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- EMDB-28037: Cryo-EM structure of the full-length human NF1 dimer -

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Basic information

Entry
Database: EMDB / ID: EMD-28037
TitleCryo-EM structure of the full-length human NF1 dimer
Map databody4
Sample
  • Complex: Full-length human NF1_body4
    • Protein or peptide: Isoform I of 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 / regulation of glial cell differentiation / observational learning / negative regulation of Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / Schwann cell proliferation / Schwann cell migration / 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 / vascular associated smooth muscle cell migration / amygdala development / Schwann cell proliferation / Schwann cell migration / negative regulation of mast cell proliferation / mast cell apoptotic process / gamma-aminobutyric acid secretion, neurotransmission / 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 / 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 oligodendrocyte differentiation / myeloid leukocyte migration / sympathetic nervous system development / peripheral nervous system development / myelination in peripheral nervous system / phosphatidylcholine binding / metanephros development / negative regulation of Ras protein signal transduction / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / phosphatidylethanolamine binding / collagen fibril organization / endothelial cell proliferation / regulation of long-term synaptic potentiation / regulation of bone resorption / regulation of postsynapse organization / neural tube development / artery morphogenesis / forebrain astrocyte development / negative regulation of neuroblast proliferation / adrenal gland development / negative regulation of protein import into nucleus / pigmentation / regulation of synaptic transmission, GABAergic / spinal cord development / Rac protein signal transduction / negative regulation of vascular associated smooth muscle cell migration / negative regulation of endothelial cell proliferation / negative regulation of osteoclast differentiation / oligodendrocyte differentiation / negative regulation of astrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / extrinsic apoptotic signaling pathway via death domain receptors / neuroblast proliferation / negative regulation of cell-matrix adhesion / regulation of angiogenesis / negative regulation of MAPK cascade / Schwann cell development / regulation of ERK1 and ERK2 cascade / negative regulation of stem cell proliferation / skeletal muscle tissue development / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell proliferation / extracellular matrix organization / positive regulation of GTPase activity / osteoclast differentiation / GTPase activator activity / negative regulation of angiogenesis / negative regulation of cell migration / liver development / stem cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of long-term neuronal synaptic plasticity / wound healing / brain development / visual learning / cerebral cortex development / long-term synaptic potentiation / cognition / protein import into nucleus / Regulation of RAS by GAPs / osteoblast differentiation / positive regulation of neuron apoptotic process / MAPK cascade / presynapse / cellular response to heat / heart development / actin cytoskeleton organization / regulation of gene expression / 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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28037.png

Downloads & links

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Map

FileDownload / File: emd_28037.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbody4
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: 0.0223
Minimum - Maximum-0.048807472 - 0.09270006
Average (Standard dev.)0.00013904223 (±0.0026211275)
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_28037_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_28037_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_28037_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_body4

EntireName: Full-length human NF1_body4
Components
  • Complex: Full-length human NF1_body4
    • Protein or peptide: Isoform I of Neurofibromin

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Supramolecule #1: Full-length human NF1_body4

SupramoleculeName: Full-length human NF1_body4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: Isoform I of Neurofibromin

