2025-08-13 REL PDBe INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation em_admin _citation.journal_volume _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _em_admin.last_update PDBe PDBe 2025-04-15 2025-07-16 2025-07-16 2025-08-13 German Research Foundation (DFG) KU2531/2 Germany German Research Foundation (DFG) KU2531/6 Germany German Research Foundation (DFG) 496113311 Germany German Research Foundation (DFG) CRC 1348 A15 Germany German Research Foundation (DFG) CRC1430 A04 Germany German Research Foundation (DFG) INST 211/667-1 Germany Structure of the human RalGAP2 complex Rasche R Klink BU Gatsogiannis C Kuemmel D Complex, GTPase activating protein, RAL, Asn thumb GAP, RalGAP, SIGNALING PROTEIN Rasche R Klink BU Apken LH Michalke E Chen M Oeckinghaus A Gatsogiannis C Kummel D Structure and mechanism of the RalGAP tumor suppressor complex. Nat Commun UK 16 7002 7002 2025 40738882 doi:10.1038/s41467-025-61743-9 2041-1723 Rasche R Apken LH Titze S Michalke E Singh RK Oeckinghaus A Kummel D The GTPase kappa B-Ras is an essential subunit of the RalGAP tumor suppressor complex. J.Biol.Chem. US 301 110460 110460 2025 40619001 doi:10.1016/j.jbc.2025.110460 1083-351X 0071 JBCHA3 EMD-53418 consensus EM volume
consensus full length RalGAP2 complex map
 EMD-53419 focused EM volume
body1: alpha2 beta heterodimer interface
 EMD-53420 focused EM volume
alpha2 N-terminus
 EMD-53421 focused EM volume
beta-beta homodimer interface
 9qwp FULLOVERLAP EMDB EMD-53418 consensus EM volume
consensus full length RalGAP2 complex map
 EMDB EMD-53419 focused EM volume
body1: alpha2 beta heterodimer interface
 EMDB EMD-53420 focused EM volume
alpha2 N-terminus
 EMDB EMD-53421 focused EM volume
beta-beta homodimer interface
 EMDB EMD-53422 associated EM volume
Structure of the human RalGAP2 complex
 Homodimer of two RalGAPa2-RalGAPb heterodimers Homodimer of two RalGAPa2-RalGAPb heterodimers 0 1 2
Co-expression of RalGAP subunit alpha2 and beta
Homo sapiens 0.17 RalGAP subunit alpha2 1 1 Homo sapiens RalGAP subunit beta 1 2 Homo sapiens Ral GTPase-activating protein subunit alpha-2 Homo sapiens 0.214046469
N-terminal 3xFLAG tag MDYKDHDGDYKDHDIDYKDDDDKLAAA
2 Homo sapiens LEVO MDYKDHDGDYKDHDIDYKDDDDKLAAAFSRRSHGDVKKSTQKVLDPKKDVLTRLKHLRALLDNVDANDLKQFFETNYSQI YFIFYENFIALENSLKLKGNNKSQREELDSILFLFEKILQFLPERIFFRWHYQSIGSTLKKLLHTGNSIKIRCEGIRLFL LWLQALQTNCAEEQVLIFACLVPGFPAVMSSRGPCTLETLINPSPSVADVKIYPEEITPLLPAISGEKIAEDQTCFFLQI LLKYMVIQAASLEWKNKENQDTGFKFLFTLFRKYYLPHLFPSFTKLTNIYKPVLDIPHLRPKPVYITTTRDNENIYSTKI PYMAARVVFIKWIVTFFLEKKYLTATQNTKNGVDVLPKIIQTVGGGAVQERAPELDGGGPTEQDKSHSNSSTLSDRRLSN