Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

2024-10-23 REL PDBe PDBe PDBe 2021-04-13 2021-06-30 2021-06-30 2024-10-23 Swiss National Science Foundation 31-149927 Switzerland Swiss National Science Foundation 31-173089 Switzerland European Commission 6th Framework EMPRO European Union European Commission 7th Framework CHAARM European Union Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist Isaikina P Tsai C-J G protein-coupled receptor (GPCR); CCR5; CCL5/RANTES; HIV entry; AIDS; membrane protein structure;, MEMBRANE PROTEIN, SIGNALING PROTEIN Isaikina P Tsai CJ Dietz N Pamula F Grahl A Goldie KN Guixa-Gonzalez R Branco C Paolini-Bertrand M Calo N Cerini F Schertler GFX Hartley O Stahlberg H Maier T Deupi X Grzesiek S Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist. Sci Adv US 7 2021 34134983 doi:10.1126/sciadv.abg8685 2375-2548 7o7f FULLOVERLAP [6P4]CCL5-CCR5-Gi-Fab16 [6P4]CCL5-CCR5-Gi-Fab16 0 1 2 3 4 5 6 7 Guanine nucleotide-binding protein G(i) subunit alpha-1 1 1 Homo sapiens Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 1 2 Bos taurus C-C chemokine receptor type 5 1 3 Homo sapiens Guanine nucleotide-binding protein G(T) subunit gamma-T1 1 4 Bos taurus C-C motif chemokine 5(0-68) 1 5 Homo sapiens Fab 1 6 7 Mus musculus Guanine nucleotide-binding protein G(i) subunit alpha-1 Homo sapiens 0.040415031000000004 1 Escherichia coli BL21(DE3) LEVO MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQS IIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLD RIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIY THFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF P63096 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 Bos taurus 0.03741693 1 LEVO MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLI IWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTS SGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGV TDDGMAVATGSWDSFLKIWN P62871 C-C chemokine receptor type 5 Homo sapiens 0.042726167999999995

UNP P51681

1 Spodoptera frugiperda LEVO MDYQVSSPIYDINYYTSEPCQKINVKQIAARLLPPLYSLVFIFGFVGNMLVILILINCKRLKSMTDIYLLNLAISDLFFL LTVPFWAHYAAAQWDFGNTMCQLLTGLYFIGFFSGIFFIILLTIDRYLAVVHAVFALKARTVTFGVVTSVITWVVAVFAS LPGIIFTRSQKEGLHYTCSSHFPYSQYQFWKNFQTLKIVILGLVLPLLVMVICYSGILKTLLRCRNEKKRHRAVRLIFTI MIVYFLFWAPYNIVLLLNTFQEFFGLNNCSSSNRLDQAMQVTETLGMTHCCINPIIYAFVGEKFRNYLLVFFQKHIAKRF CKCCSIFQQEAPERASSVYTRSTGEQEISVGLGVAGLEVLFQGPDYKDDDDK P51681 Guanine nucleotide-binding protein G(T) subunit gamma-T1 Bos taurus 0.008556917999999998

UNP P02698

1 LEVO MPVINIEDLTEKDKLKMEVDQLKKEVTLERMLVSKCCEEFRDYVEERSGEDPLVKGIPEDKNPFKELKGGCVIS P02698 C-C motif chemokine 5 Homo sapiens 0.007857122999999999

UNP P13501

1 Escherichia coli LEVO (PCA)GPPGDIVLACCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS P13501 Fab antibody fragment heavy chain Mus musculus 0.023542247999999998 1 Mus musculus LEVO DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLF LQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTV TWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPS Fab antibody fragment light chain Mus musculus 0.023921592 1 Mus musculus LEVO DIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTI SRLEAEDVGVYYCMQHLEYPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSER QNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN singleParticle particle 2.5 7.5 25.0 HEPES 150.0 NaCl 0.01 LMNG Quantifoil R1.2/1.3 COPPER 200 CARBON HOLEY GLOW DISCHARGE 30 0.025 ETHANE 100 277 FEI VITROBOT MARK IV TFS GLACIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 200 GATAN K3 (6k x 4k) 1 2466 49.0 1 FOURIER SPACE 3.15 FSC 0.143 CUT-OFF cryoSPARC 3.10 345458 NOT APPLICABLE MAXIMUM LIKELIHOOD emd_12746.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 400.32 400.32 400.32 90.0 90.0 90.0 X Y Z -1.4180621 2.1532226 -0.00004325304 0.025594182 1.112 1.112 1.112 0.16 AUTHOR ::::EMDATABANK.org::::EMD-12746:::: 5UIW C PDB experimental model 5KDO A PDB experimental model 5KDO B PDB experimental model 5KDO G PDB experimental model FLEXIBLE FIT REAL 5UIW I 11-69 PDB experimental model 6QNK H PDB experimental model 6QNK F PDB experimental model RIGID BODY FIT REAL emd_12746_msk_1.map emd_12746_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 400.32 400.32 400.32 90.0 90.0 90.0 X Y Z -0.6727154 1.1441039 0.000046380355 0.04866234 1.112 1.112 1.112 AUTHOR ::::EMDATABANK.org::::EMD-12746:::: emd_12746_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 400.32 400.32 400.32 90.0 90.0 90.0 X Y Z -0.5774972 1.1984817 0.00004152771 0.049006406 1.112 1.112 1.112 AUTHOR ::::EMDATABANK.org::::EMD-12746::::