MacromoleculeName: Isoform I of Neurofibromin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 317.410812 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAAHRPVEWV QAVVSRFDEQ LPIKTGQQNT HTKVSTEHNK ECLINISKYK FSLVISGLTT ILKNVNNMRI FGEAAEKNLY LSQLIILDT LEKCLAGQPK DTMRLDETML VKQLLPEICH FLHTCREGNQ HAAELRNSAS GVLFSLSCNN FNAVFSRIST R LQELTVCS ...String:
MAAHRPVEWV QAVVSRFDEQ LPIKTGQQNT HTKVSTEHNK ECLINISKYK FSLVISGLTT ILKNVNNMRI FGEAAEKNLY LSQLIILDT LEKCLAGQPK DTMRLDETML VKQLLPEICH FLHTCREGNQ HAAELRNSAS GVLFSLSCNN FNAVFSRIST R LQELTVCS EDNVDVHDIE LLQYINVDCA KLKRLLKETA FKFKALKKVA QLAVINSLEK AFWNWVENYP DEFTKLYQIP QT DMAECAE KLFDLVDGFA ESTKRKAAVW PLQIILLILC PEIIQDISKD VVDENNMNKK LFLDSLRKAL AGHGGSRQLT ESA AIACVK LCKASTYINW EDNSVIFLLV QSMVVDLKNL LFNPSKPFSR GSQPADVDLM IDCLVSCFRI SPHNNQHFKI CLAQ NSPST FHYVLVNSLH RIITNSALDW WPKIDAVYCH SVELRNMFGE TLHKAVQGCG AHPAIRMAPS LTFKEKVTSL KFKEK PTDL ETRSYKYLLL SMVKLIHADP KLLLCNPRKQ GPETQGSTAE LITGLVQLVP QSHMPEIAQE AMEALLVLHQ LDSIDL WNP DAPVETFWEI SSQMLFYICK KLTSHQMLSS TEILKWLREI LICRNKFLLK NKQADRSSCH FLLFYGVGCD IPSSGNT SQ MSMDHEELLR TPGASLRKGK GNSSMDSAAG CSGTPPICRQ AQTKLEVALY MFLWNPDTEA VLVAMSCFRH LCEEADIR C GVDEVSVHNL LPNYNTFMEF ASVSNMMSTG RAALQKRVMA LLRRIEHPTA GNTEAWEDTH AKWEQATKLI LNYPKAKME DGQAAESLHK TIVKRRMSHV SGGGSIDLSD TDSLQEWINM TGFLCALGGV CLQQRSNSGL ATYSPPMGPV SERKGSMISV MSSEGNADT PVSKFMDRLL SLMVCNHEKV GLQIRTNVKD LVGLELSPAL YPMLFNKLKN TISKFFDSQG QVLLTDTNTQ F VEQTIAIM KNLLDNHTEG SSEHLGQASI ETMMLNLVRY VRVLGNMVHA IQIKTKLCQL VEVMMARRDD LSFCQEMKFR NK MVEYLTD WVMGTSNQAA DDDVKCLTRD LDQASMEAVV SLLAGLPLQP EEGDGVELME AKSQLFLKYF TLFMNLLNDC SEV EDESAQ TGGRKRGMSR RLASLRHCTV LAMSNLLNAN VDSGLMHSIG LGYHKDLQTR ATFMEVLTKI LQQGTEFDTL AETV LADRF ERLVELVTMM GDQGELPIAM ALANVVPCSQ WDELARVLVT LFDSRHLLYQ LLWNMFSKEV ELADSMQTLF RGNSL ASKI MTFCFKVYGA TYLQKLLDPL LRIVITSSDW QHVSFEVDPT RLEPSESLEE NQRNLLQMTE KFFHAIISSS SEFPPQ LRS VCHCLYQVVS QRFPQNSIGA VGSAMFLRFI NPAIVSPYEA GILDKKPPPR IERGLKLMSK ILQSIANHVL FTKEEHM RP FNDFVKSNFD AARRFFLDIA SDCPTSDAVN HSLSFISDGN VLALHRLLWN NQEKIGQYLS SNRDHKAVGR RPFDKMAT L LAYLGPPEHK PVADTHWSSL NLTSSKFEEF MTRHQVHEKE EFKALKTLSI FYQAGTSKAG NPIFYYVARR FKTGQINGD LLIYHVLLTL KPYYAKPYEI VVDLTHTGPS NRFKTDFLSK WFVVFPGFAY DNVSAVYIYN CNSWVREYTK YHERLLTGLK GSKRLVFID CPGKLAEHIE HEQQKLPAAT LALEEDLKVF HNALKLAHKD TKVSIKVGST AVQVTSAERT KVLGQSVFLN D IYYASEIE EICLVDENQF TLTIANQGTP LTFMHQECEA IVQSIIHIRT RWELSQPDSI PQHTKIRPKD VPGTLLNIAL LN LGSSDPS LRSAAYNLLC ALTCTFNLKI EGQLLETSGL CIPANNTLFI VSISKTLAAN EPHLTLEFLE ECISGFSKSS IEL KHLCLE YMTPWLSNLV RFCKHNDDAK RQRVTAILDK LITMTINEKQ MYPSIQAKIW GSLGQITDLL DVVLDSFIKT SATG GLGSI KAEVMADTAV ALASGNVKLV SSKVIGRMCK IIDKTCLSPT PTLEQHLMWD DIAILARYML MLSFNNSLDV AAHLP YLFH VVTFLVATGP LSLRASTHGL VINIIHSLCT CSQLHFSEET KQVLRLSLTE FSLPKFYLLF GISKVKSAAV IAFRSS YRD RSFSPGSYER ETFALTSLET VTEALLEIME ACMRDIPTCK WLDQWTELAQ RFAFQYNPSL QPRALVVFGC ISKRVSH GQ IKQIIRILSK ALESCLKGPD TYNSQVLIEA TVIALTKLQP LLNKDSPLHK ALFWVAVAVL QLDEVNLYSA GTALLEQN L HTLDSLRIFN DKSPEEVFMA IRNPLEWHCK QMDHFVGLNF NSNFNFALVG HLLKGYRHPS PAIVARTVRI LHTLLTLVN KHRNCDKFEV NTQSVAYLAA LLTVSEEVRS RCSLKHRKSL LLTDISMENV PMDTYPIHHG DPSYRTLKET QPWSSPKGSE GYLAATYPT VGQTSPRARK SMSLDMGQPS QANTKKLLGT RKSFDHLISD TKAPKRQEME SGITTPPKMR RVAETDYEME T QRISSSQQ HPHLRKVSVS ESNVLLDEEV LTDPKIQALL LTVLATLVKY TTDEFDQRIL YEYLAEASVV FPKVFPVVHN LL DSKINTL LSLCQDPNLL NPIHGIVQSV VYHEESPPQY QTSYLQSFGF NGLWRFAGPF SKQTQIPDYA ELIVKFLDAL IDT YLPGID EETSEESLLT PTSPYPPALQ SQLSITANLN LSNSMTSLAT SQHSPGIDKE NVELSPTTGH CNSGRTRHGS ASQV QKQRS AGSFKRNSIK KIV

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: 3.8 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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