SSLCSIEEEHRMVYEMVQRILLSTRGYVNFVNEVFHQAFLLPSCEIAVTRKVVQVYRKWILQDKPVFMEEPDRKDVAQED AEKLGFSETDSKEASSESSGHKRSSSWGRTYSFTSAMSRGCVTEEENTNVKAGVQALLQVFLTNSANIFLLEPCAEVPVL LKEQVDACKAVLIIFRRMIMELTMNKKTWEQMLQILLRITEAVMQKPKDKQIKDLFAQSLAGLLFRTLMVAWIRANLCVY ISRELWDDFLGVLSSLTEWEELINEWANIMDSLTAVLARTVYGVEMTNLPLDKLSEQKEKKQRGKGCVLDPQKGTTVGRS FSLSWRSHPDVTEPMRFRSATTSGAPGVEKARNIVRQKATEVEECQQSENAPAAGSGHLTVGQQQQVLRSSSTSDIPEPL CSDSSQGQKAENTQNSSSSEPQPIQENKGHVKREHEGITILVRRSSSPAELDLKDDLQQTQGKCRERQKSESTNSDTTLG CTNEAELSMGPWQTCEEDPELNTPTDVVADADARHWLQLSPTDASNLTDSSECLTDDCSIIAGGSLTGWHPDSAAVLWRR VLGILGDVNNIQSPKIHARVFCYLYELWYKLAKIRDNLAISLDNQSSPSPPVLIPPLRMFASWLFKAATLPNEYKEGKLQ AYRLICAMMTRRQDVLPNSDFLVHFYLVMHLGLTSEDQDILNTIIRHCPPRFFSLGFPGFSMLVGDFITAAARVLSTDIL TAPRSEAVTVLGSLVCFPNTYQEIPLLQSVPEVNEAITGTEDVKHYLINILLKNATEEPNEYARCIAVCSLGVWICEELA QCTSHPQVKEAINVIGVTLKFPNKIVAQVACDVLQLLVSYWEKLQMFETSLPRKMAEILVATVAFLLPSAEYSSVETDKK FIVSLLLCLLDWCMALPVSVLLHPVSTAVLEEQHSARAPLLDYIYRVLHCCVCGSSTYTQQSHYILTLADLSSTDYDPFL PLANVKSSEPVQYHSSAELGNLLTVEEEKKRRSLELIPLTARMVMAHLVNHLGHYPLSGGPAILHSLVSENHDNAHVEGS ELSFEVFRSPNLQLFVFNDSTLISYLQTPTEGPVGGSPVGSLSDVRVIVRDISGKYSWDGKVLYGPLEGCLAPNGRNPSF LISSWHRDTFGPQKDSSQVEEGDDVLDKLLENIGHTSPECLLPSQLNLNEPSLTPCGMNYDQEKEIIEVILRQNAQEDEY IQSHNFDSAMKVTSQGQPSPVEPRGPFYFCRLLLDDLGMNSWDRRKNFHLLKKNSKLLRELKNLDSRQCRETHKIAVFYI AEGQEDKCSILSNERGSQAYEDFVAGLGWEVDLSTHCGFMGGLQRNGSTGQTAPYYATSTVEVIFHVSTRMPSDSDDSLT KKLRHLGNDEVHIVWSEHSRDYRRGIIPTAFGDVSIIIYPMKNHMFFIAITKKPEVPFFGPLFDGAIVSGKLLPSLVCAT CINASRAVKCLIPLYQSFYEERALYLEAIIQNHREVMTFEDFAAQVFSPSPSYSLSGTD Q2PPJ7 Ral GTPase-activating protein subunit beta Homo sapiens 0.17079640599999998
N-terminal 3xHA tag MYPYDVPDYAGSYPYDVPDYAGSYPYDVPDYAGS
2 Homo sapiens LEVO MYPYDVPDYAGSYPYDVPDYAGSYPYDVPDYAGSMYSEWRSLHLVIQNDQGHTSVLHSYPESVGREVANAVVRPLGQVLG TPSVAGSENLLKTDKEVKWTMEVICYGLTLPLDGETVKYCVDVYTDWIMALVLPKDSIPLPVIKEPNQYVQTILKHLQNL FVPRQEQGSSQIRLCLQVLRAIQKLARESSLMARETWEVLLLFLLQINDILLAPPTVQGGIAENLAEKLIGVLFEVWLLA CTRCFPTPPYWKTAKEMVANWRHHPAVVEQWSKVICALTSRLLRFTYGPSFPAFKVPDEDASLIPPEMDNECVAQTWFRF LHMLSNPVDLSNPAIISSTPKFQEQFLNVSGMPQELNQYPCLKHLPQIFFRAMRGISCLVDAFLGISRPRSDSAPPTPVN RLSMPQSAAVSTTPPHNRRHRAVTVNKATMKTSTVSTAHASKVQHQTSSTSPLSSPNQTSSEPRPLPAPRRPKVNSILNL FGSWLFDAAFVHCKLHNGINRDSSMTAITTQASMEFRRKGSQMSTDTMVSNPMFDASEFPDNYEAGRAEACGTLCRIFCS KKTGEEILPAYLSRFYMLLIQGLQINDYVCHPVLASVILNSPPLFCCDLKGIDVVVPYFISALETILPDRELSKFKSYVN PTELRRSSINILLSLLPLPHHFGTVKSEVVLEGKFSNDDSSSYDKPITFLSLKLRLVNILIGALQTETDPNNTQMILGAM LNIVQDSALLEAIGCQMEMGGGENNLKSHSRTNSGISSASGGSTEPTTPDSERPAQALLRDYALNTDSAAGLLIRSIHLV TQRLNSQWRQDMSISLAALELLSGLAKVKVMVDSGDRKRAISSVCTYIVYQCSRPAPLHSRDLHSMIVAAFQCLCVWLTE