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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of CXCR4 in complex with CXCL12 | |||||||||
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![]() | Chemokine receptor / CXCR4 / IMMUNE SYSTEM | |||||||||
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 / : / positive regulation of dendrite extension / Formation of definitive endoderm / positive regulation of chemotaxis / 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 / small molecule binding / 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 / adult locomotory behavior / neurogenesis / cell chemotaxis / ubiquitin binding / response to activity / Regulation of insulin secretion / G protein-coupled receptor binding / G protein-coupled receptor activity / 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||
![]() | Liu YZ / Liu AJ / Liao QW / Ye RD | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Cryo-EM structure of CXCR4 in complex with CXCL12 Authors: Liu YZ / Liu AJ / Liao QW | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.5 KB 18.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 50.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 878.8 KB | Display | ![]() |
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Full document | ![]() | 878.4 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k3zMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36869_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36869_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CXCR4-CXCL12-Gi-scFv16 complex
Entire | Name: CXCR4-CXCL12-Gi-scFv16 complex |
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Components |
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-Supramolecule #1: CXCR4-CXCL12-Gi-scFv16 complex
Supramolecule | Name: CXCR4-CXCL12-Gi-scFv16 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #6, #5, #2-#3, #1, #4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: C-X-C chemokine receptor type 4
Macromolecule | Name: C-X-C chemokine receptor type 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.826059 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KEPCFREENA NFNKIFLPTI YSIIFLTGIV GNGLVILVMG YQKKLRSMTD KYRLHLSVAD LLFVITLPFW AVDAVANWYF GNFLCKAVH VIYTVNLYSS VLILAFISLD RYLAIVHATN SQRPRKLLAE KVVYVGVWIP ALLLTIPDFI FANVSEADDR Y ICDRFYPN ...String: KEPCFREENA NFNKIFLPTI YSIIFLTGIV GNGLVILVMG YQKKLRSMTD KYRLHLSVAD LLFVITLPFW AVDAVANWYF GNFLCKAVH VIYTVNLYSS VLILAFISLD RYLAIVHATN SQRPRKLLAE KVVYVGVWIP ALLLTIPDFI FANVSEADDR Y ICDRFYPN DLWVVVFQFQ HIMVGLILPG IVILSCYCII ISKLSHSKGH QKRKALKTTV ILILAFFACW LPYYIGISID SF ILLEIIK QGCEFENTVH KWISITEALA FFHCCLNPIL YAFLGAKFKT SAQHALTSV UniProtKB: C-X-C chemokine receptor type 4 |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.198656 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD ...String: ELDQLRQEAE QLKNQIRDAR KACADATLSQ ITNNIDPVGR IQMRTRRTLR GHLAKIYAMH WGTDSRLLVS ASQDGKLIIW DSYTTNKVH AIPLRSSWVM TCAYAPSGNY VACGGLDNIC SIYNLKTREG NVRVSRELAG HTGYLSCCRF LDDNQIVTSS G DTTCALWD IETGQQTTTF TGHTGDVMSL SLAPDTRLFV SGACDASAKL WDVREGMCRQ TFTGHESDIN AICFFPNGNA FA TGSDDAT CRLFDLRADQ ELMTYSHDNI ICGITSVSFS KSGRLLLAGY DDFNCNVWDA LKADRAGVLA GHDNRVSCLG VTD DGMAVA TGSWDSFLKI WN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 40.415031 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: Stromal cell-derived factor 1
Macromolecule | Name: Stromal cell-derived factor 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.292648 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: KPVSLSYRCP CRFFESHVAR ANVKHLKILN TPNCALQIVA RLKNNNRQVC IDPKLKWIQE YL UniProtKB: Stromal cell-derived factor 1 |
-Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 6.131084 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: IAQARKLVEQ LKMEANIDRI KVSKAAADLM AYCEAHAKED PLLTPVPASE NPFRE UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #6: scFv16
Macromolecule | Name: scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 26.337307 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |