9AST: XCR1 signaling complex

Cryo-EM structure of XCR1 signaling complex. Determined by electron microscopy at 3.07 Å resolution. Released 11 Dec 2024.

Method: Electron microscopy
Resolution: 3.07 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 8,516
Mol. weight: 142.79 kDa
Released: 11 Dec 2024

Explore 9AST in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9AST contains 40 α-helices and 61 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-38	5	1
α-helix	40-41	2
α-helix	46-51	6
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-211	4
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	1
α-helix	331-351	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-24	19
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-40	3
β-strand	47-51	5	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
α-helix	95	1
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	120-125	6	6
β-strand	134-140	7	6
β-strand	146-151	6	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-181	7	7
β-strand	187-192	6	8
β-strand	198-203	6	8
β-strand	208-212	5	8
β-strand	218-222	5	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-308	5	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	336-339	4	4

Chain E: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-84	7	11
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	115-119	5	12
α-helix	125-127	3
β-strand	128-129	2	13
β-strand	134	1	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	173-178	6	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	191-196	6	13
β-strand	199-204	6	13
β-strand	214-219	6	14
β-strand	231-232	2	14

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-16	7
α-helix	17-23	7
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain L: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9-10	2	2

Chain R: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	2
α-helix	26-58	33
α-helix	65-83	19
α-helix	84-88	5
α-helix	89-93	5
α-helix	99-132	34
α-helix	134-138	5
α-helix	140-142	3
α-helix	143-158	16
α-helix	162-166	5
β-strand	168-170	3	3
β-strand	175-177	3	3
α-helix	180-214	35
α-helix	220-252	33
α-helix	259-277	19
α-helix	279-284	6
α-helix	285-289	5
α-helix	292-302	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
Lymphotactin	L	protein	11	Homo sapiens	P47992 (AlphaFold model)
Chemokine XC receptor 1	R	protein	283	Homo sapiens	P46094 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	336	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	54	Homo sapiens	P59768
scFv16	E	protein	232	Mus musculus

Sequence of entity 1 (A), FASTA

>9AST_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (L), FASTA

>9AST_2 Lymphotactin (chains L)
VGSEVSDKRTC

Sequence of entity 3 (R), FASTA

>9AST_3 Chemokine XC receptor 1 (chains R)
PCENQAWVFATLATTVLYCLVFLLSLVGNSLVLWVLVKYESLESLTNIFILNLCLSDLVF
ACLLPVWISPYHWGWVLGDFLCKLLNMIFSISLYSSIFFLTIMTIHRYLSVVSPLSTLRV
PTLRCRVLVTMAVWVASILSSILDTIFHKVLSSGCDYSELTWYLTSVYQHNLFFLLSLGI
ILFCYVEILRTLFRSRSKRRHRTVKLIFAIVVAYFLSWGPYNFTLFLQTLFRTQIIRSCE
AKQQLEYALLICRNLAFSHCCFNPVLYVFVGVKFRTHLKHVLR

Sequence of entity 4 (B), FASTA

>9AST_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
DQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWG
TDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIY
NLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHT
GDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATG
SDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADR
AGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 5 (G), FASTA

>9AST_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
IAQARKLVQQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASQNPFR

Sequence of entity 6 (E), FASTA

>9AST_6 scFv16 (chains E)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
ADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNL
ASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Primary citation

Molecular basis for chemokine recognition and activation of XCR1. Zhang, X., Schlimgen, R.R., Singh, S. et al. Proc Natl Acad Sci U S A (2024) 121:e2405732121-e2405732121. DOI 10.1073/pnas.2405732121 · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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