-aminobutyric acid secretion, neurotransmission / negative regulation of leukocyte migration / negative regulation of Schwann cell proliferation / mast cell proliferation / negative regulation of oligodendrocyte differentiation / regulation of intracellular signal transduction / smooth muscle tissue development / regulation of blood vessel endothelial cell migration / forebrain morphogenesis / sympathetic nervous system development / camera-type eye morphogenesis / cell communication / peripheral nervous system development / myelination in peripheral nervous system / metanephros development / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / hair follicle maturation / negative regulation of neurotransmitter secretion / negative regulation of osteoclast differentiation / endothelial cell proliferation / phosphatidylcholine binding / negative regulation of Ras protein signal transduction / collagen fibril organization / phosphatidylethanolamine binding / pigmentation / artery morphogenesis / neural tube development / oligodendrocyte differentiation / regulation of long-term synaptic potentiation / adrenal gland development / regulation of bone resorption / regulation of postsynapse organization / negative regulation of neuroblast proliferation / negative regulation of protein import into nucleus / neuroblast proliferation / forebrain astrocyte development / negative regulation of astrocyte differentiation / negative regulation of endothelial cell proliferation / extrinsic apoptotic signaling pathway via death domain receptors / regulation of synaptic transmission, GABAergic / spinal cord development / negative regulation of vascular associated smooth muscle cell migration / negative regulation of cell-matrix adhesion / Rac protein signal transduction / skeletal muscle tissue development / regulation of angiogenesis / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of GTPase activity / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of fibroblast proliferation / negative regulation of stem cell proliferation / regulation of ERK1 and ERK2 cascade / Schwann cell development / osteoclast differentiation / positive regulation of vascular associated smooth muscle cell proliferation / stem cell proliferation / negative regulation of MAPK cascade / extracellular matrix organization / fibroblast proliferation / positive regulation of endothelial cell proliferation / negative regulation of angiogenesis / liver development / negative regulation of cell migration / wound healing / phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / brain development / regulation of long-term neuronal synaptic plasticity / visual learning / cerebral cortex development / protein import into nucleus / cognition / long-term synaptic potentiation / osteoblast differentiation / heart development / MAPK cascade / Regulation of RAS by GAPs / neuron apoptotic process / positive regulation of neuron apoptotic process / cellular response to heat / presynapse / regulation of gene expression / actin cytoskeleton organization / angiogenesis / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsDarling JE / Merk A / Grisshammer R / Ognjenovic J
Funding support United States, 1 items
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, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28038.png

Downloads & links

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Map

FileDownload / File: emd_28038.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of the full-length human NF1 dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0321
Minimum - Maximum-0.07154444 - 0.14860432
Average (Standard dev.)0.00019031555 (±0.0035628416)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28038_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the full-length human NF1 dimer

Fileemd_28038_half_map_1.map
AnnotationCryo-EM structure of the full-length human NF1 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of the full-length human NF1 dimer

Fileemd_28038_half_map_2.map
AnnotationCryo-EM structure of the full-length human NF1 dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Full-length human NF1

EntireName: Full-length human NF1
Components
  • Complex: Full-length human NF1
    • Protein or peptide: Neurofibromin

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Supramolecule #1: Full-length human NF1

SupramoleculeName: Full-length human NF1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 kDa/nm

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Macromolecule #1: Neurofibromin

MacromoleculeName: Neurofibromin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 142.489891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NKMVEYLTDW VMGTSNQAAD DDVKCLTRDL DQASMEAVVS LLAGLPLQPE EGDGVELMEA KSQLFLKYFT LFMNLLNDCS EVEDESAQT GGRKRGMSRR LASLRHCTVL AMSNLLNANV DSGLMHSIGL GYHKDLQTRA TFMEVLTKIL QQGTEFDTLA E TVLADRFE ...String:
NKMVEYLTDW VMGTSNQAAD DDVKCLTRDL DQASMEAVVS LLAGLPLQPE EGDGVELMEA KSQLFLKYFT LFMNLLNDCS EVEDESAQT GGRKRGMSRR LASLRHCTVL AMSNLLNANV DSGLMHSIGL GYHKDLQTRA TFMEVLTKIL QQGTEFDTLA E TVLADRFE RLVELVTMMG DQGELPIAMA LANVVPCSQW DELARVLVTL FDSRHLLYQL LWNMFSKEVE LADSMQTLFR GN SLASKIM TFCFKVYGAT YLQKLLDPLL RIVITSSDWQ HVSFEVDPTR LEPSESLEEN QRNLLQMTEK FFHAIISSSS EFP PQLRSV CHCLYQATCH SLLNKATVKE KKENKKSVVS QRFPQNSIGA VGSAMFLRFI NPAIVSPYEA GILDKKPPPR IERG LKLMS KILQSIANHV LFTKEEHMRP FNDFVKSNFD AARRFFLDIA SDCPTSDAVN HSLSFISDGN VLALHRLLWN NQEKI GQYL SSNRDHKAVG RRPFDKMATL LAYLGPPEHK PVADTHWSSL NLTSSKFEEF MTRHQVHEKE EFKALKTLSI FYQAGT SKA GNPIFYYVAR RFKTGQINGD LLIYHVLLTL KPYYAKPYEI VVDLTHTGPS NRFKTDFLSK WFVVFPGFAY DNVSAVY IY NCNSWVREYT KYHERLLTGL KGSKRLVFID CPGKLAEHIE HEQQKLPAAT LALEEDLKVF HNALKLAHKD TKVSIKVG S TAVQVTSAER TKVLGQSVFL NDIYYASEIE EICLVDENQF TLTIANQGTP LTFMHQECEA IVQSIIHIRT RWELSQPDS IPQHTKIRPK DVPGTLLNIA LLNLGSSDPS LRSAAYNLLC ALTCTFNLKI EGQLLETSGL CIPANNTLFI VSISKTLAAN EPHLTLEFL EECISGFSKS SIELKHLCLE YMTPWLSNLV RFCKHNDDAK RQRVTAILDK LITMTINEKQ MYPSIQAKIW G SLGQITDL LDVVLDSFIK TSATGGLGSI KAEVMADTAV ALASGNVKLV SSKVIGRMCK IIDKTCLSPT PTLEQHLMWD DI AILARYM LMLSFNNSLD VAAHLPYLFH VVTFLVATGP LSLRASTHGL VINIIHSLCT CSQLHFSEET KQVLRLSLTE FSL PKFYLL FGISKVKSAA VIAFRSSYRD RSFSPGSYER ETFALTSLET VTEALLEIME ACMRDIPTCK WLDQWTELAQ RFAF QYNPS LQPRALVVFG CISKRVSHGQ IKQIIRILSK ALESCLKGPD TYNSQVLIEA TVIALTKLQ

UniProtKB: Neurofibromin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 9.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 161208
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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