2025-04-09 REL PDBe PDBe PDBe 2024-07-08 2025-04-09 2025-04-09 2025-04-09 Michael J. Fox Foundation MJFF-17240; MJFF-020706; MJFF-022745 United States Other government Interdisciplinary Center for Clinical Research (IZKF); Jochen-Kalden funding programme N8 Other government Fonds voor Wetenschappelijk Onderzoek; G031324N Other government VUB Strategic Research Program Financing; SRP95 Other private Friedrich-Ebert Foundation; no grant number Lysosomal transporting complex of beta-glucocerebrosidase (GCase) and lysosomal integral membrane protein 2 (LIMP-2) with bound Pro-macrobodies (consensus map) Dobert JP Schaefer JHS Dal Maso T Socher E Versees W Moeller A Zunke F Arnold P Parkinson, lysosome, Gaucher, GCase, SCARB2, Pro-macrobody, Glucosylceramide, complex, TRANSPORT PROTEIN Dobert JP Schafer JH Dal Maso T Ravindran P Huard DJE Socher E Schildmeyer LA Lieberman RL Versees W Moeller A Zunke F Arnold P Cryo-TEM structure of beta-glucocerebrosidase in complex with its transporter LIMP-2. Nat Commun UK 16 3074 3074 2025 40159502 doi:10.1038/s41467-025-58340-1 2041-1723 EMD-50502 other EM volume
primary deposition; combined map
 Lysosomal transporting complex of beta-glucocerebrosidase and lysosomal integral membrane protein 2 (LIMP-2) with two bound Pro-macrobodies. Lysosomal transporting complex of beta-glucocerebrosidase and lysosomal integral membrane protein 2 (LIMP-2) with two bound Pro-macrobodies. 0 1 2 3 4
Maltose-binding protein (MBP) domains of Pro-macrobodies were not resolved, only nanobody domains are included in the model.
Homo sapiens 0.25 Lysosomal acid glucosylceramidase Homo sapiens Homo sapiens LEVO ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKG FGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPL IHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGL LSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPA KATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFL ETISPGYSIHTYLWRRQ P04062 3.2.1.45 Nanobody Nb6 unidentified
Pro-Macrobody; nanobody fused to maltose-binding protein (MBP) via Pro-Pro linker; MBP not resolved and not modeled.
Escherichia coli MC1061 LEVO QVQLVESGGGLVQPGGSLRLSCAASGSIFSINTMGWYRQAPGKEREMVAYIITFGSTNYADSVKGRFTISGDNANNTMWL QMNSLKPEDTAVYYCYAAIRPTDSSTYTSYWGQGTQVTVPP Lysosomal membrane protein 2 Homo sapiens Homo sapiens LEVO KKIVLRNGTEAFDSWEKPPLPVYTQFYFFNVTNPEEILRGETPRVEEVGPYTYRELRNKANIQFGDNGTTISAVSNKAYV FERDQSVGDPKIDLIRTLNIPVLTVIEWSQVHFLREIIEAMLKAYQQKLFVTHTVDELLWGYKDEILSLIHVFRPDISPY FGLFYEKNGTNDGDYVFLTGEDSYLNFTKIVEWNGKTSLDWWITDKCNMINGTDGDSFHPLITKDEVLYVFPSDFCRSVY ITFSDYESVQGLPAFRYKVPAEILANTSDNAGFCIPEGNCLGSGVLNVSICKNGAPIIMSFPHFYQADERFVSYLDFLAP NQEDHETFVDINPLTGIILKAAKRFQINIYVKKLDDFVETGDIRTMVFPVMYLNESVHIDKETASRLKSMI Q14108 Nanobody Nb1 unidentified
Pro-Macrobody; nanobody fused to maltose-binding protein (MBP) via Pro-Pro linker; MBP not resolved and not modeled.
Escherichia coli MC1061 LEVO QVQLVESGGGLVQPGGSLRLSCAASGFTLDYYAIGWFRQAPGKEREGVSCISSSDGSTYYADSAKGRFTISRDNAKNTVY LQMNSLKPEDTAVYYCATDRGQCTYYSSGYYRDLRWYDYWGQGTQVTVPP singleParticle particle 0.6 7.4 20.0 C6H13NO4S MES; 2-(N-morpholino)ethanesulfonic acid 150.0 NaCl sodium chloride
20 mM MES; 150 mM NaCl, pH: 7.4
 C-flat-1.2/1.3 COPPER 300 CARBON HOLEY 2.0 ETHANE 100 277 FEI VITROBOT MARK IV
Monodisperse, complex seperated from monomers via size exclusion chhromatography.
 TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 0.6 2.0 130000.0 NITROGEN TFS Selectris 10 FEI FALCON IV (4k x 4k) COUNTING 1 10550 50.0 1 3.7 FSC 0.143 CUT-OFF cryoSPARC 4.2 397385 NOT APPLICABLE NOT APPLICABLE emd_50936.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 296.0 296.0 296.0 90.0 90.0 90.0 X Y Z -0.8482906 1.2634709 -0.00006666664 0.018381333 0.925 0.925 0.925 0.08 AUTHOR Sharpened Concensus Map of GCase/LIMP-2 transport complex with two bound Pro-macrobodies. Obtained via non-uniform refinement. B-factor: -152.7 6TN1 AAA 1-497 PDB experimental model
GCase
 FLEXIBLE FIT
Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix
REAL 4Q4F A 37-430 PDB experimental model
LIMP-2
 RIGID BODY FIT
Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix
REAL 9ENA PDB experimental model
Nanobody Nb1; Unpublished
 RIGID BODY FIT
Initial fitting with ChimeraX, manual flexible fitting with Coot, refinement with Phenix
REAL emd_50936_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 296.0 296.0 296.0 90.0 90.0 90.0 X Y Z -0.1699071 0.35628814 0.00017124396 0.011435881 0.925 0.925 0.925 AUTHOR Half map A emd_50936_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 296.0 296.0 296.0 90.0 90.0 90.0 X Y Z -0.13970773 0.31359664 0.00017222107 0.011438269 0.925 0.925 0.925 AUTHOR Half map B