2024-05-01 REL PDBe PDBe PDBe 2020-10-22 2020-12-02 2020-12-02 2024-05-01 Austrian Science Fund P33367 Austria Structure of the actin filament Arp2/3 complex branch junction in cells Faessler F Dimchev G Actin, Arp2-3 complex, Cytoskeleton, STRUCTURAL PROTEIN Fassler F Dimchev G Hodirnau VV Wan W Schur FKM Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nat Commun UK 11 6437 6437 2020 33353942 doi:10.1038/s41467-020-20286-x 2041-1723 EMD-11870 other EM volume
D_1292111823 contains a representative tomogram associated with this entry
 7aqk FULLOVERLAP Actin Filament Arp2/3 Complex Branch Junction Actin Filament Arp2/3 Complex Branch Junction 0 1 2 3 4 5 6 7 8
Structure obtained from the actin network of extracted and fixed mouse fibroblast lamellipodia
Mus musculus Actin-related protein 2, Arp2 Mus musculus 0.044818711000000004
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MDSQGRKVVVCDNGTGFVKCGYAGSNFPEHIFPALVGRPIIRSTTKVGNIEIKDLMVGDEASELRSMLEVNYPMENGIVR NWDDMKHLWDYTFGPEKLNIDTRNCKILLTEPPMNPTKNREKIVEVMFETYQFSGVYVAIQAVLTLYAQGLLTGVVVDSG DGVTHICPVYEGFSLPHLTRRLDIAGRDITRYLIKLLLLRGYAFNHSADFETVRMIKEKLCYVGYNIEQEQKLALETTVL VESYTLPDGRIIKVGGERFEAPEALFQPHLINVEGVGVAELLFNTIQAADIDTRSEFYKHIVLSGGSTMYPGLPSRLERE LKQLYLERVLKGDVEKLSKFKIRIEDPPRRKHMVFLGGAVLADIMKDKDNFWMTRQEYQEKGVRVLEKLGVTVR Actin-related protein 3, Arp3 Mus musculus 0.047428031
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEKPTYATKWPIRH GIVEDWDLMERFMEQVIFKYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNVPGLYIAVQAVLALAASWTSRQVGE RTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVK EFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERFLGPEIFFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIV LSGGSTMFRDFGRRLQRDLKRTVDARLKLSEELSGGRLKPKPIDVQVITHHMQRYAVWFGGSMLASTPEFYQVCHTKKDY EEIGPSICRHNPVFGVMS Actin-related protein 2/3 complex subunit 1b, ArpC1b Mus musculus 0.041016738
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MAYHSFLVEPISCHAWNKDRTQIAICPNNHEVHIYEKSGNKWVQVHELKEHNGQVTGVDWAPDSNRIVTCGTDRNAYVWT LKGRTWKPTLVILRINRAARCVRWAPNEKKFAVGSGSRVISICYFEQENDWWVCKHIKKPIRSTVLSLDWHPNSVLLAAG SCDFKCRIFSAYIKEVEERPAPTPWGSKMPFGELMFESSSSCGWVHGVCFSANGSRVAWVSHDSTVCLADADKKMAVATL ASETLPLLAVTFITESSLVAAGHDCFPVLFTYDSAAGKLSFGGRLDVPKQSSQRGLTARERFQNLDKKASSEGSAAAGAG LDSLHKNSVSQISVLSGGKAKCSQFCTTGMDGGMSIWDVRSLESALKDLKIV Actin-related protein 2/3 complex subunit 2, ArpC2 Mus musculus 0.03440204299999999
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MILLEVNNRIIEETLALKFENAAAGNKPEAVEVTFADFDGVLYHISNPNGDKTKVMVSISLKFYKELQAHGADELLKRVY GSYLVNPESGYNVSLLYDLENLPASKDSIVHQAGMLKRNCFASVFEKYFQFQEEGKEGENRAVIHYRDDETMYVESKKDR VTVVFSTVFKDDDDVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTNASARDNT INLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTITGKTFSSR Actin-related protein 2/3 complex subunit 3, ArpC3 Mus musculus 0.020572666
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MPAYHSSLMDPDTKLIGNMALLPIRSQFKGPAPRETKDTDIVDEAIYYFKANVFFKNYEIKNEADRTLIYITLYISECLK KLQKCNSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQLRQETGLRLCEKVFDPQNDKPSKWW TCFVKRQFMNKSLSGPGQ Actin-related protein 2/3 complex subunit 4, ArpC4 Mus musculus 0.019697047
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MTATLRPYLSAVRATLQAALCLENFSSQVVERHNKPEVEVRSSKELLLQPVTISRNEKEKVLIEGSINSVRVSIAVKQAD EIEKILCHKFMRFMMMRAENFFILRRKPVEGYDISFLITNFHTEQMYKHKLVDFVIHFMEEIDKEISEMKLSVNARARIV AEEFLKNF Actin-related protein 2/3 complex subunit 5, ArpC5 Mus musculus 0.016295316999999997
As models derived from Bos taurus Arp2/3 complexes have been used for fitting, also the Bos taurus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
1 LEVO MSKNTVSSARFRKVDVDEYDENKFVDEDDGGDGQAGPDEGEVDSCLRQGNMTAALQAALKNPPINTKSQAVKDRAGSIVL KVLISFKANDIEKAVQSLDKNGVDLLMKYIYKGFESPSDNSSAVLLQWHEKALAAGGVGSIVRVLTARKTV Actin, alpha skeletal muscle, ACTA1 Mus musculus 0.042096953
As models derived from Oryctolagus cuniculus actin have been used for fitting, also the Oryctolagus cuniculus sequence (as well as the corresponding UniProt identifier) is given here, even though they were fit into a mouse structure.
