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Open data
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Basic information
Entry | Database: PDB / ID: 8k3z | ||||||
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Title | Cryo-EM structure of CXCR4 in complex with CXCL12 | ||||||
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![]() | IMMUNE SYSTEM / Chemokine receptor / CXCR4 | ||||||
Function / homology | ![]() 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 / : / C-C chemokine receptor activity / positive regulation of dendrite extension / positive regulation of chemotaxis / induction of positive chemotaxis / Formation of definitive endoderm / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / C-C chemokine binding / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / positive regulation of monocyte chemotaxis / chemokine-mediated signaling pathway / blood circulation / Chemokine receptors bind chemokines / chemokine activity / anchoring junction / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / positive regulation of calcium ion import / epithelial cell development / cell leading edge / small molecule binding / 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 / positive regulation of T cell migration / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / 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 / neurogenesis / adult locomotory behavior / cell chemotaxis / response to activity / ubiquitin binding / axon guidance / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / calcium-mediated signaling / 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 / brain development / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å | ||||||
![]() | Liu, Y.Z. / Liu, A.J. / Liao, Q.W. / Ye, R.D. | ||||||
Funding support | 1items
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![]() | ![]() Title: Cryo-EM structure of CXCR4 in complex with CXCL12 Authors: Liu, Y.Z. / Liu, A.J. / Liao, Q.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 248.9 KB | Display | ![]() |
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PDB format | ![]() | 195.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 36869MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules AD
#1: Protein | Mass: 33826.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Protein | Mass: 7292.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Guanine nucleotide-binding protein ... , 3 types, 3 molecules BCG
#2: Protein | Mass: 37198.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 40415.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#5: Protein | Mass: 6131.084 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Antibody , 1 types, 1 molecules S
#6: Antibody | Mass: 26337.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: CXCR4-CXCL12-Gi-scFv16 complex / Type: COMPLEX / Entity ID: #6, #5, #2-#3, #1, #4 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373108 / Symmetry type: POINT |