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- PDB-9l16: A local Cryo_EM structure of CCR7 complex with CCL21 -

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Basic information

Entry
Database: PDB / ID: 9l16
TitleA local Cryo_EM structure of CCR7 complex with CCL21
Components
  • C-C chemokine receptor type 7
  • C-C motif chemokine 21
KeywordsMEMBRANE PROTEIN / GPCR / CCL21 / CCR7
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 / : / 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 / : / 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 / positive regulation of T cell chemotaxis / immunological synapse formation / 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 / response to nitric oxide / positive regulation of cell-matrix adhesion / 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 / cell maturation / T cell costimulation / release of sequestered calcium ion into cytosol / positive regulation of interleukin-12 production / positive regulation of cell adhesion / cell chemotaxis / positive regulation of JNK cascade / calcium-mediated signaling / G protein-coupled receptor activity / positive regulation of receptor-mediated endocytosis / antimicrobial humoral immune response mediated by antimicrobial peptide / cell-cell signaling / cellular response to prostaglandin E stimulus / positive regulation of cytosolic calcium ion concentration / response to lipopolysaccharide / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of canonical NF-kappaB signal transduction / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / external side of plasma membrane / cell surface / mitochondrion / extracellular space / extracellular region / plasma membrane
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 coupled receptors family 1 signature. ...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 coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile.
Similarity search - Domain/homology
C-C motif chemokine 21 / C-C chemokine receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDuan, J. / Yuan, Q. / Cao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A local Cryo_EM structure of CCR7 complex with CCL21
Authors: Duan, J. / Yuan, Q. / Cao, Y.
History
DepositionDec 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 17, 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

Downloads & links

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Assembly

Deposited unit
L: C-C motif chemokine 21
R: C-C chemokine receptor type 7


Theoretical massNumber of molelcules
Total (without water)48,0512
Polymers48,0512
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

#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
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 local Cryo_EM structure of CCR7 complex with CCR21 / Type: COMPLEX / Entity ID: all / 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
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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 469279 / Symmetry type: POINT

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