Structure of alpha6beta1 integrin in complex with laminin-511

2024-10-16 REL PDBj PDBj PDBj 2020-06-22 2021-06-23 2021-06-23 2024-10-16 Japan Society for the Promotion of Science (JSPS) 18H02389 Japan Japan Agency for Medical Research and Development (AMED) 19am0101075 Japan Structure of alpha6beta1 integrin in complex with laminin-511 Arimori T Miyazaki N Integrin, Laminin, Fv-clasp, CELL ADHESION, CELL ADHESION-IMMUNE SYSTEM complex Arimori T Miyazaki N Mihara E Takizawa M Taniguchi Y Cabanas C Sekiguchi K Takagi J Structural mechanism of laminin recognition by integrin. Nat Commun UK 12 4012 4012 2021 34188035 doi:10.1038/s41467-021-24184-8 2041-1723 7cec FULLOVERLAP Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp Quaternary complex of alpha6beta1 integrin, laminin-511, TS2/16 Fv-clasp, and HUTS-4 Fv-clasp 0 1 2 3 4 5 6 7 8 9 Homo sapiens 0.286 Integrin alpha-6 Homo sapiens 0.06977602299999999 1 Homo sapiens LEVO FNLDTREDNVIRKYGDPGSLFGFSLAMHWQLQPEDKRLLLVGAPRAEALPLQRANRTGGLYSCDITARGPCTRIEFDNDA DPTSESKEDQWMGVTVQSQGPGGKVVTCAHRYEKRQHVNTKQESRDIFGRCYVLSQNLRIEDDMDGGDWSFCDGRLRGHE KFGSCQQGVAATFTKDFHYIVFGAPGTYNWKGIVRVEQKNNTFFDMNIFEDGPYEVGGETEHDESLVPVPANSYLGFSLD SGKGIVSKDEITFVSGAPRANHSGAVVLLKRDMKSAHLLPEHIFDGEGLASSFGYDVAVVDLNKDGWQDIVIGAPQYFDR DGEVGGAVYVYMNQQGRWNNVKPIRLNGTKDSMFGIAVKNIGDINQDGYPDIAVGAPYDDLGKVFIYHGSANGINTKPTQ VLKGISPYFGYSIAGNMDLDRNSYPDVAVGSLSDSVTIFRSRPVINIQKTITVTPNRIDLRQKTACGAPSGICLQVKSCF EYTANPAGYNPSISIVGTLEAEKERRKSGLSSRVQFRNQGSEPKYTQELTLKRQKQKVCMEETLWLQDNIRDKLRPIPIT ASVEIQEPSSRRRVNSLPEVLPILNSDEPKTAHIDVHFLKEGCGDDNVCNSNLKLEYKGSLENLYFQ P23229 Integrin beta-1 Homo sapiens 0.050510929999999996 1 Homo sapiens LEVO QTDENRCLKANAKSCGECIQAGPNCGWCTNSTFLQEGMPTSARCDDLEALKKKGCPPDDIENPRGSKDIKKNKNVTNRSK GTAEKLKPEDITQIQPQQLVLRLRSGEPQTFTLKFKRAEDYPIDLYYLMDLSYSMKDDLENVKSLGTDLMNEMRRITSDF RIGFGSFVEKTVMPYISTTPAKLRNPCTSEQNCTSPFSYKNVLSLTNKGEVFNELVGKQRISGNLDSPEGGFDAIMQVAV CGSLIGWRNVTRLLVFSTDAGFHFAGDGKLGGIVLPNDGQCHLENNMYTMSHYYDYPSIAHLVQKLSENNIQTIFAVTEE FQPVYKELKNLIPKSAVGTLSANSSNVIQLIIDAYNSLSSEVILENGKLSEGVTISYKSYCKNGVNGTGENGRKCSNISI GDEVQFEISITSNKCPKKDSDSFKIRPLGFTEEVEVILQYICECEGGLENLYFQ P05556 Laminin subunit alpha-5 Homo sapiens 0.073414203 1 Homo sapiens LEVO GENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKV KVPMKFNGRSGVQLRTPRDLADLAAYTALKFYLQGPEPEPGQGTEDRFVMYMGSRQATGDYMGVSLRDKKVHWVYQLGEA GPAVLSIDEDIGEQFAAVSLDRTLQFGHMSVTVERQMIQETKGDTVAPGAEGLLNLRPDDFVFYVGGYPSTFTPPPLLRF PGYRGCIEMDTLNEEVVSLYNFERTFQLDTAVDRPCARSKSTGDPWLTDGSYLDGTGFARISFDSQISTTKRFEQELRLV SYSGVLFFLKQQSQFLCLAVQEGSLVLLYDFGAGLKKAVPLQPPPPLTSASKAIQVFLLGGSRKRVLVRVERATVYSVEQ DNDLELADAYYLGGVPPDQLPPSLRRLFPTGGSVRGCVKGIKALGKYVDLKRLNTTGVSAGCTADLLVGRAMTFHGHGFL RLALSNVAPLTGNVYSGFGFHSAQDSALLYYRASPDGLCQVSLQQGRVSLQLLRTEVKTQAGFADGAPHYVAFYSNATGV WLYVDDQLQQMKPHRGPPPELQPQPEGPPRLLLGGLPESGTIYNFSGCISNVFVQRLLGPQRVFDLQQNLGSVNVSTGCA PALQAQTPGLGPRGLQATARKASRRSRQPARHPA O15230 Laminin subunit beta-1 Homo sapiens 0.008552753 1 Homo sapiens LEVO GDARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCL P07942 Laminin subunit gamma-1 Homo sapiens 0.009483723999999999 1 Homo sapiens LEVO GDTVDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCFNTPSI EKP P11047 TS2/16 VH(S112C)-SARAH,TS2/16 VH(S112C)-SARAH Homo sapiens 0.019463991999999996

