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- EMDB-12746: Structural basis of the activation of the CC chemokine receptor 5... -

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Basic information

Entry
Database: EMDB / ID: EMD-12746
TitleStructural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist
Map data
Sample
  • Complex: [6P4]CCL5-CCR5-Gi-Fab16
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: 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(T) subunit beta-1
    • Complex: C-C chemokine receptor type 5
      • Protein or peptide: C-C chemokine receptor type 5
    • Complex: Guanine nucleotide-binding protein G(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
    • Complex: C-C motif chemokine 5(0-68)
      • Protein or peptide: C-C motif chemokine 5
    • Complex: Fab
      • Protein or peptide: Fab antibody fragment heavy chain
      • Protein or peptide: Fab antibody fragment light chain
KeywordsG protein-coupled receptor (GPCR) / CCR5 / CCL5/RANTES / HIV entry / AIDS / membrane protein structure / MEMBRANE PROTEIN / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine (C-C motif) ligand 5 signaling pathway / chemokine receptor antagonist activity / chemokine (C-C motif) ligand 5 binding / phospholipase D-activating G protein-coupled receptor signaling pathway / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / Olfactory Signaling Pathway / receptor signaling protein tyrosine kinase activator activity / chemokine receptor activity / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / CCR5 chemokine receptor binding / positive regulation of receptor signaling pathway via STAT / positive regulation of T cell chemotaxis / CCR chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / eye photoreceptor cell development / signaling / Inactivation, recovery and regulation of the phototransduction cascade / positive regulation of homotypic cell-cell adhesion / positive regulation of G protein-coupled receptor signaling pathway / neutrophil activation / Activation of the phototransduction cascade / C-C chemokine receptor activity / phosphatidylinositol-4,5-bisphosphate phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / chemokine-mediated signaling pathway / C-C chemokine binding / eosinophil chemotaxis / positive regulation of calcium ion transport / response to cholesterol / positive regulation of monocyte chemotaxis / positive regulation of innate immune response / cell surface receptor signaling pathway via STAT / chemokine activity / regulation of T cell activation / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / dendritic cell chemotaxis / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / positive regulation of smooth muscle cell migration / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / negative regulation of G protein-coupled receptor signaling pathway / Extra-nuclear estrogen signaling / G alpha (s) signalling events / G alpha (q) signalling events / leukocyte cell-cell adhesion / phospholipase activator activity / negative regulation of viral genome replication / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of macrophage chemotaxis / chemoattractant activity / exocytosis / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of translational initiation / cellular response to interleukin-1 / host-mediated suppression of viral transcription / phototransduction / positive regulation of TOR signaling / Binding and entry of HIV virion / positive regulation of T cell migration / cellular defense response / adenylate cyclase inhibitor activity / positive regulation of viral genome replication / positive regulation of protein localization to cell cortex / T cell migration / Adenylate cyclase inhibitory pathway / coreceptor activity / D2 dopamine receptor binding / response to prostaglandin E / G protein-coupled serotonin receptor binding / adenylate cyclase regulator activity / cellular response to fibroblast growth factor stimulus
Similarity search - Function
CC chemokine receptor 5 / 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 ...CC chemokine receptor 5 / 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 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
Guanine nucleotide-binding protein G(T) subunit gamma-T1 / C-C motif chemokine 5 / C-C chemokine receptor type 5 / 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) / Bos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsIsaikina P / Tsai C-J
Funding support Switzerland, European Union, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation31-149927 Switzerland
Swiss National Science Foundation31-173089 Switzerland
European Commission6th Framework EMPROEuropean Union
European Commission7th Framework CHAARMEuropean Union
CitationJournal: Sci Adv / Year: 2021
Title: Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist.
Authors: Polina Isaikina / Ching-Ju Tsai / Nikolaus Dietz / Filip Pamula / Anne Grahl / Kenneth N Goldie / Ramon Guixà-González / Camila Branco / Marianne Paolini-Bertrand / Nicolas Calo / Fabrice ...Authors: Polina Isaikina / Ching-Ju Tsai / Nikolaus Dietz / Filip Pamula / Anne Grahl / Kenneth N Goldie / Ramon Guixà-González / Camila Branco / Marianne Paolini-Bertrand / Nicolas Calo / Fabrice Cerini / Gebhard F X Schertler / Oliver Hartley / Henning Stahlberg / Timm Maier / Xavier Deupi / Stephan Grzesiek /
Abstract: The human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in cancer, HIV, and COVID-19. Despite its importance as a drug ...The human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in cancer, HIV, and COVID-19. Despite its importance as a drug target, the molecular activation mechanism of CCR5, i.e., how chemokine agonists transduce the activation signal through the receptor, is yet unknown. Here, we report the cryo-EM structure of wild-type CCR5 in an active conformation bound to the chemokine super-agonist [6P4]CCL5 and the heterotrimeric G protein. The structure provides the rationale for the sequence-activity relation of agonist and antagonist chemokines. The N terminus of agonist chemokines pushes onto specific structural motifs at the bottom of the orthosteric pocket that activate the canonical GPCR microswitch network. This activation mechanism differs substantially from other CC chemokine receptors that bind chemokines with shorter N termini in a shallow binding mode involving unique sequence signatures and a specialized activation mechanism.
History
DepositionApr 13, 2021-
Header (metadata) releaseJun 30, 2021-
Map releaseJun 30, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7o7f
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12746.png

