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- EMDB-62470: A local Cryo_EM structure of CCR7 complex with CCL19 -

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Basic information

Entry
Database: EMDB / ID: EMD-62470
TitleA local Cryo_EM structure of CCR7 complex with CCL19
Map data
Sample
  • Complex: A local Cryo_EM structure of CCR7 complex with CCL19
    • Protein or peptide: C-C motif chemokine 19
    • Protein or peptide: C-C chemokine receptor type 7
KeywordsGPCR / CCR7 / CCL19 / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive 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 ...positive 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 / CCR10 chemokine receptor binding / positive regulation of humoral immune response / lymphocyte migration into lymph node / mature conventional dendritic cell differentiation / positive regulation of dendritic cell antigen processing and presentation / positive regulation of T-helper 1 cell differentiation / 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 / regulation of cell projection assembly / immunological synapse formation / CCR chemokine receptor binding / regulation of type II interferon production / positive regulation of pseudopodium assembly / cell communication / 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 / chemokine-mediated signaling pathway / eosinophil chemotaxis / ruffle organization / regulation of Cdc42 protein signal transduction / 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 / Interleukin-10 signaling / positive regulation of Rac protein signal transduction / homeostasis of number of cells / positive regulation of endocytosis / cell maturation / T cell costimulation / positive regulation of T cell proliferation / release of sequestered calcium ion into cytosol / positive regulation of interleukin-12 production / positive regulation of cell adhesion / positive regulation of interleukin-1 beta production / cell chemotaxis / positive regulation of JNK cascade / calcium-mediated signaling / positive regulation of non-canonical NF-kappaB signal transduction / G protein-coupled receptor activity / cellular response to virus / positive regulation of receptor-mediated endocytosis / response to virus / intracellular calcium ion homeostasis / positive regulation of tumor necrosis factor production / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B 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 / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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 ...CC chemokine receptor 7 / Chemokine CC, DCCL motif-cointaining domain / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / 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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
C-C chemokine receptor type 7 / C-C motif chemokine 19
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYuan Q / Duan J / Cao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A local Cryo_EM structure of CCR7 complex with CCL19
Authors: Yuan Q / Duan J / Cao Y
History
DepositionNov 20, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62470.png

Downloads & links

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Map

FileDownload / File: emd_62470.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å		0.73 Å/pix.
x 360 pix.
= 262.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.279
Minimum - Maximum-3.5252943 - 3.776824
Average (Standard dev.)0.00026071956 (±0.038700107)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 262.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62470_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62470_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : A local Cryo_EM structure of CCR7 complex with CCL19

EntireName: A local Cryo_EM structure of CCR7 complex with CCL19
Components
  • Complex: A local Cryo_EM structure of CCR7 complex with CCL19
    • Protein or peptide: C-C motif chemokine 19
    • Protein or peptide: C-C chemokine receptor type 7

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Supramolecule #1: A local Cryo_EM structure of CCR7 complex with CCL19

SupramoleculeName: A local Cryo_EM structure of CCR7 complex with CCL19 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-C motif chemokine 19

MacromoleculeName: C-C motif chemokine 19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.865106 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
GTNDAEDCCL SVTQKPIPGY IVRNFHYLLI KDGCRVPAVV FTTLRGRQLC APPDQPWVER IIQRLQRTS

UniProtKB: C-C motif chemokine 19

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Macromolecule #2: C-C chemokine receptor type 7

MacromoleculeName: C-C chemokine receptor type 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.243426 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: QDEVTDDYIG DNTTVDYTLF ESLCSKKDVR NFKAWFLPIM YSIICFVGLL GNGLVVLTYI YFKRLKTMTD TYLLNLAVAD ILFLLTLPF WAYSAAKSWV FGVHFCKLIF AIYKMSFFSG MLLLLCISID RYVAIVQAVS AHRHRARVLL ISKLSCVGIW I LATVLSIP ...String:
QDEVTDDYIG DNTTVDYTLF ESLCSKKDVR NFKAWFLPIM YSIICFVGLL GNGLVVLTYI YFKRLKTMTD TYLLNLAVAD ILFLLTLPF WAYSAAKSWV FGVHFCKLIF AIYKMSFFSG MLLLLCISID RYVAIVQAVS AHRHRARVLL ISKLSCVGIW I LATVLSIP ELLYSDLQRS SSEQAMRCSL ITEHVEAFIT IQVAQMVIGF LVPLLAMSFC YLVIIRTLLQ ARNFERNKAI KV IIAVVVV FIVFQLPYNG VVLAQTVANF NITSSTCELS KQLNIAYDVT YSLACVRCCV NPFLYAFIGV KFRNDLFKLF KDL GCLSQE QLRQWSSCRH IRRSSMSV

UniProtKB: C-C chemokine receptor type 7

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.04
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 18.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 178837
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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