2024-10-16 REL PDBe PDBe PDBe 2020-09-15 2020-12-02 2020-12-02 2024-10-16 German Research Foundation (DFG) SCHU 3196/1-1 Germany Max Planck Society Germany Cryo-EM structure of human ER membrane protein complex in lipid nanodiscs Braeuning B Prabu JR ER membrane protein, EMC, Membrane protein biogenesis, MEMBRANE PROTEIN Miller-Vedam LE Brauning B Popova KD Schirle Oakdale NT Bonnar JL Prabu JR Boydston EA Sevillano N Shurtleff MJ Stroud RM Craik CS Schulman BA Frost A Weissman JS Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. Elife US 9 2020 33236988 doi:10.7554/eLife.62611 2050-084X 7ado FULLOVERLAP Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs Human endoplasmic reticulum membrane protein complex (EMC) in POPC nanodiscs 0 1 2 3 4 5 6 7 8 9 10 Homo sapiens 0.3 ER membrane protein complex subunit 1 Homo sapiens 0.111886141 1 Homo sapiens LEVO MAAEWASRFWLWATLLIPAAAVYEDQVGKFDWRQQYVGKVKFASLEFSPGSKKLVVATEKNVIAALNSRTGEILWRHVDK GTAEGAVDAMLLHGQDVITVSNGGRIMRSWETNIGGLNWEITLDSGSFQALGLVGLQESVRYIAVLKKTTLALHHLSSGH LKWVEHLPESDSIHYQMVYSYGSGVVWALGVVPFSHVNIVKFNVEDGEIVQQVRVSTPWLQHLSGACGVVDEAVLVCPDP SSRSLQTLALETEWELRQIPLQSLDLEFGSGFQPRVLPTQPNPVDASRAQFFLHLSPSHYALLQYHYGTLSLLKNFPQTA LVSFATTGEKTVAAVMACRNEVQKSSSSEDGSMGSFSEKSSSKDSLACFNQTYTINLYLVETGRRLLDTTITFSLEQSGT RPERLYIQVFLKKDDSVGYRALVQTEDHLLLFLQQLAGKVVLWSREESLAEVVCLEMVDLPLTGAQAELEGEFGKKADGL LGMFLKRLSSQLILLQAWTSHLWKMFYDARKPRSQIKNEINIDTLARDEFNLQKMMVMVTASGKLFGIESSSGTILWKQY LPNVKPDSSFKLMVQRTTAHFPHPPQCTLLVKDKESGMSSLYVFNPIFGKWSQVAPPVLKRPILQSLLLPVMDQDYAKVL LLIDDEYKVTAFPATRNVLRQLHELAPSIFFYLVDAEQGRLCGYRLRKDLTTELSWELTIPPEVQRIVKVKGKRSSEHVH SQGRVMGDRSVLYKSLNPNLLAVVTESTDAHHERTFIGIFLIDGVTGRIIHSSVQKKAKGPVHIVHSENWVVYQYWNTKA RRNEFTVLELYEGTEQYNATAFSSLDRPQLPQVLQQSYIFPSSISAMEATITERGITSRHLLIGLPSGAILSLPKALLDP RRPEIPTEQSREENLIPYSPDVQIHAERFINYNQTVSRMRGIYTAPSGLESTCLVVAYGLDIYQTRVYPSKQFDVLKDDY DYVLISSVLFGLVFATMITKRLAQVKLLNRAWR Q8N766 ER membrane protein complex subunit 2 Homo sapiens 0.034882531 1 Homo sapiens LEVO MAKVSELYDVTWEEMRDKMRKWREENSRNSEQIVEVGEELINEYASKLGDDIWIIYEQVMIAALDYGRDDLALFCLQELR RQFPGSHRVKRLTGMRFEAMERYDDAIQLYDRILQEDPTNTAARKRKIAIRKAQGKNVEAIRELNEYLEQFVGDQEAWHE LAELYINEHDYAKAAFCLEELMMTNPHNHLYCQQYAEVKYTQGGLENLELSRKYFAQALKLNNRNMRALFGLYMSASHIA SNPKASAKTKKDNMKYASWAASQINRAYQFAGRSKKETKYSLKAVEDMLETLQITQS Q15006 ER membrane protein complex subunit 3 Homo sapiens 0.029981923999999997 1 Homo sapiens LEVO MAGPELLLDSNIRLWVVLPIVIITFFVGMIRHYVSILLQSDKKLTQEQVSDSQVLIRSRVLRENGKYIPKQSFLTRKYYF NNPEDGFFKKTKRKVVPPSPMTDPTMLTDMMKGNVTNVLPMILIGGWINMTFSGFVTTKVPFPLTLRFKPMLQQGIELLT LDASWVSSASWYFLNVFGLRSIYSLILGQDNAADQSRMMQEQMTGAAMAMPADTNKAFKTEWEALELTDHQWALDDVEEE LMAKDLHFEGMFKKELQTSIF Q9P0I2 ER membrane protein complex subunit 4 Homo sapiens 0.020104571999999998
There is no mutations but sequence from model and input are not aligning well.
