+Open data
-Basic information
Entry | Database: PDB / ID: 8u4o | ||||||
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Title | Structure of CXCL12-bound CXCR4/Gi complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN / GPCR / chemokine receptor / chemokine | ||||||
Function / homology | Function and homology information C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / chemokine (C-X-C motif) ligand 12 signaling pathway / negative regulation of leukocyte tethering or rolling / positive regulation of vascular wound healing / positive regulation of macrophage migration inhibitory factor signaling pathway / positive regulation of mesenchymal stem cell migration / neuron recognition / response to ultrasound / response to tacrolimus / telencephalon cell migration / regulation of actin polymerization or depolymerization / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / chemokine receptor binding / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / CXCR chemokine receptor binding / positive regulation of axon extension involved in axon guidance / endothelial tube morphogenesis / positive regulation of dopamine secretion / endothelial cell differentiation / Signaling by ROBO receptors / regulation of chemotaxis / cellular response to organonitrogen compound / positive regulation of chemotaxis / positive regulation of dendrite extension / Formation of definitive endoderm / induction of positive chemotaxis / C-C chemokine receptor activity / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / C-C chemokine binding / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / blood circulation / Chemokine receptors bind chemokines / chemokine activity / anchoring junction / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / cell leading edge / positive regulation of calcium ion import / epithelial cell development / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / positive regulation of cell adhesion / Adenylate cyclase inhibitory pathway / positive regulation of T cell migration / positive regulation of protein localization to cell cortex / small molecule binding / Binding and entry of HIV virion / regulation of cAMP-mediated signaling / animal organ regeneration / regulation of cell adhesion / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / cardiac muscle contraction / Nuclear signaling by ERBB4 / regulation of mitotic spindle organization / cellular response to forskolin / positive regulation of endothelial cell proliferation / positive regulation of neuron differentiation / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / adult locomotory behavior / neurogenesis / cell chemotaxis / ubiquitin binding / response to activity / Regulation of insulin secretion / G protein-coupled receptor activity / G protein-coupled receptor binding / calcium-mediated signaling / axon guidance / growth factor activity / neuron migration / G-protein beta/gamma-subunit complex binding / response to virus / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / brain development / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
Authors | Saotome, K. / McGoldrick, L.L. / Franklin, M.C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biorxiv / Year: 2024 Title: Structural insights into CXCR4 modulation and oligomerization Authors: Saotome, K. / McGoldrick, L.L. / Ho, J. / Ramlall, T. / Shah, S. / Moore, M.J. / Kim, J.H. / Leidich, R. / Olson, W.C. / Franklin, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u4o.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u4o.ent.gz | 152.3 KB | Display | PDB format |
PDBx/mmJSON format | 8u4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u4o_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8u4o_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8u4o_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 8u4o_validation.cif.gz | 54.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/8u4o ftp://data.pdbj.org/pub/pdb/validation_reports/u4/8u4o | HTTPS FTP |
-Related structure data
Related structure data | 41889MC 8u4nC 8u4pC 8u4qC 8u4rC 8u4sC 8u4tC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules RJ
#1: Protein | Mass: 71063.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCR4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61073 |
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#5: Protein | Mass: 7978.460 Da / Num. of mol.: 1 / Fragment: UNP residues 22-89 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CXCL12, SDF1, SDF1A, SDF1B / Production host: Escherichia coli (E. coli) / References: UniProt: P48061 |
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules ABC
#2: Protein | Mass: 41591.312 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 |
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#3: Protein | Mass: 38534.062 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 |
#4: Protein | Mass: 7861.143 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 |
-Non-polymers , 1 types, 1 molecules
#6: Chemical | ChemComp-CLR / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CXCL12-bound CXCR4/Gi complex / Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87963 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.5 Å2 | ||||||||||||||||||||||||
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