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- EMDB-62469: A Cryo_EM structure of CCR7 complex with CCL21 -

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Basic information

Entry
Database: EMDB / ID: EMD-62469
TitleA Cryo_EM structure of CCR7 complex with CCL21
Map data
Sample
  • Complex: A Cryo_EM structure of CCR7 complex with CCL21
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: SCFV16
    • Protein or peptide: C-C motif chemokine 21
    • Protein or peptide: C-C chemokine receptor type 7
KeywordsGPCR / CCR7 / CCL19 / MEMBRANE PROTEIN/IMMUNE SYSTEM / 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)
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 Cryo_EM structure of CCR7 complex with CCL21
Authors: Yuan Q / Duan J / Cao Y
History
DepositionNov 19, 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_62469.png

Downloads & links

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Map

FileDownload / File: emd_62469.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.0045251898 - 1.9841999
Average (Standard dev.)0.0028045063 (±0.035027154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62469_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_62469_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 Cryo_EM structure of CCR7 complex with CCL21

EntireName: A Cryo_EM structure of CCR7 complex with CCL21
Components
  • Complex: A Cryo_EM structure of CCR7 complex with CCL21
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Protein or peptide: SCFV16
    • Protein or peptide: C-C motif chemokine 21
    • Protein or peptide: C-C chemokine receptor type 7

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Supramolecule #1: A Cryo_EM structure of CCR7 complex with CCL21

SupramoleculeName: A Cryo_EM structure of CCR7 complex with CCL21 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#6, #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: C-C motif chemokine 21

MacromoleculeName: C-C motif chemokine 21 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.807232 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
SDGGAQDCCL KYSQRKIPAK VVRSYRKQEP SLGCSIPAIL FLPRKRSQAE LCADPKELWV QQLMQHLDKT PSPQKPAQ

UniProtKB: C-C motif chemokine 21

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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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Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.459086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String:
MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKSTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TETKNVQFVF DAVTDVIIKN NLKDCGLF

UniProtKB: Guanine nucleotide-binding protein G(i) subunit alpha-1

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Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.095797 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSLLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWNGS SGGGGSGGGG SSGVSGWRLF KKIS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.729947 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFCAIL

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #6: SCFV16

MacromoleculeName: SCFV16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.521564 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SAGGGGSGGG GSGGGGSADI VMTQATSSVP VTPGESVSIS C RSSKSLLH ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SAGGGGSGGG GSGGGGSADI VMTQATSSVP VTPGESVSIS C RSSKSLLH SNGNTYLYWF LQRPGQSPQL LIYRMSNLAS GVPDRFSGSG SGTAFTLTIS RLEAEDVGVY YCMQHLEYPL TF GAGTKLE LK

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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: 469279
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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