[English] 日本語
Yorodumi
- EMDB-47970: Cryo-EM structure of Drosophila melanogaster insulin receptor (dm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47970
TitleCryo-EM structure of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation
Map dataCryo-EM map of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation
Sample
  • Complex: Drosophila melanogaster insulin receptor in complex with one DILP2, asymmetric conformation
    • Protein or peptide: Insulin-like receptor
    • Protein or peptide: DILP2 B-chain
    • Protein or peptide: DILP2 A-chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInsulin receptor / DILP / STRUCTURAL PROTEIN
Function / homology
Function and homology information


primary spermatocyte growth / negative regulation of peptide hormone secretion / Extra-nuclear estrogen signaling / response to anoxia / negative regulation of entry into reproductive diapause / Insulin signaling pathway / Insulin receptor recycling / female mating behavior / embryonic development via the syncytial blastoderm / larval feeding behavior ...primary spermatocyte growth / negative regulation of peptide hormone secretion / Extra-nuclear estrogen signaling / response to anoxia / negative regulation of entry into reproductive diapause / Insulin signaling pathway / Insulin receptor recycling / female mating behavior / embryonic development via the syncytial blastoderm / larval feeding behavior / male germ-line stem cell asymmetric division / female germ-line stem cell population maintenance / germ-band shortening / carbohydrate homeostasis / germ-line stem-cell niche homeostasis / imaginal disc growth / open tracheal system development / positive regulation of neuron remodeling / germ-line stem cell division / negative regulation of circadian sleep/wake cycle, sleep / follicle cell of egg chamber development / lymph gland development / positive regulation of border follicle cell migration / female germ-line stem cell asymmetric division / positive regulation of fat cell proliferation / regulation of growth rate / intestinal stem cell homeostasis / growth cone membrane / positive regulation of organ growth / response to amino acid starvation / female gonad development / positive regulation of lipid storage / insulin receptor complex / regulation of organ growth / insulin receptor activity / embryo development ending in birth or egg hatching / positive regulation of multicellular organism growth / sleep / insulin binding / triglyceride homeostasis / response to food / negative regulation of glycogen catabolic process / negative regulation of feeding behavior / negative regulation of macroautophagy / positive regulation of wound healing / positive regulation of neuroblast proliferation / regulation of cell size / lipid homeostasis / locomotor rhythm / insulin receptor substrate binding / regulation of multicellular organism growth / developmental growth / positive regulation of cell size / phosphatidylinositol 3-kinase binding / positive regulation of TORC1 signaling / axon guidance / cholesterol homeostasis / cellular response to starvation / determination of adult lifespan / insulin receptor binding / response to cocaine / growth factor activity / locomotory behavior / cellular response to glucose stimulus / receptor protein-tyrosine kinase / circadian rhythm / hormone activity / SH3 domain binding / multicellular organism growth / insulin receptor signaling pathway / glucose homeostasis / nervous system development / regulation of cell population proliferation / protein autophosphorylation / positive regulation of cell growth / response to oxidative stress / protein tyrosine kinase activity / protein phosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / receptor ligand activity / axon / positive regulation of cell population proliferation / extracellular space / extracellular region / ATP binding / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Long hematopoietin receptor, single chain family signature. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily ...Long hematopoietin receptor, single chain family signature. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Insulin-like receptor / Insulin-like peptide 2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBai XC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural basis of the activation of the Drosophila insulin receptor by three Drosophila insulin-like peptides
Authors: Bai XC
History
DepositionNov 19, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47970.png

Downloads & links

-
Map

FileDownload / File: emd_47970.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.022650352 - 0.041419268
Average (Standard dev.)0.000003832174 (±0.0008249223)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Cryo-EM map of Drosophila melanogaster insulin receptor (dmIR)...

Fileemd_47970_half_map_1.map
AnnotationCryo-EM map of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation, half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM map of Drosophila melanogaster insulin receptor (dmIR)...

Fileemd_47970_half_map_2.map
AnnotationCryo-EM map of Drosophila melanogaster insulin receptor (dmIR) bound with one DILP2, asymmetric conformation, half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Drosophila melanogaster insulin receptor in complex with one DILP...

EntireName: Drosophila melanogaster insulin receptor in complex with one DILP2, asymmetric conformation
Components
  • Complex: Drosophila melanogaster insulin receptor in complex with one DILP2, asymmetric conformation
    • Protein or peptide: Insulin-like receptor
    • Protein or peptide: DILP2 B-chain
    • Protein or peptide: DILP2 A-chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Drosophila melanogaster insulin receptor in complex with one DILP...

SupramoleculeName: Drosophila melanogaster insulin receptor in complex with one DILP2, asymmetric conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Drosophila melanogaster (fruit fly)

