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- EMDB-73069: Human CI-M6PR/IGF2R (cation-independent mannose-6-phosphate recep... -

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Basic information

Entry
Database: EMDB / ID: EMD-73069
TitleHuman CI-M6PR/IGF2R (cation-independent mannose-6-phosphate receptor) cryo-EM structure low pH conformation
Map data
Sample
  • Organelle or cellular component: ci-m6pr / igf2r
    • Protein or peptide: Cation-independent mannose-6-phosphate receptor
KeywordsCI-MPR / CI-M6PR / M6PR / IGF2R / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


response to tetrachloromethane / Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor binding / Golgi to lysosome transport / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / protein targeting to lysosome ...response to tetrachloromethane / Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor binding / Golgi to lysosome transport / insulin-like growth factor II binding / trans-Golgi network transport vesicle / host-mediated activation of viral process / protein targeting to lysosome / retinoic acid binding / post-embryonic development / D-mannose binding / cargo receptor activity / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / animal organ regeneration / response to retinoic acid / endocytic vesicle / G-protein alpha-subunit binding / transport vesicle / liver development / secretory granule membrane / trans-Golgi network membrane / trans-Golgi network / clathrin-coated endocytic vesicle membrane / phosphoprotein binding / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome / endosome membrane / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / enzyme binding / cell surface / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. ...Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsCasner RG / Sevvana M / Batchelor J
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: pH-dependent conformational change and low-pH structure of human CI-M6PR
Authors: Casner RG / Batchelor J
History
DepositionOct 8, 2025-
Header (metadata) releaseOct 14, 2026-
Map releaseOct 14, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73069.png

Downloads & links

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Map

FileDownload / File: emd_73069.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å		0.71 Å/pix.
x 512 pix.
= 363.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.71 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.1874135 - 0.3547193
Average (Standard dev.)0.00025482866 (±0.009426663)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 363.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73069_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73069_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ci-m6pr / igf2r

EntireName: ci-m6pr / igf2r
Components
  • Organelle or cellular component: ci-m6pr / igf2r
    • Protein or peptide: Cation-independent mannose-6-phosphate receptor

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Supramolecule #1: ci-m6pr / igf2r

SupramoleculeName: ci-m6pr / igf2r / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cation-independent mannose-6-phosphate receptor

