9XHI: CCL21-CCR7-Gi-scFv16 complex

Structure of the CCL21-CCR7-Gi-scFv16 complex. Determined by electron microscopy at 3.2 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 9,449
Mol. weight: 240.29 kDa
Ligands: CLR
Released: 22 Apr 2026

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

Secondary structure: helices and β-sheets

9XHI contains 33 α-helices and 65 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-40	7	4
α-helix	46-54	9
β-strand	185-191	7	4
β-strand	194-200	7	4
α-helix	208-210	3
α-helix	213-215	3
β-strand	220-226	7	4
α-helix	242-254	13
β-strand	263-269	7	4
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-322	4	4
α-helix	331-351	21

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	29-32	4
α-helix	37-39	3
β-strand	49-50	2	5
β-strand	57-62	6	6
β-strand	68-73	6	6
β-strand	77-82	6	6
β-strand	88-93	6	6
β-strand	99-104	6	7
β-strand	110-115	6	7
β-strand	120-124	5	7
β-strand	133-138	6	7
β-strand	145-150	6	8
β-strand	155-160	6	8
β-strand	164-169	6	8
β-strand	174-180	7	8
α-helix	185	1
β-strand	186-191	6	9
β-strand	197-202	6	9
β-strand	206-211	6	9
β-strand	217-221	5	9
β-strand	228-233	6	10
β-strand	239-244	6	10
β-strand	249-253	5	10
β-strand	259-263	5	10
β-strand	272-277	6	11
β-strand	283-288	6	11
β-strand	293-297	5	11
β-strand	303-307	5	11
β-strand	314-319	6	5
β-strand	326-330	5	5
β-strand	335-337	3	5

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	30-43	14

Chain D: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	5	1
β-strand	6	1	13
α-helix	7-8	2
β-strand	17-23	7	13
β-strand	25	1	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
β-strand	58-60	3	14
α-helix	62-64	3
β-strand	68-73	6	13
β-strand	78-84	7	13
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	110-111	2	14
β-strand	115-117	3	14
β-strand	129-130	2	15
β-strand	136	1	16
β-strand	143-148	6	15
β-strand	162-167	6	17
β-strand	174-178	5	17
β-strand	182-183	2	17
β-strand	191-196	6	15
β-strand	199-204	6	15
β-strand	214-219	6	17
β-strand	231	1	17
β-strand	234	1	16

Chain L: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	22-28	7	1
α-helix	29-30	2
β-strand	31	1	2
β-strand	38-43	6	1
β-strand	51-53	3	1
α-helix	58-68	11

Chain R: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	1
α-helix	51-86	36
α-helix	92-119	28
α-helix	126-158	33
α-helix	161-166	6
α-helix	168-189	22
α-helix	191-195	5
β-strand	197-200	4	3
β-strand	209-212	4	3
β-strand	213	1	2
α-helix	217-228	12
α-helix	229-233	5
α-helix	234-251	18
α-helix	257-290	34
α-helix	298-326	29
α-helix	331-341	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C motif chemokine 21	L	protein	126	Homo sapiens	O00585 (AlphaFold model)
C-C chemokine receptor type 7,Non structural polyprotein	R	protein	551	Homo sapiens	A0A482LYE4, P32248 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding…	A, C	protein	432	Homo sapiens	P59768 (AlphaFold model), P63097
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	371	Homo sapiens	P62873
Antibody fragment scFv16	D	protein	256	Mus musculus

Sequence of entity 1 (L), FASTA

>9XHI_1 C-C motif chemokine 21 (chains L)
SDGGAQDCCLKYSQRKIPAKVVRSYRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWV
QQLMQHLDKTPSPQKPAQGCRKDRGASKTGKKGKGSKGCKRTERSQTPKGPGSGSGSAAA
LEVLFQ

Sequence of entity 2 (R), FASTA

>9XHI_2 C-C chemokine receptor type 7,Non structural polyprotein (chains R)
DYKDDDDGSQDEVTDDYIGDNTTVDYTLFESLCSKKDVRNFKAWFLPIMYSIICFVGLLG
NGLVVLTYIYFKRLKTMTDTYLLNLAVADILFLLTLPFWAYSAAKSWVFGVHFCKLIFAI
YKMSFFSGMLLLLCISIDRYVAIVQAVSAHRHRARVLLISKLSCVGIWILATVLSIPELL
YSDLQRSSSEQAMRCSLITEHVEAFITIQVAQMVIGFLVPLLAMSFCYLVIIRTLLQARN
FERNKAIKVIIAVVVVFIVFQLPYNGVVLAQTVANFNITSSTCELSKQLNIAYDVTYSLA
CVRCCVNPFLYAFIGVKFRNDLFKLFKDLGCLSQEQLRQWSSCRHIRRSSMSVEAETTTT
FSPSRGSSGGGGSGGGGSSGVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVT
PIQRIVRSGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVI
DGVTPNMLNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINSGG
GGSHHHHHHHH

Sequence of entity 3 (A, C), FASTA

>9XHI_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2,Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A, C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAILGSAGSAGSAGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAG
ESGKNTIVKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARAD
DARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRI
AQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAII
FCVALSDYDLVLAEDEEMNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSP
LTICYPEYAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDV
IIKNNLKDCGLF

Sequence of entity 4 (B), FASTA

>9XHI_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VSGWRLFKKIS

Sequence of entity 5 (D), FASTA

>9XHI_5 Antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structural insights into biased signaling at chemokine receptor CCR7. Tanaka, K., Nishikawa, K., Shiimura, Y. et al. Proc Natl Acad Sci U S A (2026) 123:e2533975123-e2533975123. DOI 10.1073/pnas.2533975123 · PubMed

Other PDB entries of the same protein (UniProt O00585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EKI 1.9 Å, Crystal Structure of Truncated CCL21
9KO4 3.3 Å, A Cryo_EM structure of CCR7 complex with CCL21
9L16 3.5 Å, A local Cryo_EM structure of CCR7 complex with CCL21
2L4N Solution Structure of the Chemokine CCL21

Browse structure collections

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