9KO4: A Cryo_EM structure of CCR7 complex with CCL21
A Cryo_EM structure of CCR7 complex with CCL21. Determined by electron microscopy at 3.3 Å resolution. Released 26 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 3.3 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 8,908
- Mol. weight
- 162.86 kDa
- Released
- 26 Nov 2025
Explore 9KO4 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9KO4 contains 34 α-helices and 64 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 | 7-31 | 25 | |
| β-strand | 34-40 | 7 | 3 |
| α-helix | 42-52 | 11 | |
| β-strand | 185-191 | 7 | 3 |
| β-strand | 194-200 | 7 | 3 |
| α-helix | 208-210 | 3 | |
| α-helix | 213-215 | 3 | |
| β-strand | 220-226 | 7 | 3 |
| α-helix | 227-230 | 4 | |
| α-helix | 242-255 | 14 | |
| α-helix | 257-259 | 3 | |
| β-strand | 263-269 | 7 | 3 |
| α-helix | 271-280 | 10 | |
| α-helix | 283-285 | 3 | |
| α-helix | 296-308 | 13 | |
| β-strand | 319-323 | 5 | 3 |
| α-helix | 328-350 | 23 | |
Chain B: 0 helices, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 47-50 | 4 | 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 |
| 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 | 148-153 | 6 | 7 |
| β-strand | 156-160 | 5 | 7 |
| β-strand | 166-169 | 4 | 7 |
| β-strand | 176-180 | 5 | 7 |
| β-strand | 189-192 | 4 | 8 |
| β-strand | 198-202 | 5 | 8 |
| β-strand | 208-212 | 5 | 8 |
| β-strand | 220 | 1 | 8 |
| β-strand | 229-234 | 6 | 9 |
| β-strand | 240-245 | 6 | 9 |
| β-strand | 250-254 | 5 | 9 |
| β-strand | 257-264 | 8 | 9 |
| β-strand | 273-278 | 6 | 10 |
| β-strand | 285-289 | 5 | 10 |
| β-strand | 294-298 | 5 | 10 |
| β-strand | 303-307 | 5 | 10 |
| β-strand | 317-320 | 4 | 4 |
| β-strand | 327-330 | 4 | 4 |
| β-strand | 336-339 | 4 | 4 |
Chain G: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 30-43 | 14 | |
Chain H: 4 helices, 24 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 | 59-60 | 2 | 12 |
| β-strand | 68-73 | 6 | 11 |
| β-strand | 78-84 | 7 | 11 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 12 |
| β-strand | 110-111 | 2 | 12 |
| β-strand | 115-119 | 5 | 12 |
| β-strand | 140-141 | 2 | 13 |
| β-strand | 146-148 | 3 | 14 |
| β-strand | 155-161 | 7 | 13 |
| β-strand | 166 | 1 | 15 |
| β-strand | 172 | 1 | 15 |
| β-strand | 174-179 | 6 | 14 |
| β-strand | 185-189 | 5 | 14 |
| β-strand | 195 | 1 | 14 |
| β-strand | 203-207 | 5 | 13 |
| β-strand | 211-216 | 6 | 13 |
| α-helix | 221-223 | 3 | |
| β-strand | 225-231 | 7 | 14 |
| α-helix | 237 | 1 | |
| β-strand | 239 | 1 | 14 |
| β-strand | 243-246 | 4 | 14 |
Chain L: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| α-helix | 19-21 | 3 | |
| β-strand | 22-25 | 4 | 1 |
| β-strand | 39-43 | 5 | 1 |
| α-helix | 49-50 | 2 | |
| β-strand | 51-53 | 3 | 1 |
| α-helix | 58-66 | 9 | |
Chain R: 14 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-43 | 3 | |
| β-strand | 46 | 1 | 1 |
| α-helix | 51-86 | 36 | |
| α-helix | 92-119 | 28 | |
| α-helix | 126-158 | 33 | |
| α-helix | 161-164 | 4 | |
| α-helix | 168-189 | 22 | |
| α-helix | 191-196 | 6 | |
| β-strand | 198-202 | 5 | 2 |
| β-strand | 206-211 | 6 | 2 |
| α-helix | 217-225 | 9 | |
| α-helix | 226-233 | 8 | |
| α-helix | 234-250 | 17 | |
| α-helix | 259-291 | 33 | |
| α-helix | 298-322 | 25 | |
| α-helix | 323-327 | 5 | |
| α-helix | 331-342 | 12 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| C-C motif chemokine 21 | L | protein | 78 | Homo sapiens | O00585 (AlphaFold model) |
| C-C chemokine receptor type 7 | R | protein | 344 | Homo sapiens | P32248 (AlphaFold model) |
| Guanine nucleotide-binding protein G(i) subunit alpha-1 | A | protein | 354 | Homo sapiens | P63096 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 370 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 70 | Homo sapiens | P59768 |
| SCFV16 | H | protein | 249 | Homo sapiens | |
Sequence of entity 1 (L), FASTA
>9KO4_1 C-C motif chemokine 21 (chains L)
SDGGAQDCCLKYSQRKIPAKVVRSYRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWV
QQLMQHLDKTPSPQKPAQ
Sequence of entity 2 (R), FASTA
>9KO4_2 C-C chemokine receptor type 7 (chains R)
QDEVTDDYIGDNTTVDYTLFESLCSKKDVRNFKAWFLPIMYSIICFVGLLGNGLVVLTYI
YFKRLKTMTDTYLLNLAVADILFLLTLPFWAYSAAKSWVFGVHFCKLIFAIYKMSFFSGM
LLLLCISIDRYVAIVQAVSAHRHRARVLLISKLSCVGIWILATVLSIPELLYSDLQRSSS
EQAMRCSLITEHVEAFITIQVAQMVIGFLVPLLAMSFCYLVIIRTLLQARNFERNKAIKV
IIAVVVVFIVFQLPYNGVVLAQTVANFNITSSTCELSKQLNIAYDVTYSLACVRCCVNPF
LYAFIGVKFRNDLFKLFKDLGCLSQEQLRQWSSCRHIRRSSMSV
Sequence of entity 3 (A), FASTA
>9KO4_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTETKNVQFVFDAVTDVIIKNNLKDCGLF
Sequence of entity 4 (B), FASTA
>9KO4_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLA
KIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGG
LDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQ
TTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFP
NGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNV
WDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSGV
SGWRLFKKIS
Sequence of entity 5 (G), FASTA
>9KO4_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL
Sequence of entity 6 (H), FASTA
>9KO4_6 SCFV16 (chains H)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
AGGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQ
RPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTF
GAGTKLELK
Primary citation
A Cryo_EM structure of CCR7 complex with CCL21. Yuan, Q., Duan, J., Cao, Y. To be published.
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
- 9XHI 3.2 Å, Structure of the CCL21-CCR7-Gi-scFv16 complex
- 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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