MacromoleculeName: Cation-independent mannose-6-phosphate receptor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 248.22075 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAAPFPELCS YTWEAVDTKN NVLYKINICG SVDIVQCGPS SAVCMHDLKT RTYHSVGDSV LRSATRSLLE FNTTVSCDQQ GTNHRVQSS IAFLCGKTLG TPEFVTATEC VHYFEWRTTA ACKKDIFKAN KEVPCYVFDE ELRKHDLNPL IKLSGAYLVD D SDPDTSLF ...String:
QAAPFPELCS YTWEAVDTKN NVLYKINICG SVDIVQCGPS SAVCMHDLKT RTYHSVGDSV LRSATRSLLE FNTTVSCDQQ GTNHRVQSS IAFLCGKTLG TPEFVTATEC VHYFEWRTTA ACKKDIFKAN KEVPCYVFDE ELRKHDLNPL IKLSGAYLVD D SDPDTSLF INVCRDIDTL RDPGSQLRAC PPGTAACLVR GHQAFDVGQP RDGLKLVRKD RLVLSYVREE AGKLDFCDGH SP AVTITFV CPSERREGTI PKLTAKSNCR YEIEWITEYA CHRDYLESKT CSLSGEQQDV SIDLTPLAQS GGSSYISDGK EYL FYLNVC GETEIQFCNK KQAAVCQVKK SDTSQVKAAG RYHNQTLRYS DGDLTLIYFG GDECSSGFQR MSVINFECNK TAGN DGKGT PVFTGEVDCT YFFTWDTEYA CVKEKEDLLC GATDGKKRYD LSALVRHAEP EQNWEAVDGS QTETEKKHFF INICH RVLQ EGKARGCPED AAVCAVDKNG SKNLGKFISS PMKEKGNIQL SYSDGDDCGH GKKIKTNITL VCKPGDLESA PVLRTS GEG GCFYEFEWHT AAACVLSKTE GENCTVFDSQ AGFSFDLSPL TKKNGAYKVE TKKYDFYINV CGPVSVSPCQ PDSGACQ VA KSDEKTWNLG LSNAKLSYYD GMIQLNYRGG TPYNNERHTP RATLITFLCD RDAGVGFPEY QEEDNSTYNF RWYTSYAC P EEPLECVVTD PSTLEQYDLS SLAKSEGGLG GNWYAMDNSG EHVTWRKYYI NVCRPLNPVP GCNRYASACQ MKYEKDQGS FTEVVSISNL GMAKTGPVVE DSGSLLLEYV NGSACTTSDG RQTTYTTRIH LVCSRGRLNS HPIFSLNWEC VVSFLWNTEA ACPIQTTTD TDQACSIRDP NSGFVFNLNP LNSSQGYNVS GIGKIFMFNV CGTMPVCGTI LGKPASGCEA ETQTEELKNW K PARPVGIE KSLQLSTEGF ITLTYKGPLS AKGTADAFIV RFVCNDDVYS GPLKFLHQDI DSGQGIRNTY FEFETALACV PS PVDCQVT DLAGNEYDLT GLSTVRKPWT AVDTSVDGRK RTFYLSVCNP LPYIPGCQGS AVGSCLVSEG NSWNLGVVQM SPQ AAANGS LSIMYVNGDK CGNQRFSTRI TFECAQISGS PAFQLQDGCE YVFIWRTVEA CPVVRVEGDN CEVKDPRHGN LYDL KPLGL NDTIVSAGEY TYYFRVCGKL SSDVCPTSDK SKVVSSCQEK REPQGFHKVA GLLTQKLTYE NGLLKMNFTG GDTCH KVYQ RSTAIFFYCD RGTQRPVFLK ETSDCSYLFE WRTQYACPPF DLTECSFKDG AGNSFDLSSL SRYSDNWEAI TGTGDP EHY LINVCKSLAP QAGTEPCPPE AAACLLGGSK PVNLGRVRDG PQWRDGIIVL KYVDGDLCPD GIRKKSTTIR FTCSESQ VN SRPMFISAVE DCEYTFAWPT ATACPMKSNE HDDCQVTNPS TGHLFDLSSL SGRAGFTAAY SEKGLVYMSI CGENENCP P GVGACFGQTR ISVGKANKRL RYVDQVLQLV YKDGSPCPSK SGLSYKSVIS FVCRPEARPT NRPMLISLDK QTCTLFFSW HTPLACEQAT ECSVRNGSSI VDLSPLIHRT GGYEAYDESE DDASDTNPDF YINICQPLNP MHGVPCPAGA AVCKVPIDGP PIDIGRVAG PPILNPIANE IYLNFESSTP CLADKHFNYT SLIAFHCKRG VSMGTPKLLR TSECDFVFEW ETPVVCPDEV R MDGCTLTD EQLLYSFNLS SLSTSTFKVT RDSRTYSVGV CTFAVGPEQG GCKDGGVCLL SGTKGASFGR LQSMKLDYRH QD EAVVLSY VNGDRCPPET DDGVPCVFPF IFNGKSYEEC IIESRAKLWC STTADYDRDH EWGFCRHSNS YRTSSIIFKC DED EDIGRP QVFSEVRGCD VTFEWKTKVV CPPKKLECKF VQKHKTYDLR LLSSLTGSWS LVHNGVSYYI NLCQKIYKGP LGCS ERASI CRRTTTGDVQ VLGLVHTQKL GVIGDKVVVT YSKGYPCGGN KTASSVIELT CTKTVGRPAF KRFDIDSCTY YFSWD SRAA CAVKPQEVQM VNGTITNPIN GKSFSLGDIY FKLFRASGDM RTNGDNYLYE IQLSSITSSR NPACSGANIC QVKPND QHF SRKVGTSDKT KYYLQDGDLD VVFASSSKCG KDKTKSVSST IFFHCDPLVE DGIPEFSHET ADCQYLFSWY TSAVCPL GV GFDSEN

UniProtKB: Cation-independent mannose-6-phosphate receptor

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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: 4.5 / Details: 250 mM acetic acid pH 4.5 150 mM ammonium acetate
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 202676
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9yl1:
Human CI-M6PR/IGF2R (cation-independent mannose-6-phosphate receptor) cryo-EM structure low pH conformation

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