Downloads & links

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Map

FileDownload / File: emd_12746.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.)
1.11 Å/pix.
x 360 pix.
= 400.32 Å		1.11 Å/pix.
x 360 pix.
= 400.32 Å		1.11 Å/pix.
x 360 pix.
= 400.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.112 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16 / Movie #1: 0.2
Minimum - Maximum-1.4180621 - 2.1532226
Average (Standard dev.)-0.00004325304 (±0.025594182)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 400.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1121.1121.112
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z400.320400.320400.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.4182.153-0.000

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Supplemental data

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Mask #1

Fileemd_12746_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_12746_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_12746_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : [6P4]CCL5-CCR5-Gi-Fab16

EntireName: [6P4]CCL5-CCR5-Gi-Fab16
Components
  • Complex: [6P4]CCL5-CCR5-Gi-Fab16
    • Complex: Guanine nucleotide-binding protein G(i) subunit alpha-1
      • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Complex: 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(T) subunit beta-1
    • Complex: C-C chemokine receptor type 5
      • Protein or peptide: C-C chemokine receptor type 5
    • Complex: Guanine nucleotide-binding protein G(T) subunit gamma-T1
      • Protein or peptide: Guanine nucleotide-binding protein G(T) subunit gamma-T1
    • Complex: C-C motif chemokine 5(0-68)
      • Protein or peptide: C-C motif chemokine 5
    • Complex: Fab
      • Protein or peptide: Fab antibody fragment heavy chain
      • Protein or peptide: Fab antibody fragment light chain

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Supramolecule #1: [6P4]CCL5-CCR5-Gi-Fab16

SupramoleculeName: [6P4]CCL5-CCR5-Gi-Fab16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1

SupramoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

SupramoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #4: C-C chemokine receptor type 5

SupramoleculeName: C-C chemokine receptor type 5 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Guanine nucleotide-binding protein G(T) subunit gamma-T1

SupramoleculeName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #6: C-C motif chemokine 5(0-68)

SupramoleculeName: C-C motif chemokine 5(0-68) / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Fab

SupramoleculeName: Fab / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Mus musculus (house mouse)

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

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.415031 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 FDVGGQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCA TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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

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Macromolecule #2: 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: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 37.41693 KDa
SequenceString: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String:
MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN

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

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Macromolecule #3: C-C chemokine receptor type 5

