2026-09-02 REL PDBe INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY EXPERIMENTAL_SUMMARY em_admin _em_admin.last_update REMEDIATION REPOSITORY Metalloprotein remediation DERIVED_CALCULATIONS em_admin pdbx_nonpoly_atom_coordination pdbx_nonpoly_atom_coordination_sphere pdbx_nonpoly_atom_coordination_sphere_order pdbx_validate_close_contact struct_conn struct_conn_type _em_admin.last_update PDBe PDBe 2023-03-04 2024-03-13 2024-03-13 2026-09-02 European Research Council (ERC) 852880 European Union Netherlands Organisation for Scientific Research (NWO) NWO.STU.018-2.007 Netherlands Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3 Kuhm TI Jakobi AJ Jakobi AJ Cell-autonomous immunity, intracellular pathogens, GTPase, IMMUNE SYSTEM Kuhm T Taisne C de Agrela Pinto C Gross L Giannopoulou EA Huber ST Pardon E Steyaert J Tans SJ Jakobi AJ Structural basis of antimicrobial membrane coat assembly by human GBP1. Nat.Struct.Mol.Biol. US 32 172 184 2025 39394410 doi:10.1038/s41594-024-01400-9 1545-9985 8cqb FULLOVERLAP EMDB EMD-16794 associated EM volume
Cryo-EM structure of the human GBP1 dimer bound to GDP-AlF3
 Homodimeric complex of GBP1 stabilised by GDP-AlF3 Homodimeric complex of GBP1 stabilised by GDP-AlF3 0 1 Homo sapiens 0.134 Guanylate-binding protein 1 Homo sapiens 0.06802161699999999 2 Escherichia coli LEVO MASEIHMTGPMCLIENTNGRLMANPEALKILSAITQPMVVVAIVGLYRTGKSYLMNKLAGKKKGFSLGSTVQSHTKGIWM WCVPHPKKPGHILVLLDTEGLGDVEKGDNQNDSWIFALAVLLSSTFVYNSIGTINQQAMDQLYYVTELTHRIRSKSSPDE NENEVEDSADFVSFFPDFVWTLRDFSLDLEADGQPLTPDEYLTYSLKLKKGTSQKDETFNLPRLCIRKFFPKKKCFVFDR PVHRRKLAQLEKLQDEELDPEFVQQVADFCSYIFSNSKTKTLSGGIQVNGPRLESLVLTYVNAISSGDLPCMENAVLALA QIENSAAVQKAIAHYEQQMGQKVQLPTETLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEKKRDDFCKQNQ EASSDRCSALLQVIFSPLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESMTDAILQTDQ TLTEKEKEIEVERVKAESAQASAKMLQEMQRKNEQMMEQKERSYQEHLKQLTEKMENDRVQLLKEQERTLALKLQEQEQL LKEGFQKESRIMKNEIQDLQTKMRRRKACTIS P32455 3.6.5.- GUANOSINE-5'-DIPHOSPHATE 0.000443201 2 GDP ALUMINUM FLUORIDE 8.3977e-05 2 AF3 MAGNESIUM ION 2.4305e-05 2 MG singleParticle particle 0.7 7.4 50.0 C8H18N2O4S HEPES 150.0 NaCl Sodium chloride 1.0 C4H10O2S2 Dithiothreitol 200.0 C10H15N5O11P2 Guanosine diphosphate 10.0 NaF Sodium fluoride 300.0 AlCl3 Aluminium chloride 5.0 MgCl2 Magnesium chloride
5u mM HEPES pH7.4, 150 mM NaCl, 1 mM DTT, 200 uM GDP, 10 mM NaF, 300 uM AlCl3, 5 mM MgCl2
 Quantifoil COPPER 300 CARBON HOLEY GLOW DISCHARGE ETHANE 99 22 LEICA EM GP FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 2.7 0.6 2.2 105000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 5760 4092 2 5214 60.0 1 447651
447,651 particles were used to perform ab initio reconstruction to generate five different models. Three classes were selected for heterogeneous refinements without imposing symmetry. A single class with 147095 particles was used for non-uniform refinement.
 cryoSPARC 3.1 PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model was generated ab initio
 C1 3.7 FSC 0.143 CUT-OFF cryoSPARC 3.3 147095 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD 3 cryoSPARC 3.3 emd_16794.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 328 328 328 0 0 0 328 328 328 273.552 273.552 273.552 90.0 90.0 90.0 X Y Z -2.143496 3.13021 0.00024753826 0.043452296 0.834 0.834 0.834 0.25 AUTHOR Primary map 1FN5 A 323-478 PDB experimental model 2B92 A 6-304 PDB experimental model 2B92 B 6-304 PDB experimental model OTHER Real-space cross correlation RECIPROCAL emd_16794_msk_1.map emd_16794_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 328 328 328 0 0 0 328 328 328 273.552 273.552 273.552 90.0 90.0 90.0 X Y Z -0.11852084 0.48633564 0.0011299354 0.012542595 0.834 0.834 0.834 AUTHOR Locally sharpened map (LocScale) emd_16794_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 328 328 328 0 0 0 328 328 328 273.552 273.552 273.552 90.0 90.0 90.0 X Y Z -0.33781573 1.0702333 0.0008507307 0.0312773 0.834 0.834 0.834 AUTHOR Half map 1 emd_16794_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 328 328 328 0 0 0 328 328 328 273.552 273.552 273.552 90.0 90.0 90.0 X Y Z -0.35394463 1.0790339 0.0008404657 0.031328786 0.834 0.834 0.834 AUTHOR Half map 2