11 LEVO MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITN WDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDG VTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEIT ALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF subtomogramAveraging cell 6.1 10.0 MES 150.0 sodium chloride 5.0 EGTA 5.0 Glucose 5.0 Magnesium chloride
Adjust to pH 6.1 using NaOH
 Quantifoil R2/2 GOLD 200 CARBON HOLEY GLOW DISCHARGE AIR
After glow discharging of the grid and prior to the seeding of cells, the grid was coated using 25ug/ml Fibronectin
 ETHANE 80 277
Leica GP2, 3,5sec back-blotting, sensor on, 0,1mm movement after contact, manually pre-blotted within the chamber prior to the application of fiducials.
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 -0.00175 -0.0055 42000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN GIF Bioquantum 20 GATAN K3 BIOQUANTUM (6k x 4k) 1.21 2.79
Images were collected in movie-mode at 7 frames per tilt
 1 1 C1 9.0 FSC 0.143 CUT-OFF RELION 3.0.9
Final reconstruction in RELION was performed after Multiple particle refinement in M version 1.0.9.
14296 131 39300 Reference generated from manually selected particles Template Matching Dynamo 1.133 Warp 1.07
After first classification in Dynamo and re-extraction in Warp 17,146 subvolumes remained.
 1 14296.0 RELION 3.0.9 MAXIMUM LIKELIHOOD RELION 3.0.9
Multiple particle refinement in M version 1.0.9 was performed after 3D Refinement in RELION.
 emd_11869.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 512.88 512.88 512.88 90.0 90.0 90.0 X Y Z -0.0034114548 0.014956028 0.0000346011 0.00058454473 2.137 2.137 2.137 0.00404 AUTHOR Structure of the actin filament Arp2/3 complex branch junction 1TYQ A 2-39 PDB experimental model 1TYQ A 52-353 PDB experimental model 1TYQ A 360-418 PDB experimental model 1TYQ B 151-345 PDB experimental model 1TYQ C 1-288 PDB experimental model 1TYQ C 319-372 PDB experimental model 1TYQ D 1-208 PDB experimental model 1TYQ D 217-281 PDB experimental model 1TYQ E 2-150 PDB experimental model 1TYQ E 155-174 PDB experimental model 1TYQ F 3-168 PDB experimental model 1TYQ G 36-151 PDB experimental model 4JD2 B 4-150 PDB experimental model 4JD2 B 346-387 PDB experimental model 1K8K C 297-309 PDB experimental model 6T20 A 5-375 PDB experimental model 6T20 B 5-375 PDB experimental model 6T20 C 5-375 PDB experimental model 6T20 D 5-375 PDB experimental model 6T20 E 5-375 PDB experimental model FLEXIBLE FIT REAL emd_11869_msk_1.map emd_11869_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 512.88 512.88 512.88 90.0 90.0 90.0 X Y Z -0.02197018 0.025533509 0.000035110188 0.002866008 2.137 2.137 2.137 AUTHOR Half map 1 emd_11869_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 240 240 240 0 0 0 240 240 240 512.88 512.88 512.88 90.0 90.0 90.0 X Y Z -0.022162538 0.024147235 0.000034091987 0.0028456938 2.137 2.137 2.137 AUTHOR Half map 2