[English] 日本語
Yorodumi
- EMDB-28037: Cryo-EM structure of the full-length human NF1 dimer -

+
Open data


ID or keywords:

Loading...

-
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 / Schwann cell migration / vascular associated smooth muscle cell migration / amygdala development / 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 / vascular associated smooth muscle cell migration / amygdala development / 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 / mast 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 / 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 / collagen fibril organization / regulation of long-term synaptic potentiation / endothelial cell proliferation / regulation of postsynapse organization / regulation of bone resorption / neural tube development / artery morphogenesis / forebrain astrocyte development / adrenal gland development / negative regulation of neuroblast proliferation / negative regulation of protein import into nucleus / pigmentation / spinal cord development / regulation of synaptic transmission, GABAergic / negative regulation of astrocyte differentiation / negative regulation of vascular associated smooth muscle cell migration / negative regulation of endothelial cell proliferation / Rac protein signal transduction / negative regulation of osteoclast differentiation / oligodendrocyte differentiation / RAS signaling downstream of NF1 loss-of-function variants / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of cell-matrix adhesion / neuroblast proliferation / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / Schwann cell development / skeletal muscle tissue development / negative regulation of stem cell proliferation / negative regulation of MAPK cascade / negative regulation of fibroblast proliferation / positive regulation of vascular associated smooth muscle cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of endothelial cell proliferation / positive regulation of GTPase activity / extracellular matrix organization / GTPase activator activity / osteoclast differentiation / negative regulation of angiogenesis / negative regulation of cell migration / stem cell proliferation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / liver development / regulation of long-term neuronal synaptic plasticity / cerebral cortex development / brain development / visual learning / Regulation of RAS by GAPs / cognition / long-term synaptic potentiation / protein import into nucleus / osteoblast differentiation / MAPK cascade / positive regulation of neuron apoptotic process / presynapse / regulation of gene expression / cellular response to heat / heart development / actin cytoskeleton organization / fibroblast proliferation / angiogenesis / neuron apoptotic process / 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)
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

-
Structure visualization

Supplemental images

emd_28037.png

Downloads & links

-
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 °

-
Supplemental data

-
Mask #1

Fileemd_28037_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
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)

-
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)

-
Sample components

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
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

+
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