HPDMLDEKDCLKEVLEIVELGISGSKSKNNEQEVKYKGDKEPNPASMRVKDAAEATLTCIMQLLGAFPSPSGPASPCSLV NETTLIKYSRLPTINKHSFRYFVLDNSVILAMLEQPLGNEQNDFFPSVTVLVRGMSGRLAWAQQLCLLPRGAKANQKLFV PEPRPVPKNDVGFKYSVKHRPFPEEVDKIPFVKADLSIPDLHEIVTEELEERHEKLRSGMAQQIAYEIHLEQQSEEELQK RSFPDPVTDCKPPPPAQEFQTARLFLSHFGFLSLEALKEPANSRLPPHLIALDSTIPGFFDDIGYLDLLPCRPFDTVFIF YMKPGQKTNQEILKNVESSRTVQPHFLEFLLSLGWSVDVGRHPGWTGHVSTSWSINCCDDGEGSQQEVISSEDIGASIFN GQKKVLYYADALTEIAFVVPSPVESLTDSLESNISDQDSDSNMDLMPGILKQPSLTLELFPNHTDNLNSSQRLSPSSRMR KLPQGRPVPPLGPETRVSVVWVERYDDIENFPLSELMTEISTGVETTANSSTSLRSTTLEKEVPVIFIHPLNTGLFRIKI QGATGKFNMVIPLVDGMIVSRRALGFLVRQTVINICRRKRLESDSYSPPHVRRKQKITDIVNKYRNKQLEPEFYTSLFQE VGLKNCSS Q86X10 singleParticle particle 0.7 7.5 20.0 C8H18N2O4S HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) 150.0 NaCl sodium chloride 2.0 MgCl2 magnesium chloride 1.0 C9H15O6P TCEP (tris(2-carboxyethyl)phosphine) Quantifoil R2/1 COPPER 300 GLOW DISCHARGE AIR 0.01 ETHANE 100 286 FEI VITROBOT MARK IV
double blotting.
Co-expression of RalGAP alpha2 and beta Monodisperse sample from size exclusion chromatography
 TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 50.0 2.7 0.5 4.2 215000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN TFS Selectris X 10 FEI FALCON IV (4k x 4k) 4096 4096 4 64606 3.2 60.0
Images were collected in EER mode with 793-819 fractions were generated for motion correction. Micrographs were collected at 0, 10 and 30 degree tilt, in 5 subsets of data.
 1 5519589 RELION 5 PHASE FLIPPING AND AMPLITUDE CORRECTION A model of the RGalpha2/RGbeta complex was calculated using AlphaFold2 1 C1 FOURIER SPACE 3.8 FSC 0.143 CUT-OFF RELION 5 420975 MAXIMUM LIKELIHOOD RELION 5 MAXIMUM LIKELIHOOD RELION 5 4 221930.0 RELION 5 emd_53422.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 417.59998 417.59998 417.59998 90.0 90.0 90.0 Z Y X -27.712185000000002 56.165095999999998 0.0019600154 1.0653441 1.16 1.16 1.16 9.130000000000001 AUTHOR Composite cryo EM map of the human RalGAP2 complex AlphaFold in silico model AB INITIO MODEL
A model of the RGalpha2/RGbeta complex was calculated using AlphaFold2 running on a local high performance computing cluster (PALMA II), docked into map from 3D reconstruction with ChimeraX and energy optimized with ISOLDE. In an iterative process, the model was optimized using real space refinement in Phenix Refine against the full density map, and manual model building with Coot using the full density map as well as the resampled multi body refinement maps.
cross correlation REAL 129.719999999999999