1 Homo sapiens LEVO MTAQGGLVANRGRRFKWAIELSGPGGGSRGRSDRGSGQGDSLYPVGYLDKQVPDTSVQETDRILVEKRCWDIALGPLKQI PMNLFIMYMAGNTISIFPTMMVCMMAWRPIQALMAISATFKMLESSSQKFLQGLVYLIGNLMGLALAVYKCQSMGLLPTH ASDWLAFIEPPERMEFSGGGLLL Q5J8M3 Membrane magnesium transporter 1 Homo sapiens 0.015703762 1 Homo sapiens LEVO MAPSLWKGLVGIGLFALAHAAFSAAQHRSYMRLTEKEDESLPIDIVLQTLLAFAVTCYGIVHIAGEFKDMDATSELKNKT FDTLRNHPSFYVFNHRGRVLFRPSDTANSSNQDALSSNTSLKLRKLESLRRDYKDDDDK Q8N4V1 ER membrane protein complex subunit 6 Homo sapiens 0.012029248 1 Homo sapiens LEVO MAAVVAKREGPPFISEAAVRGNAAVLDYCRTSVSALSGATAGILGLTGLYGFIFYLLASVLLSLLLILKAGRRWNKYFKS RRPLFTGGLIGGLFTYVLFWTFLYGMVHVY Q9BV81 ER membrane protein complex subunit 7 Homo sapiens 0.026501585999999997 1 Homo sapiens LEVO MAAALWGFFPVLLLLLLSGDVQSSEVPGAAAEGSGGSGVGIGDRFKIEGRAVVPGVKPQDWISAARVLVDGEEHVGFLKT DGSFVVHDIPSGSYVVEVVSPAYRFDPVRVDITSKGKMRARYVNYIKTSEVVRLPYPLQMKSSGPPSYFIKRESWGWTDF LMNPMVMMMVLPLLIFVLLPKVVNTSDPDMRREMEQSMNMLNSNHELPDVSEFMTRLFSSKSSGKSSSGSSKTGKSGAGK RR Q9NPA0 ER membrane protein complex subunit 8 Homo sapiens 0.023807076
Map modelled as EMC8; both EMC8 and its paralog EMC9 (44% identity) were co-expressed and turns out they can both occupy same position on complex in mutually exclusive manner. We chose to model as EMC8 but note that map is likely superposition of both.
1 Homo sapiens LEVO MPGVKLTTQAYCKMVLHGAKYPHCAVNGLLVAEKQKPRKEHLPLGGPGAHHTLFVDCIPLFHGTLALAPMLEVALTLIDS WCKDHSYVIAGYYQANERVKDASPNQVAEKVASRIAEGFSDTALIMVDNTKFTMDCVAPTIHVYEHHENRWRCRDPHHDY CEDWPEAQRISASLLDSRSYETLVDFDNHLDDIRNDWTNPEINKAVLHLC O43402 ER membrane protein complex subunit 10 Homo sapiens 0.027446875 1 Homo sapiens LEVO MAAAASAGATRLLLLLLMAVAAPSRARGSGCRAGTGARGAGAEGREGEACGTVGLLLEHSFEIDDSANFRKRGSLLWNQQ DGTLSLSQRQLSEEERGRLRDVAALNGLYRVRIPRRPGALDGLEAGGYVSSFVPACSLVESHLSDQLTLHVDVAGNVVGV SVVTHPGGCRGHEVEDVDLELFNTSVQLQPPTTAPGPETAAFIERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMM SGAPDTGGQGGGGGGGGGGGSGR Q5UCC4 Unassigned helix Homo sapiens 0.0013796919999999999
This is transmembrane alpha-helix which was modeled as poly-alanine.
1 Homo sapiens LEVO (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 4 NAG 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE 0.0007871209999999999 5 PCW singleParticle particle 2 6.0
10 mM ammonium citrate pH 6.0, 100 mM sodium chloride, 0.25 mM TCEP
 Quantifoil R1.2/1.3 COPPER 300 PLASMA CLEANING ETHANE 100 277 FEI VITROBOT MARK III FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 GATAN K3 BIOQUANTUM (6k x 4k) 3.0 72.0 1 C1 3.39 FSC 0.143 CUT-OFF RELION cryoSPARC 177560 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_11732.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -1.1078776 2.3187323 -0.00031519795 0.054983426 0.8511999 0.8511999 0.8511999 0.36 AUTHOR Consensus map of hEMC in nanodiscs AB INITIO MODEL emd_11732_msk_1.map emd_11732_additional_4.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.8164965 1.8980675 -0.0007206715 0.05246959 0.8511999 0.8511999 0.8511999 AUTHOR Consensus map of hEMC in nanodiscs - subclassified on EMC7 lumenal domain. emd_11732_additional_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.04575734 0.10645637 0.00005677768 0.0015949854 0.8511999 0.8511999 0.8511999 AUTHOR Focused lumen map of hEMC in nanodiscs emd_11732_additional_3.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.07505329 0.13534804 0.00012042141 0.002011281 0.8511999 0.8511999 0.8511999 AUTHOR Sidesplitter map of hEMC in nanodiscs emd_11732_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.042767935 0.09585735 0.000035605204 0.001192094 0.8511999 0.8511999 0.8511999 AUTHOR Focused cytoplasm map of hEMC in nanodiscs emd_11732_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.7656558 1.5157886 0.0013924729 0.09491929 0.8511999 0.8511999 0.8511999 AUTHOR Consensus map of hEMC in nanodiscs - Halfmap 1 emd_11732_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 400 400 400 0 0 0 400 400 400 340.47998 340.47998 340.47998 90.0 90.0 90.0 X Y Z -0.7506482 1.4911425 0.0013902222 0.094902 0.8511999 0.8511999 0.8511999 AUTHOR Consensus map of hEMC in nanodiscs - Halfmap 2