2024-10-23 REL PDBj PDBj PDBj 2016-06-29 2016-11-02 2017-01-18 2024-10-23 Three-dimensional reconstruction of human LRP6 ectodomain complexed with Dkk1 Matoba K Mihara E Wnt signaling, Wnt co-receptor, LRP6, glycoprotein, antagonist, Dkk1, conformational change, SIGNALING PROTEIN Matoba K Mihara E Tamura-Kawakami K Miyazaki N Maeda S Hirai H Thompson S Iwasaki K Takagi J Conformational Freedom of the LRP6 Ectodomain Is Regulated by N-glycosylation and the Binding of the Wnt Antagonist Dkk1 Cell Rep US 18 32 40 2017 28052259 doi:10.1016/j.celrep.2016.12.017 2211-1247 5gje FULLOVERLAP Human LRP6 ectodomain complexed with full length of Dkk1 Human LRP6 ectodomain complexed with full length of Dkk1 0 1 2 3
Human Dkk1 fused with human growth hormone at the N-terminal (hGH-Dkk1) was co-expressed with LRP6ec in the HEK293S GnT1- cells.
Homo sapiens 0.21 LRP6 ectodomain 1 1 2 Human Dickkopf-related protein1 1 3
N-terminal human growth hormone fused full length of Dkk1
 Low-density lipoprotein receptor-related protein 6 Homo sapiens 0.069034883 1 Cricetulus griseus LEVO APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTEFNKTESVQNVVVSGLLSPDG LACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQPRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINS EIYWPNGLTLDYEEQKLYWADAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLR EIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLENGKTCKDGATELLLLARRTDL RRISLDTPDFTDIVLQLEDIRHAIAIDYDPVEGYIYWTDDEVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYW TDTGTDRIEVTRLNGTMRKILISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGWPNGLALDY DEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQRRSIERVHKRSAEREVIIDQLPDLMGLK ATNVHRVIGSNPCAEENGGCSHLCLYRPQGLRCACPIGFELISDMKTCIVP O75581 Low-density lipoprotein receptor-related protein 6 Homo sapiens 0.069810609 1 Spodoptera frugiperda LEVO EAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGM AVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNV GRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQ GHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVID EQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYW TCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALD SRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSD IHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSCGEP O75581 Dickkopf-related protein 1 Homo sapiens 0.009607075999999999 1 Spodoptera frugiperda LEVO KGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGEGLSCRIQKDHHQASNSSRLH TCQRH O94907 PHOSPHATE ION 9.4971e-05 2 PO4 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 3 NAG GLYCEROL 9.209399999999999e-05 1 GOL water 1.8015e-05 13 HOH singleParticle particle 7.2 NONE Uranyl acetate COPPER 200 CARBON CONTINUOUS GLOW DISCHARGE
This sample was monodisperse.
 HITACHI H-9500SD SPOT SCAN BRIGHT FIELD LAB6 200 2.8 80000.0 SIDE ENTRY, EUCENTRIC TVIPS TEMCAM-F224 (2k x 2k) 2048 2048 2.0 20.0 1
The selected images were band-pass filtered.
10974 tilt pairs for RCT
 10974 C1 BACK PROJECTION 21.0 FSC 0.5 CUT-OFF SPIDER 5390 PROJECTION MATCHING 83 SPIDER
The projections generated from RCT were used for initial angle assignment
 PROJECTION MATCHING 83 SPIDER emd_9501.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 200 200 200 0 0 0 200 200 200 440.0 440.0 440.0 90.0 90.0 90.0 X Y Z -0.079741 1.0378006 0.00088656624 0.036129534 2.2 2.2 2.2 0.198 AUTHOR 4DG6 A 1-611 PDB experimental model 3S2K B 631-1243 PDB experimental model 3S2K C 182-266 PDB experimental model RIGID BODY FIT