9XHH: CCL19-CCR7-Gi-scFv16 complex

Structure of the CCL19-CCR7-Gi-scFv16 complex. Determined by electron microscopy at 3.0 Å resolution. Released 22 Apr 2026.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 9,463
Mol. weight: 236.82 kDa
Ligands: CLR
Released: 22 Apr 2026

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

Secondary structure: helices and β-sheets

9XHH contains 41 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: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	34-39	6	10
α-helix	46-54	9
β-strand	185-191	7	10
β-strand	194-200	7	10
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	10
α-helix	227-229	3
β-strand	233	1	11
β-strand	241	1	11
α-helix	242-254	13
β-strand	263-269	7	10
α-helix	271-280	10
α-helix	283-285	3
α-helix	296-309	14
β-strand	319-323	5	10
α-helix	331-351	21

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	29-31	3
α-helix	37-39	3
β-strand	42	1	3
β-strand	49-51	3	4
β-strand	57-62	6	5
β-strand	68-73	6	5
β-strand	77-82	6	5
β-strand	88-93	6	5
β-strand	99-104	6	6
β-strand	110-115	6	6
β-strand	120-124	5	6
β-strand	133-138	6	6
β-strand	145-150	6	7
β-strand	155-160	6	7
β-strand	164-169	6	7
β-strand	174-180	7	7
α-helix	185	1
β-strand	186-191	6	8
β-strand	197-202	6	8
β-strand	206-211	6	8
β-strand	217-221	5	8
β-strand	228-233	6	9
β-strand	239-244	6	9
β-strand	249-253	5	9
β-strand	259-263	5	9
β-strand	272-277	6	3
β-strand	283-288	6	3
β-strand	293-297	5	3
β-strand	303-307	5	3
β-strand	316-319	4	4
β-strand	326-329	4	4
β-strand	334-337	4	4

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	27-29	3
α-helix	30-43	14
α-helix	53-55	3

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	18-23	6	13
β-strand	25	1	12
α-helix	29-31	3
β-strand	33-39	7	14
β-strand	45-51	7	14
α-helix	53-55	3
β-strand	58-60	3	14
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	93-99	7	14
β-strand	110-111	2	14
β-strand	115	1	14
β-strand	129-130	2	15
β-strand	134-136	3	16
β-strand	143-148	6	15
β-strand	163-167	5	16
β-strand	174-178	5	16
β-strand	182-183	2	16
β-strand	191-196	6	15
β-strand	199-204	6	15
β-strand	214-218	5	16
β-strand	226	1	14
β-strand	231-234	4	16

Chain L: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	16-18	3
α-helix	19-21	3
β-strand	25-28	4	1
α-helix	30-32	3
β-strand	38-42	5	1
β-strand	48-51	4	1
α-helix	56-67	12

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	51-85	35
α-helix	92-119	28
α-helix	126-154	29
α-helix	155-159	5
α-helix	161-166	6
α-helix	168-189	22
α-helix	191-195	5
β-strand	197-200	4	2
β-strand	209-212	4	2
α-helix	217-228	12
α-helix	229-233	5
α-helix	234-250	17
α-helix	257-274	18
α-helix	277-290	14
α-helix	298-326	29
α-helix	331-341	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C motif chemokine 19	L	protein	92	Homo sapiens	Q99731 (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(T) subunit beta-1	B	protein	371	Homo sapiens	P62873 (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, P63097
Antibody fragment scFv16	D	protein	256	Mus musculus

Sequence of entity 1 (L), FASTA

>9XHH_1 C-C motif chemokine 19 (chains L)
GTNDAEDCCLSVTQKPIPGYIVRNFHYLLIKDGCRVPAVVFTTLRGRQLCAPPDQPWVER
IIQRLQRTSAKMKRRSSGSGSGSAAALEVLFQ

Sequence of entity 2 (R), FASTA

>9XHH_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 (B), FASTA

>9XHH_3 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 4 (A, C), FASTA

>9XHH_4 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 5 (D), FASTA

>9XHH_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 Q99731 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7STA 2.5 Å, X-ray Crystal Structure of Truncated Human Chemokine CCL19 (7-70)
9KO2 2.98 Å, A Cryo_EM structure of CCR7 complex with CCL19
9KO6 3.3 Å, A local Cryo_EM structure of CCR7 complex with CCL19
2MP1 Solution structure of the human chemokine CCL19

Browse structure collections

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