chimera of TS2/16 VH(S112C)-SARAH

1 Escherichia coli LEVO MDVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVATISSGGSYTYYPDSVKGRFTISRDKAKNTL YLQMGSLKSEDTAMYYCTRIGYDEDYAMDHWGQGTSVTVCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQS KRQPILDAIEAK TS2/16 VL-SARAH(S37C),TS2/16 VL-SARAH(S37C) Homo sapiens 0.018270741999999996

chimera of TS2/16 VL-SARAH(S37C)

1 Escherichia coli LEVO GSHMQIVVTQRPTTMAASPGDKIIITCSVSSIISSNYLHWYSQKPGFSPKLLIYRTSNLASGVPPRFSGSGSGTSYSLTI GTMEAEDVATYYCQQGSDIPLTFGDGTKLDLKRGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDA IEAK HUTS-4 VH(S112C)-SARAH,HUTS-4 VH(S112C)-SARAH Homo sapiens 0.019760207

chimera of HUTS-4 VH(S112C)-SARAH

1 Escherichia coli LEVO MQVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWLAHIYWDDDKRYHPSLKSRLTISKDTSSNQ VFLKITSVDTADTATYYCARSIYDGYYDYFDVWGAGTTVTVCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKY QSKRQPILDAIEAK HUTS-4 VL(C87Y)-SARAH(S37C),HUTS-4 VL(C87Y)-SARAH(S37C) Homo sapiens 0.017701023

chimera of HUTS-4 VL(C87Y)-SARAH(S37C)

1 Escherichia coli LEVO MQIVLSQSPAILSASPGEKVTMTCRATSSVTYMHWYQQKPGSSPKPWIYATSNLASGVPARFSGSGSGTSYSLTISRVEA ADAATYYCQQWTSNPPTFGGGTKLEIKRGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK CALCIUM ION 4.0078e-05 4 CA 2-acetamido-2-deoxy-beta-D-glucopyranose 0.000221208 6 NAG MANGANESE (II) ION 5.4938e-05 3 MN singleParticle particle 0.07 7.5 20.0 C4H11NO3 tris(hydroxymethyl)aminomethane 150.0 NaCl sodium chloride 1.0 MnCl2 manganese chloride 0.1 CaCl2 calcium chloride Quantifoil R2/1 MOLYBDENUM 300 CARBON CONTINUOUS GLOW DISCHARGE 30 ETHANE 100 277 FEI VITROBOT MARK IV FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 0.8 59000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN VOLTA PHASE PLATE FEI FALCON III (4k x 4k) INTEGRATING 4096 4096 1 7768 40.0 1 2660283 C1 3.9 FSC 0.143 CUT-OFF RELION 3.0 429521 MAXIMUM LIKELIHOOD RELION 3.0 MAXIMUM LIKELIHOOD RELION 3.0 4 130000.0 RELION 3.0 emd_30342.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 300 300 300 0 0 0 300 300 300 333.90002 333.90002 333.90002 90.0 90.0 90.0 X Y Z -0.054479014 0.15038915 0.00052672107 0.0049025496 1.113 1.113 1.113 0.05 AUTHOR ::::EMDATABANK.org::::EMD-30342::::