2026-04-29 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY PDBj PDBj 2025-04-29 2026-04-29 2026-04-29 2026-04-29 Other government 32100963 China Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a Jiao HZ Sang XH Huang ZW Hu HL CXC motif chemokine receptor 4, agonist, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex Sang X Jiao H Meng Q Fang X Sundaram KS Zhou J Xu Y Alvarado AIW Nuryyev RL Ourenik J Ourednik V Huang IS Liu X Mei Y Qian T Ciechanover A Pizzo DP Lane MA Zholudeva LV An J Snyder EY Hu H Huang Z The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS. Biorxiv US 2025 40672153 doi:10.1101/2025.07.08.663251 2692-8205 9upu FULLOVERLAP EMDB EMD-64402 associated EM volume
Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
 SDV1a-CXCR4-DNGi-scFv16 SDV1a-CXCR4-DNGi-scFv16 0 1 2 3 4 5 6 Homo sapiens Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 Homo sapiens 0.042005894999999994 1 Spodoptera frugiperda LEVO HHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIY AMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSREL AGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCR QTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDA LKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGASGASGASGASVSGWRLFKKIS P62873 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 Homo sapiens 0.007861143 1 Spodoptera frugiperda LEVO MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFREKKFFCAIL P59768 Guanine nucleotide-binding protein G(i) subunit alpha-1 Homo sapiens 0.040445059 1 Spodoptera frugiperda LEVO MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQS IIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLD RIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIY THFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF P63096 single-chain variable fragment scFv16 Homo sapiens 0.027784896 1 Spodoptera frugiperda LEVO DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLF LQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG AGTKLELKAAAHHHHHHHH Stromal cell-derived factor 1 Homo sapiens 0.0009511219999999999 1 LEVO KPVSLSYR P48061 Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase catalytic subunit Oplophorus gracilirostris 0.072689641 1 Spodoptera frugiperda LEVO MKTIIALSYIFCLVFADYKDDDDKGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPD SPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLLVPRGSMEGISIYTSDNYTEEMGSGDYD SMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW YFGNFLCKAVHVIYTVSLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADD RYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISID SFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVST ESESSSFHSSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKIDIHVIIPYEGLSADQ MAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSM LFRVTINS P0ABE7 P61073 Q9GV45 1.13.12.13 CHOLESTEROL 0.000386654 1 CLR singleParticle particle 7.5 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 1.2 1.8 GIF Bioquantum 20 GATAN K3 (6k x 4k) 54.2 1 PHASE FLIPPING AND AMPLITUDE CORRECTION 2.8 FSC 0.143 CUT-OFF cryoSPARC 211499 RANDOM ASSIGNMENT PROJECTION MATCHING emd_64402.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 272.0 272.0 272.0 90.0 90.0 90.0 Z Y X -17.170652 57.102989999999998 -0.000000000001072 1.0 0.85 0.85 0.85 7.0 AUTHOR optimized by Locscale2.0 and sharpened by phenix.autosharpen emd_64402_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 272.0 272.0 272.0 90.0 90.0 90.0 X Y Z -0.47850084 0.8795322 -0.0007451521 0.0201647 0.85 0.85 0.85 AUTHOR emd_64402_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 272.0 272.0 272.0 90.0 90.0 90.0 X Y Z -0.62468815 0.98962563 0.000118007694 0.07870629 0.85 0.85 0.85 AUTHOR emd_64402_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 272.0 272.0 272.0 90.0 90.0 90.0 X Y Z -0.65784335 0.9226206 0.00012070814 0.07878989 0.85 0.85 0.85 AUTHOR