2024-07-10 REL PDBe PDBe PDBe 2021-01-29 2022-03-02 2022-03-02 2024-07-10 European Research Council (ERC) 615984 Cryo-EM structure of the human FERRY complex Quentin D Klink BU Raunser S Human FERRY complex, Five-subunit Early endosome RNA and Ribosome intermediarY complex, Intracellular RNA transport, Early Endosome-associated transport of RNA, RNA BINDING PROTEIN Quentin D Schuhmacher JS Klink BU Lauer J Shaikh TR Huis In 't Veld PJ Welp LM Urlaub H Zerial M Raunser S Structural basis of mRNA binding by the human FERRY Rab5 effector complex. Mol.Cell US 83 1856 1871.e9 2023 37267906 doi:10.1016/j.molcel.2023.05.009 1097-2765 2168 MOCEFL 7nd2 FULLOVERLAP Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex Human FERRY (Five-subunit Early endosome RNA and Ribosome intermediarY) complex 0 1 2 3 Protein phosphatase 1 regulatory subunit 21 1 1 Homo sapiens Quinone oxidoreductase-like protein 1 1 2 Homo sapiens Glutamine amidotransferase-like class 1 domain-containing protein 1 1 3 Homo sapiens Protein phosphatase 1 regulatory subunit 21 Homo sapiens 0.08878283599999999 2 Spodoptera frugiperda LEVO MAAAMASAELQGKYQKLAQEYSKLRAQNQVLKKGVVDEQANSAALKEQLKMKDQSLRKLQQEMDSLTFRNLQLAKRVELL QDELALSEPRGKKNKKSGESSSQLSQEQKSVFDEDLQKKIEENERLHIQFFEADEQHKHVEAELRSRLATLETEAAQHQA VVDGLTRKYMETIEKLQNDKAKLEVKSQTLEKEAKECRLRTEECQLQLKTLHEDLSGRLEESLSIINEKVPFNDTKYSQY NALNVPLHNRRHQLKMRDIAGQALAFVQDLVTALLNFHTYTEQRIQIFPVDSAIDTISPLNQKFSQYLHENASYVRPLEE GMLHLFESITEDTVTVLETTVKLKTFSEHLTSYICFLRKILPYQLKSLEEECESSLCTSALRARNLELSQDMKKMTAVFE KLQTYIALLALPSTEPDGLLRTNYSSVLTNVGAALHGFHDVMKDISKHYSQKAAIEHELPTATQKLITTNDCILSSVVAL TNGAGKIASFFSNNLDYFIASLSYGPKAASGFISPLSAECMLQYKKKAAAYMKSLRKPLLESVPYEEALANRRILLSSTE SREGLAQQVQQSLEKISKLEQEKEHWMLEAQLAKIKLEKENQRIADKLKNTGSAQLVGLAQENAAVSNTAGQDEATAKAV LEPIQSTSLIGTLTRTSDSEVPDVESREDLIKNHYMARIVELTSQLQLADSKSVHFYAECRALSKRLALAEKSKEALTEE MKLASQNISRLQDELTTTKRSYEDQLSMMSDHLCSMNETLSKQREEIDTLKMSSKGNSKKNKSR Q6ZMI0 Quinone oxidoreductase-like protein 1 Homo sapiens 0.03966141399999999
N-terminal His-6 tag
2 Escherichia coli BL21(DE3) LEVO MSHHHHHHKGLYFQQSSTDEEITFVFQEKEDLPVTEDNFVKLQVKACALSQINTKLLAEMKMKKDLFPVGREIAGIVLDV GSKVSFFQPDDEVVGILPLDSEDPGLCEVVRVHEHYLVHKPEKVTWTEAAGSIRDGVRAYTALHYLSHLSPGKSVLIMDG ASAFGTIAIQLAHHRGAKVISTACSLEDKQCLERFRPPIARVIDVSNGKVHVAESCLEETGGLGVDIVLDAGVRLYSKDD EPAVKLQLLPHKHDIITLLGVGGHWVTTEENLQLDPPDSHCLFLKGATLAFLNDEVWNLSNVQQGKYLCILKDVMEKLST GVFRPQLDEPIPLYEAKVSMEAVQKNQGRKKQVVQF O95825 1.-.-.- Glutamine amidotransferase-like class 1 domain-containing protein 1 Homo sapiens 0.024237488 4 Escherichia coli BL21(DE3) LEVO MSHHHHHHASERLPNRPACLLVASGAAEGVSAQSFLHCFTMASTAFNLQVATPGGKAMEFVDVTESNARWVQDFRLKAYA SPAKLESIDGARYHALLIPSCPGALTDLASSGSLARILQHFHSESKPICAVGHGVAALCCATNEDRSWVFDSYSLTGPSV CELVRAPGFARLPLVVEDFVKDSGACFSASEPDAVHVVLDRHLVTGQNASSTVPAVQNLLFLCGSRK Q8NB37 singleParticle particle 0.7 7.5 20.0 HEPES 250.0 NaCl 20.0 KCl 20.0 MgCl2 UltrAuFoil R1.2/1.3 GOLD 300 GLOW DISCHARGE AIR ETHANE 100 286 FEI VITROBOT MARK III
3s blotting time.
TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.6 2.8000000000000003 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K2 SUMMIT (4k x 4k) 1879 15.0 75.8 1 1800000
Ab initio 3D structure obtained with RVIPER of the SPHIRE software package
 C2 4.0 FSC 0.143 CUT-OFF SPHIRE 18300 MAXIMUM LIKELIHOOD SPHIRE MAXIMUM LIKELIHOOD SPHIRE SPHIRE
ISAC classification in SPHIRE
 emd_12273.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 285.12003 285.12003 285.12003 90.0 90.0 90.0 X Y Z -0.025887525 0.04872177 0.00011392889 0.0011070273 1.08 1.08 1.08 0.011 AUTHOR Cryo-EM structure of the FERRY complex core
To build the model for the (CRYZL1)2(PPP1r21)2(GATD1)4 core of the FERRY complex, the obtained crystal structures of CRYZL1 and GATD1 were initially fitted into the corresponding density using the rigid body fitting tool in Chimera. trRosetta, a de novo protein structure prediction algorithm that is based on direct energy minimization with restrained Rosetta, was used to obtain initial models for PPP1r21. The predicted model for the 6-helix bundle domain, containing residues 246 to 498, that matched our experimental density best was subsequently fitted similar as CRYZL1 and GATD1 using rigid body fit. Manual model building for the regions N- and C-terminal 6-helix bundle, which comprise residues 218 to 245 and 499 to 552, respectively, was further guided by secondary structure predictions of individual trRosetta runs for these regions, that include the vertical helix as well as the beginning of the two terminal coiled-coils of PPP1r21. With the resulting combined model, containing residues 2 to 349, 218 to 552 and 8 to 217 of CRYZL1, PPP1r21 and GATD1, respectively, a restrained refinement in PHENIX was performed. In the next step, the model was further refined using a combination of manual building in COOT and real-space refinement in PHENIX.
 emd_12273_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 264 264 264 0 0 0 264 264 264 285.12003 285.12003 285.12003 90.0 90.0 90.0 X Y Z -0.5211247 0.7053428 0.0008167816 0.016118886 1.08 1.08 1.08 AUTHOR L-AFTER filtered Cryo-EM density map of the FERRY complex core