Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist

2026-09-09 REL PDBj INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_ASTM _citation.journal_id_CSD _citation.journal_id_ISSN _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update DATABASE_REFERENCES citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.journal_volume _citation.page_first _citation.page_last _citation_author.identifier_ORCID _citation_author.name _em_admin.last_update PDBj PDBj 2026-01-26 2026-04-22 2026-04-22 2026-09-09 Science and Engineering Research Board (SERB) IPA/2020/000405 India Wellcome Trust IA/S/20/1/504916 United Kingdom Science and Engineering Research Board (SERB) CRG/2022/002646 India Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist Banerjee R Ganguly M Banerjee N Tiwari D Muratspahic E Baker D Shukla AK GPCR, G protein, SIGNALING PROTEIN, SIGNALING PROTEIN-IMMUNE SYSTEM complex Muratspahic E Feldman D Kim DE Qu X Bratovianu AM Rivera-Sanchez P Voss JH Hertz EPT Jeppesen M Dimitri F Sakamoto K Nallathambi A Peceli P Cao J Cary BP Belousoff MJ Keov P Trinh PNH Chen Q Ren Y Fine J Mishra S Dalal A Sinha S Banerjee R Ganguly M Karuppusamy KV Sappington I Schlichthaerle T Zhang JZ Pillai A Coventry B Mihaljevic L Bauer MS Torres SV Motmaen A Lee GR Tran L Wang X Goreshnik I Vafeados DK Svendsen JE Hosseinzadeh P Lindegaard N Brandt M Waltenspuhl Y Deibler K Deweid L Bennett A Schoppe J Dong T Yan X Oostdyk L Cao W Anantharaman L Weisser JJ Bastlund JF Bundgaard C Asuni AA English JG Stewart LJ Halloran L Spangler JB Lieber A Shukla AK Sexton PM Roth BL Krumm BE Wootten D Tate CG Norn C Baker D De novo design of miniproteins targeting GPCRs. Nature UK 656 1044 1053 2026 42168559 doi:10.1038/s41586-026-10656-8 1476-4687 0006 NATUAS 22xc FULLOVERLAP EMDB EMD-68747 associated EM volume

Structure of CXCR4 in complex with a synthetic protein antagonist, dCX001

C-X-C chemokine receptor type 4 in complex with dCX001 C-X-C chemokine receptor type 4 in complex with dCX001 0 1 2 Homo sapiens C-X-C chemokine receptor type 4 / CXCR4 1 2 dCX001 binder antagonist 1 1 dCX001 binder antagonist synthetic construct 0.009994728999999999 3 Escherichia coli LEVO MSGMVLKAVSMPTGIYSKLKKEYGEEIEKKAKELGVKISYGYRNGEMLIGFSGKKEEVDKLVKYVKKIVTEISRKRNGSL EHHHHHH C-X-C chemokine receptor type 4 Homo sapiens 0.04568885899999999 3 Spodoptera frugiperda LEVO MGKTIIALSYIFCLVFADYKDDDDAANFTPVNGSSGNQSVRLVTSSSLEVLFQGPGSEGISIYTSDNYTEEMGSGDYDSM KEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYF GNFLCKAVHVIYTVNLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRY ICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSF ILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTES ESSSFHSS P61073 CHOLESTEROL 0.000386654 3 CLR (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate 0.0006749289999999999 3 D21 singleParticle particle 7.4 ETHANE TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.8 1.8 GATAN K3 (6k x 4k) COUNTING 75.0 1 NONE 8U4S C3 3.28 FSC 0.143 CUT-OFF cryoSPARC 18396 MAXIMUM LIKELIHOOD MAXIMUM LIKELIHOOD emd_68747.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 271.35934 271.35934 271.35934 90.0 90.0 90.0 X Y Z -0.120801084 1.2735469 0.017532445 0.017906358 0.94222 0.94222 0.94222 0.1 AUTHOR ::::EMDATABANK.org::::EMD-68747:::: FLEXIBLE FIT REAL emd_68747_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 271.35934 271.35934 271.35934 90.0 90.0 90.0 X Y Z -0.36578998 0.55330056 0.00039377232 0.030892067 0.94222 0.94222 0.94222 AUTHOR ::::EMDATABANK.org::::EMD-68747:::: emd_68747_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 288 288 288 0 0 0 288 288 288 271.35934 271.35934 271.35934 90.0 90.0 90.0 X Y Z -0.37771523 0.52452207 0.00038454012 0.030900346 0.94222 0.94222 0.94222 AUTHOR ::::EMDATABANK.org::::EMD-68747::::