-
Macromolecule #1: Insulin-like receptor

MacromoleculeName: Insulin-like receptor / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 240.078078 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MFNMPRGVTK SKSKRGKIKM ENDMAAAATT TACTLGHICV LCRQEMLLDT CCCRQAVEAV DSPASSEEAY SSSNSSSCQA SSEISAEEV WFLSHDDIVL CRRPKFDEVE TTGKKRDVKC SGHQCSNECD DGSTKNNRQQ RENFNIFSNC HNILRTLQSL L LLMFNCGI ...String:
MFNMPRGVTK SKSKRGKIKM ENDMAAAATT TACTLGHICV LCRQEMLLDT CCCRQAVEAV DSPASSEEAY SSSNSSSCQA SSEISAEEV WFLSHDDIVL CRRPKFDEVE TTGKKRDVKC SGHQCSNECD DGSTKNNRQQ RENFNIFSNC HNILRTLQSL L LLMFNCGI FNKRRRRQHQ QQHHHHYQHH HQQHHQQHHQ RQQANVSYTK FLLLLQTLAA ATTRLSLSPK NYKQQQQLQH NQ QLPRATP QQKQQEKDRH KCFHYKHNYS YSPGISLLLF ILLANTLAIQ AVVLPAHQQH LLHNDIADGL DKTALSVSGT QSR WTRSES NPTMRLSQNV KPCKSMDIRN MVSHFNQLEN CTVIEGFLLI DLINDASPLN RSFPKLTEVT DYIIIYRVTG LHSL SKIFP NLSVIRGNKL FDGYALVVYS NFDLMDLGLH KLRSITRGGV RIEKNHKLCY DRTIDWLEIL AENETQLVVL TENGK EKEC RLSKCPGEIR IEEGHDTTAI EGELNASCQL HNNRRLCWNS KLCQTKCPEK CRNNCIDEHT CCSQDCLGGC VIDKNG NES CISCRNVSFN NICMDSCPKG YYQFDSRCVT ANECITLTKF ETNSVYSGIP YNGQCITHCP TGYQKSENKR MCEPCPG GK CDKECSSGLI DSLERAREFH GCTIITGTEP LTISIKRESG AHVMDELKYG LAAVHKIQSS LMVHLTYGLK SLKFFQSL T EISGDPPMDA DKYALYVLDN RDLDELWGPN QTVFIRKGGV FFHFNPKLCV STINQLLPML ASKPKFFEKS DVGADSNGN RGSCGTAVLN VTLQSVGANS AMLNVTTKVE IGEPQKPSNA TIVFKDPRAF IGFVFYHMID PYGNSTKSSD DPCDDRWKVS SPEKSGVMV LSNLIPYTNY SYYVRTMAIS SELTNAESDV KNFRTNPGRP SKVTEVVATA ISDSKINVTW SYLDKPYGVL T RYFIKAKL INRPTRNNNR DYCTEPLVKA MENDLPATTP TKKISDPLAG DCKCVEGSKK TSSQEYDDRK VQAGMEFENA LQ NFIFVPN IRKSKNGSSD KSDGAEGAAL DSNAIPNGGA TNPSRRRRDV ALEPELDDVE GSVLLRHVRS ITDDTDAFFE KDD ENTYKD EEDLSSNKQF YEVFAKELPP NQTHFVFEKL RHFTRYAIFV VACREEIPSE KLRDTSFKKS LCSDYDTVFQ TTKR KKFAD IVMDLKVDLE HANNTESPVR VRWTPPVDPN GEIVTYEVAY KLQKPDQVEE KKCIPAADFN QTAGYLIKLN EGLYS FRVR ANSIAGYGDF TEVEHIKVEP PPSYAKVFFW LLGIGLAFLI VSLFGYVCYL HKRKVPSNDL HMNTEVNPFY ASMQYI PDD WEVLRENIIQ LAPLGQGSFG MVYEGILKSF PPNGVDRECA IKTVNENATD RERTNFLSEA SVMKEFDTYH VVRLLGV CS RGQPALVVME LMKKGDLKSY LRAHRPEERD EAMMTYLNRI GVTGNVQPPT YGRIYQMAIE IADGMAYLAA KKFVHRDL A ARNCMVADDL TVKIGDFGMT RDIYETDYYR KGTKGLLPVR WMPPESLRDG VYSSASDVFS FGVVLWEMAT LAAQPYQGL SNEQVLRYVI DGGVMERPEN CPDFLHKLMQ RCWHHRSSAR PSFLDIIAYL EPQCPNSQFK EVSFYHSEAG LQHREKERKE RNQLDAFAA VPLDQDLQDR EQQEDATTPL RMGDYQQNSS LDQPPESPIA MVDDQGSHLP FSLPSGFIAS STPDGQTVMA T AFQNIPAA QGDISATYVV PDADALDGDR GYEIYDPSPK CAELPTSRSG STGGGKLSGE QHLLPRKGRQ PTIMSSSMPD DV IGGSSLQ PSTASAGSSN ASSHTGRPSL KKTVADSVRN KANFINRHLF NHKRTGSNAS HKSNASNAPS TSSNTNLTSH PVA MGNLGT IESGGSGSAG SYTGTPRFYT PSATPGGGSG MAISDNPNYR LLDESIASEQ ATILTTSSPN PNYEMMHPPT SLVS TNPNY MPMNETPVQM AGVTISHNPN YQPMQAPLNA RQSQSSSDED NEQEEDDEDE DDDVDDEHVE HIKMERMPLS RPRQR ALPS KTQPPRSRSV SQTRKSPTNP NSGIGATGAG NRSNLLKENW LRPASTPRPP PPNGFIGREA

UniProtKB: Insulin-like receptor

-
Macromolecule #2: DILP2 B-chain

MacromoleculeName: DILP2 B-chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 2.75017 KDa
SequenceString:
TLCSEKLNEV LSMVCEEYNP VIPH

UniProtKB: Insulin-like peptide 2

-
Macromolecule #3: DILP2 A-chain

MacromoleculeName: DILP2 A-chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 3.025617 KDa
SequenceString:
QGIVERCCKK SCDMKALREY CSVVRN

UniProtKB: Insulin-like peptide 2

-
Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 50277
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

+
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