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- PDB-9ko4: A Cryo_EM structure of CCR7 complex with CCL21 -

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Basic information

Entry
Database: PDB / ID: 9ko4
TitleA Cryo_EM structure of CCR7 complex with CCL21
Components
  • (Guanine nucleotide-binding protein ...) x 3
  • C-C chemokine receptor type 7
  • C-C motif chemokine 21
  • SCFV16
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / GPCR / CCR7 / CCL19 / MEMBRANE PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / positive regulation of hypersensitivity / chemokine (C-C motif) ligand 19 binding / chemokine (C-C motif) ligand 21 binding / C-C motif chemokine 19 receptor activity / C-C motif chemokine 21 receptor activity / positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation / regulation of dendritic cell dendrite assembly ...mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / positive regulation of hypersensitivity / chemokine (C-C motif) ligand 19 binding / chemokine (C-C motif) ligand 21 binding / C-C motif chemokine 19 receptor activity / C-C motif chemokine 21 receptor activity / positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation / regulation of dendritic cell dendrite assembly / myeloid dendritic cell chemotaxis / CCL19-activated CCR7 signaling pathway / CCL21-activated CCR7 signaling pathway / CCR7 chemokine receptor binding / positive regulation of immunological synapse formation / positive regulation of T cell costimulation / positive regulation of phospholipase C/protein kinase C signal transduction / positive regulation of humoral immune response / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / mature conventional dendritic cell differentiation / positive regulation of dendritic cell antigen processing and presentation / positive regulation of myeloid dendritic cell chemotaxis / negative regulation of leukocyte tethering or rolling / positive regulation of glycoprotein biosynthetic process / positive regulation of dendritic cell chemotaxis / establishment of T cell polarity / regulation of interleukin-1 beta production / chemokine receptor binding / immunological synapse formation / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / regulation of type II interferon production / positive regulation of pseudopodium assembly / negative thymic T cell selection / negative regulation of interleukin-12 production / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / C-C chemokine receptor activity / cellular response to chemokine / chemokine-mediated signaling pathway / eosinophil chemotaxis / ruffle organization / regulation of Cdc42 protein signal transduction / positive regulation of cell adhesion mediated by integrin / chemokine activity / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / positive regulation of filopodium assembly / dendritic cell chemotaxis / positive regulation of cell motility / positive regulation of cell-matrix adhesion / response to nitric oxide / cellular response to cytokine stimulus / positive regulation of actin filament polymerization / positive regulation of T cell receptor signaling pathway / positive regulation of Rac protein signal transduction / homeostasis of number of cells / positive regulation of T cell migration / adenylate cyclase inhibitor activity / cell maturation / positive regulation of protein localization to cell cortex / T cell costimulation / T cell migration / Adenylate cyclase inhibitory pathway / D2 dopamine receptor binding / response to prostaglandin E / release of sequestered calcium ion into cytosol / positive regulation of interleukin-12 production / adenylate cyclase regulator activity / G protein-coupled serotonin receptor binding / adenylate cyclase-inhibiting serotonin receptor signaling pathway / positive regulation of cell adhesion / cellular response to forskolin / regulation of mitotic spindle organization / cell chemotaxis / positive regulation of JNK cascade / Regulation of insulin secretion / positive regulation of cholesterol biosynthetic process / calcium-mediated signaling / negative regulation of insulin secretion / G protein-coupled receptor binding / response to peptide hormone / G protein-coupled receptor activity / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of receptor-mediated endocytosis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / centriolar satellite / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42
Similarity search - Function
CC chemokine receptor 7 / Chemokine CC, DCCL motif-cointaining domain / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein alpha subunit, group I ...CC chemokine receptor 7 / Chemokine CC, DCCL motif-cointaining domain / Chemokine receptor family / : / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / G-protein alpha subunit, group I / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / G protein alpha subunit / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
C-C motif chemokine 21 / C-C chemokine receptor type 7 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYuan, Q. / Duan, J. / Cao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A Cryo_EM structure of CCR7 complex with CCL21
Authors: Yuan, Q. / Duan, J. / Cao, Y.
History
DepositionNov 19, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: C-C motif chemokine 21
R: C-C chemokine receptor type 7
A: Guanine nucleotide-binding protein G(i) subunit alpha-1
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
H: SCFV16


Theoretical massNumber of molelcules
Total (without water)162,8576
Polymers162,8576
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules LR

#1: Protein C-C motif chemokine 21 / 6Ckine / Beta-chemokine exodus-2 / Secondary lymphoid-tissue chemokine / SLC / Small-inducible cytokine A21


Mass: 8807.232 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL21, SCYA21, UNQ784/PRO1600 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00585
#2: Protein C-C chemokine receptor type 7 / C-C CKR-7 / CC-CKR-7 / CCR-7 / BLR2 / CDw197 / Epstein-Barr virus-induced G-protein coupled ...C-C CKR-7 / CC-CKR-7 / CCR-7 / BLR2 / CDw197 / Epstein-Barr virus-induced G-protein coupled receptor 1 / EBI1 / EBV-induced G-protein coupled receptor 1 / MIP-3 beta receptor


Mass: 39243.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCR7, CMKBR7, EBI1, EVI1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P32248

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Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABG

#3: Protein Guanine nucleotide-binding protein G(i) subunit alpha-1 / Adenylate cyclase-inhibiting G alpha protein


Mass: 40459.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNAI1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P63096, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#4: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 40095.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#5: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7729.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Antibody , 1 types, 1 molecules H

#6: Antibody SCFV16


Mass: 26521.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: A Cryo_EM structure of CCR7 complex with CCL21 / Type: COMPLEX / Entity ID: #3-#6, #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.04
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 18000 nm / Nominal defocus min: 8000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 469279 / Symmetry type: POINT
RefinementHighest resolution: 3.3 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049098
ELECTRON MICROSCOPYf_angle_d0.56212372
ELECTRON MICROSCOPYf_dihedral_angle_d11.8143125
ELECTRON MICROSCOPYf_chiral_restr0.0421444
ELECTRON MICROSCOPYf_plane_restr0.0041555

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