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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Structure of tetrameric CXCR4 in complex with REGN7663 Fab | |||||||||
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![]() | GPCR / chemokine receptor / tetramer / oligomer / antibody / SIGNALING PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() C-X-C motif chemokine 12 receptor activity / regulation of viral process / 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 / C-X-C chemokine receptor activity ...C-X-C motif chemokine 12 receptor activity / regulation of viral process / 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 / C-X-C chemokine receptor activity / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / positive regulation of vasculature development / regulation of programmed cell death / endothelial tube morphogenesis / endothelial cell differentiation / Signaling by ROBO receptors / regulation of chemotaxis / cellular response to organonitrogen compound / positive regulation of dendrite extension / positive regulation of chemotaxis / Formation of definitive endoderm / C-C chemokine receptor activity / C-C chemokine binding / Chemokine receptors bind chemokines / anchoring junction / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / cell leading edge / epithelial cell development / cellular response to cytokine stimulus / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / small molecule binding / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / cardiac muscle contraction / neurogenesis / cell chemotaxis / response to activity / ubiquitin binding / G protein-coupled receptor activity / calcium-mediated signaling / neuron migration / response to virus / brain development / cellular response to xenobiotic stimulus / late endosome / virus receptor activity / actin binding / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / cytoplasmic vesicle / lysosome / early endosome / response to hypoxia / positive regulation of cell migration / inflammatory response / immune response / G protein-coupled receptor signaling pathway / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / cell surface / protein-containing complex / extracellular exosome / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.38 Å | |||||||||
![]() | Saotome K / McGoldrick LL / Franklin MC | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into CXCR4 modulation and oligomerization Authors: Saotome K / McGoldrick LL / Ho J / Ramlall T / Shah S / Moore MJ / Kim JH / Leidich R / Olson WC / Franklin MC | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 167.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
Images | ![]() | 151.4 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 164.7 MB 164.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 17.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u4tMC ![]() 8u4nC ![]() 8u4oC ![]() 8u4pC ![]() 8u4qC ![]() 8u4rC ![]() 8u4sC C: citing same article ( M: atomic model generated by this map |
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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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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_41894_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41894_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Tetrameric CXCR4 in complex with REGN7663 Fab
Entire | Name: Tetrameric CXCR4 in complex with REGN7663 Fab |
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Components |
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-Supramolecule #1: Tetrameric CXCR4 in complex with REGN7663 Fab
Supramolecule | Name: Tetrameric CXCR4 in complex with REGN7663 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: REGN7663 Fab light chain
Macromolecule | Name: REGN7663 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.185904 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: DVVMTQSPLS LPVTLGQPAS ISCRSSQSLV YTDGNTYLNW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSGTDFTLKI SRVEAEDVG FYYCMQNTHW PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String: DVVMTQSPLS LPVTLGQPAS ISCRSSQSLV YTDGNTYLNW FQQRPGQSPR RLIYKVSNRD SGVPDRFSGS GSGTDFTLKI SRVEAEDVG FYYCMQNTHW PLTFGGGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C |
-Macromolecule #2: REGN7663 Fab heavy chain
Macromolecule | Name: REGN7663 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.799934 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYGISWVRQA PGQGIEWMGW ISTYNGNRNY AQKVQGRVTM TTDRSTSTAY MDLRSLRSD DTAVYYCARH GITGARNYYY HYGMDVWGQG TTVTVSSAST KGPSVFPLAP CSRSTSESTA ALGCLVKDYF P EPVTVSWN ...String: QVQLVQSGAE VKKPGASVKV SCKASGYTFT SYGISWVRQA PGQGIEWMGW ISTYNGNRNY AQKVQGRVTM TTDRSTSTAY MDLRSLRSD DTAVYYCARH GITGARNYYY HYGMDVWGQG TTVTVSSAST KGPSVFPLAP CSRSTSESTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTKTYT CNVDHKPSNT KVDKRVESKY GPPCPPCPAP PV |
-Macromolecule #3: C-X-C chemokine receptor type 4
Macromolecule | Name: C-X-C chemokine receptor type 4 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 71.063609 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKTIIALSYI FCLVFAGAPE GISIYTSDNY TEEMGSGDYD SMKEPCFREE NANFNKIFLP TIYSIIFLTG IVGNGLVILV MGYQKKLRS MTDKYRLHLS VADLLFVITL PFWAVDAVAN WYFGNFLCKA VHVIYTVSLY SSVLILAFIS LDRYLAIVHA T NSQRPRKL ...String: MKTIIALSYI FCLVFAGAPE GISIYTSDNY TEEMGSGDYD SMKEPCFREE NANFNKIFLP TIYSIIFLTG IVGNGLVILV MGYQKKLRS MTDKYRLHLS VADLLFVITL PFWAVDAVAN WYFGNFLCKA VHVIYTVSLY SSVLILAFIS LDRYLAIVHA T NSQRPRKL LAEKVVYVGV WIPALLLTIP DFIFANVSEA DDRYICDRFY PNDLWVVVFQ FQHIMVGLIL PGIVILSCYC II ISKLSHS KGHQKRKALK TTVILILAFF ACWLPYYIGI SIDSFILLEI IKQGCEFENT VHKWISITEA LAFFHCCLNP ILY AFLGAK FKTSAQHALT SVSRGSSLKI LSKGKRGGHS SVSTESESSS FHSSGRPLEV LFQGPGGGGS VSKGEELFTG VVPI LVELD GDVNGHKFSV SGEGEGDATY GKLTLKFICT TGKLPVPWPT LVTTLTYGVQ CFSRYPDHMK QHDFFKSAMP EGYVQ ERTI FFKDDGNYKT RAEVKFEGDT LVNRIELKGI DFKEDGNILG HKLEYNYNSH NVYIMADKQK NGIKVNFKIR HNIEDG SVQ LADHYQQNTP IGDGPVLLPD NHYLSTQSKL SKDPNEKRDH MVLLEFVTAA GITLGMDELY KDYKDDDDK UniProtKB: C-X-C chemokine receptor type 4 |
-Macromolecule #4: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 16 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Macromolecule #5: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec...
Macromolecule | Name: (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate type: ligand / ID: 5 / Number of copies: 4 / Formula: D21 |
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Molecular weight | Theoretical: 674.929 Da |
Chemical component information | ![]() ChemComp-D21: |
-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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31775 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |