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- EMDB-64403: Cryo-EM structure of CXCR4 complexed with agonist SDVX1 -

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Entry
Database: EMDB / ID: EMD-64403
TitleCryo-EM structure of CXCR4 complexed with agonist SDVX1
Map dataoptimized by Locscale2.0 and sharpened by phenix.autosharpen
Sample
  • Complex: SDVX1-CXCR4-DNGi-scFv16
    • Protein or peptide: 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(O) subunit gamma-2
    • Protein or peptide: Stromal cell-derived factor 1
    • Protein or peptide: Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase catalytic subunit
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: single-chain variable fragment scFv16
  • Ligand: CHOLESTEROL
KeywordsCXC motif chemokine receptor 4 / agonist / SIGNALING PROTEIN
Function / homology
Function and homology information


Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / C-X-C motif chemokine 12 receptor activity / response to ultrasound / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding ...Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / telencephalon cell migration / chemokine (C-X-C motif) ligand 12 signaling pathway / C-X-C motif chemokine 12 receptor activity / response to ultrasound / negative regulation of leukocyte tethering or rolling / regulation of actin polymerization or depolymerization / positive regulation of macrophage migration inhibitory factor signaling pathway / myosin light chain binding / CXCL12-activated CXCR4 signaling pathway / Specification of primordial germ cells / chemokine receptor binding / myelin maintenance / Developmental Lineage of Multipotent Pancreatic Progenitor Cells / CXCR chemokine receptor binding / C-X-C chemokine receptor activity / positive regulation of axon extension involved in axon guidance / positive regulation of vasculature development / Signaling by ROBO receptors / induction of positive chemotaxis / negative regulation of dendritic cell apoptotic process / Formation of definitive endoderm / integrin activation / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of dopamine secretion / cellular response to chemokine / C-C chemokine receptor activity / C-C chemokine binding / positive regulation of monocyte chemotaxis / anchoring junction / chemokine activity / Chemokine receptors bind chemokines / dendritic cell chemotaxis / blood circulation / positive regulation of calcium ion import / cellular response to cytokine stimulus / cell leading edge / detection of temperature stimulus involved in sensory perception of pain / positive regulation of oligodendrocyte differentiation / animal organ regeneration / Binding and entry of HIV virion / detection of mechanical stimulus involved in sensory perception of pain / positive regulation of T cell migration / Nuclear signaling by ERBB4 / regulation of cell adhesion / coreceptor activity / adenylate cyclase inhibitor activity / positive regulation of protein localization to cell cortex / positive regulation of endothelial cell proliferation / T cell migration / positive regulation of relaxation of smooth muscle / Adenylate cyclase inhibitory pathway / positive regulation of neuron differentiation / D2 dopamine receptor binding / neurogenesis / positive regulation of cell adhesion / adenylate cyclase-inhibiting serotonin receptor signaling pathway / G protein-coupled serotonin receptor binding / axon guidance / cellular response to forskolin / bioluminescence / regulation of mitotic spindle organization / chemokine-mediated signaling pathway / growth factor activity / cell chemotaxis / adult locomotory behavior / ubiquitin binding / Regulation of insulin secretion / calcium-mediated signaling / neuropeptide signaling pathway / defense response / response to prostaglandin E / electron transport chain / brain development / positive regulation of cholesterol biosynthetic process / negative regulation of insulin secretion / G protein-coupled receptor binding / integrin binding / response to peptide hormone / G protein-coupled receptor activity / neuron migration / chemotaxis / response to virus / centriolar satellite / G-protein beta/gamma-subunit complex binding / intracellular calcium ion homeostasis / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G protein-coupled acetylcholine receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Glucagon signaling in metabolic regulation / Prostacyclin signalling through prostacyclin receptor
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CXC Chemokine domain / 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 ...CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / CXC Chemokine domain / 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 / : / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Calycin / G-protein alpha subunit, group I / G protein alpha subunit, helical insertion / G protein alpha subunit / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit / G-alpha domain profile. / 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. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 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
Soluble cytochrome b562 / Stromal cell-derived factor 1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / C-X-C chemokine receptor type 4 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(i) subunit alpha-1 / Oplophorus-luciferin 2-monooxygenase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human) / Oplophorus gracilirostris (arthropod)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsJiao HZ / Sang XH / Huang ZW / Hu HL
Funding support China, 1 items
OrganizationGrant numberCountry
Other government32100963 China
CitationJournal: bioRxiv / Year: 2025
Title: The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS.
Authors: Xiaohong Sang / Haizhan Jiao / Qian Meng / Xiong Fang / Kartik S Sundaram / Jiao Zhou / Yan Xu / Asuka I W Alvarado / Ruslan L Nuryyev / Jitka Ourenik / Vaclav Ourednik / Iris S Huang / ...Authors: Xiaohong Sang / Haizhan Jiao / Qian Meng / Xiong Fang / Kartik S Sundaram / Jiao Zhou / Yan Xu / Asuka I W Alvarado / Ruslan L Nuryyev / Jitka Ourenik / Vaclav Ourednik / Iris S Huang / Xiang Liu / Yuheng Mei / Tingli Qian / Aaron Ciechanover / Donald P Pizzo / Michael A Lane / Lyandysha V Zholudeva / Jing An / Evan Y Snyder / Hongli Hu / Ziwei Huang /
Abstract: G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor ...G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1α. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1α in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1α that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1 mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.
History
DepositionApr 29, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64403.png

Downloads & links

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Map

FileDownload / File: emd_64403.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoptimized by Locscale2.0 and sharpened by phenix.autosharpen
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
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Contour LevelBy AUTHOR: 7.0
Minimum - Maximum-23.614661999999999 - 64.764403999999999
Average (Standard dev.)-0.000000000002192 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_64403_additional_1.map
Annotationunsharpened map
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Half map: #2

Fileemd_64403_half_map_1.map
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Half map: #1

Fileemd_64403_half_map_2.map
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Sample components

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Entire : SDVX1-CXCR4-DNGi-scFv16

EntireName: SDVX1-CXCR4-DNGi-scFv16
Components
  • Complex: SDVX1-CXCR4-DNGi-scFv16
    • Protein or peptide: 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(O) subunit gamma-2
    • Protein or peptide: Stromal cell-derived factor 1
    • Protein or peptide: Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase catalytic subunit
    • Protein or peptide: Guanine nucleotide-binding protein G(i) subunit alpha-1
    • Protein or peptide: single-chain variable fragment scFv16
  • Ligand: CHOLESTEROL

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Supramolecule #1: SDVX1-CXCR4-DNGi-scFv16

SupramoleculeName: SDVX1-CXCR4-DNGi-scFv16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 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: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.005895 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: HHHHHHHHHH LEVLFQGPGS SGSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE L AGHTGYLS ...String:
HHHHHHHHHH LEVLFQGPGS SGSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSR LLVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE L AGHTGYLS CCRFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CR QTFTGHE SDINAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDA LKADRA GVLAGHDNRV SCLGVTDDGM AVATGSWDSF LKIWNGASGA SGASGASVSG WRLFKKIS

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

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.861143 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #3: Stromal cell-derived factor 1

MacromoleculeName: Stromal cell-derived factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 951.122 Da
SequenceString:
KPVSLSYR

UniProtKB: Stromal cell-derived factor 1

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Macromolecule #4: Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophoru...

MacromoleculeName: Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase catalytic subunit
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Oplophorus-luciferin 2-monooxygenase
Source (natural)Organism: Oplophorus gracilirostris (arthropod)
Molecular weightTheoretical: 72.689641 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKGSADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLLVPRGSM EGISIYTSDN YTEEMGSGDY D SMKEPCFR ...String:
MKTIIALSYI FCLVFADYKD DDDKGSADLE DNWETLNDNL KVIEKADNAA QVKDALTKMR AAALDAQKAT PPKLEDKSPD SPEMKDFRH GFDILVGQID DALKLANEGK VKEAQAAAEQ LKTTRNAYIQ KYLLVPRGSM EGISIYTSDN YTEEMGSGDY D SMKEPCFR EENANFNKIF LPTIYSIIFL TGIVGNGLVI LVMGYQKKLR SMTDKYRLHL SVADLLFVIT LPFWAVDAVA NW YFGNFLC KAVHVIYTVS LYSSVLILAF ISLDRYLAIV HATNSQRPRK LLAEKVVYVG VWIPALLLTI PDFIFANVSE ADD RYICDR FYPNDLWVVV FQFQHIMVGL ILPGIVILSC YCIIISKLSH SKGHQKRKAL KTTVILILAF FACWLPYYIG ISID SFILL EIIKQGCEFE NTVHKWISIT EALAFFHCCL NPILYAFLGA KFKTSAQHAL TSVSRGSSLK ILSKGKRGGH SSVST ESES SSFHSSVFTL EDFVGDWEQT AAYNLDQVLE QGGVSSLLQN LAVSVTPIQR IVRSGENALK IDIHVIIPYE GLSADQ MAQ IEEVFKVVYP VDDHHFKVIL PYGTLVIDGV TPNMLNYFGR PYEGIAVFDG KKITVTGTLW NGNKIIDERL ITPDGSM LF RVTINS

UniProtKB: Soluble cytochrome b562, C-X-C chemokine receptor type 4, Oplophorus-luciferin 2-monooxygenase catalytic subunit

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Macromolecule #5: Guanine nucleotide-binding protein G(i) subunit alpha-1

MacromoleculeName: Guanine nucleotide-binding protein G(i) subunit alpha-1
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.445059 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF

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

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Macromolecule #6: single-chain variable fragment scFv16

MacromoleculeName: single-chain variable fragment scFv16 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.784896 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 KAAAHHHHHH HH

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Macromolecule #7: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 7 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 194772
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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