MacromoleculeName: C-C chemokine receptor type 5 / type: protein_or_peptide / ID: 3 / Details: UNP P51681 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.726168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDYQVSSPIY DINYYTSEPC QKINVKQIAA RLLPPLYSLV FIFGFVGNML VILILINCKR LKSMTDIYLL NLAISDLFFL LTVPFWAHY AAAQWDFGNT MCQLLTGLYF IGFFSGIFFI ILLTIDRYLA VVHAVFALKA RTVTFGVVTS VITWVVAVFA S LPGIIFTR ...String:
MDYQVSSPIY DINYYTSEPC QKINVKQIAA RLLPPLYSLV FIFGFVGNML VILILINCKR LKSMTDIYLL NLAISDLFFL LTVPFWAHY AAAQWDFGNT MCQLLTGLYF IGFFSGIFFI ILLTIDRYLA VVHAVFALKA RTVTFGVVTS VITWVVAVFA S LPGIIFTR SQKEGLHYTC SSHFPYSQYQ FWKNFQTLKI VILGLVLPLL VMVICYSGIL KTLLRCRNEK KRHRAVRLIF TI MIVYFLF WAPYNIVLLL NTFQEFFGLN NCSSSNRLDQ AMQVTETLGM THCCINPIIY AFVGEKFRNY LLVFFQKHIA KRF CKCCSI FQQEAPERAS SVYTRSTGEQ EISVGLGVAG LEVLFQGPDY KDDDDK

UniProtKB: C-C chemokine receptor type 5

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Macromolecule #4: Guanine nucleotide-binding protein G(T) subunit gamma-T1

MacromoleculeName: Guanine nucleotide-binding protein G(T) subunit gamma-T1
type: protein_or_peptide / ID: 4 / Details: UNP P02698 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 8.556918 KDa
SequenceString:
MPVINIEDLT EKDKLKMEVD QLKKEVTLER MLVSKCCEEF RDYVEERSGE DPLVKGIPED KNPFKELKGG CVIS

UniProtKB: Guanine nucleotide-binding protein G(T) subunit gamma-T1

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Macromolecule #5: C-C motif chemokine 5

MacromoleculeName: C-C motif chemokine 5 / type: protein_or_peptide / ID: 5 / Details: UNP P13501 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.857123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(PCA)GPPGDIVLA CCFAYIARPL PRAHIKEYFY TSGKCSNPAV VFVTRKNRQV CANPEKKWVR EYINSLEMS

UniProtKB: C-C motif chemokine 5

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Macromolecule #6: Fab antibody fragment heavy chain

MacromoleculeName: Fab antibody fragment heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.542248 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSAKTTPPSV YPLAPGCGDT TGSSVTLGCL VKGYFPESVT V TWNSGSLS SSVHTFPALL QSGLYTMSSS VTVPSSTWPS QTVTCSVAHP ASSTTVDKKL EPS

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Macromolecule #7: Fab antibody fragment light chain

MacromoleculeName: Fab antibody fragment light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.921592 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVMTQATSS VPVTPGESVS ISCRSSKSLL HSNGNTYLYW FLQRPGQSPQ LLIYRMSNLA SGVPDRFSGS GSGTAFTLTI SRLEAEDVG VYYCMQHLEY PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW ...String:
DIVMTQATSS VPVTPGESVS ISCRSSKSLL HSNGNTYLYW FLQRPGQSPQ LLIYRMSNLA SGVPDRFSGS GSGTAFTLTI SRLEAEDVG VYYCMQHLEY PLTFGAGTKL ELKRADAAPT VSIFPPSSEQ LTSGGASVVC FLNNFYPKDI NVKWKIDGSE R QNGVLNSW TDQDSKDSTY SMSSTLTLTK DEYERHNSYT CEATHKTSTS PIVKSFNRN

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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

Concentration2.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
25.0 mMHEPES
150.0 mMNaCl
0.01 %LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Pressure: 0.025 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 2466 / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.10) / Number images used: 345458
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5uiw

chain_id: C, source_name: PDB, initial_model_type: experimental model

5kdo

chain_id: A, source_name: PDB, initial_model_type: experimental model

5kdo

chain_id: B, source_name: PDB, initial_model_type: experimental model

5kdo

chain_id: G, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7o7f:
Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

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Atomic model buiding 2

Initial model
PDB IDChain

5uiw

chain_id: I, residue_range: 11-69, source_name: PDB, initial_model_type: experimental model

6qnk

chain_id: H, source_name: PDB, initial_model_type: experimental model

6qnk

chain_id: F, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7o7f:
Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist

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  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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