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- PDB-8u4t: Structure of tetrameric CXCR4 in complex with REGN7663 Fab -

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Basic information

Entry
Database: PDB / ID: 8u4t
TitleStructure of tetrameric CXCR4 in complex with REGN7663 Fab
Components
  • C-X-C chemokine receptor type 4
  • REGN7663 Fab heavy chain
  • REGN7663 Fab light chain
KeywordsSIGNALING PROTEIN/IMMUNE SYSTEM / GPCR / chemokine receptor / tetramer / oligomer / antibody / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


C-X-C motif chemokine 12 receptor activity / positive regulation of macrophage migration inhibitory factor signaling pathway / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / C-X-C chemokine receptor activity / positive regulation of vasculature development / Signaling by ROBO receptors / regulation of chemotaxis ...C-X-C motif chemokine 12 receptor activity / positive regulation of macrophage migration inhibitory factor signaling pathway / Specification of primordial germ cells / CXCL12-activated CXCR4 signaling pathway / myosin light chain binding / myelin maintenance / C-X-C chemokine receptor activity / positive regulation of vasculature development / Signaling by ROBO receptors / regulation of chemotaxis / Formation of definitive endoderm / C-C chemokine receptor activity / Developmental Lineage of Pancreatic Acinar Cells / C-C chemokine binding / Chemokine receptors bind chemokines / anchoring junction / dendritic cell chemotaxis / cellular response to cytokine stimulus / cell leading edge / positive regulation of oligodendrocyte differentiation / Binding and entry of HIV virion / regulation of cell adhesion / coreceptor activity / neurogenesis / ubiquitin binding / cell chemotaxis / calcium-mediated signaling / G protein-coupled receptor activity / brain development / response to virus / late endosome / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / virus receptor activity / actin binding / cytoplasmic vesicle / G alpha (i) signalling events / early endosome / response to hypoxia / lysosome / immune response / positive regulation of cell migration / G protein-coupled receptor signaling pathway / inflammatory response / external side of plasma membrane / apoptotic process / ubiquitin protein ligase binding / cell surface / protein-containing complex / extracellular exosome / plasma membrane / cytoplasm
Similarity search - Function
CXC chemokine receptor 4 N-terminal domain / CXCR4 Chemokine receptor N terminal / CXC chemokine receptor 4/atypical chemokine receptor 2 / Chemokine receptor family / : / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
CHOLESTEROL / Chem-D21 / C-X-C chemokine receptor type 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsSaotome, K. / McGoldrick, L.L. / Franklin, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Structural insights into CXCR4 modulation and oligomerization.
Authors: Kei Saotome / Luke L McGoldrick / Jo-Hao Ho / Trudy F Ramlall / Sweta Shah / Michael J Moore / Jee Hae Kim / Raymond Leidich / William C Olson / Matthew C Franklin /
Abstract: Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an ...Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood. Here, we use cryo-electron microscopy to investigate various modes of human CXCR4 regulation. CXCL12 activates CXCR4 by inserting its N terminus deep into the CXCR4 orthosteric pocket. The binding of US Food and Drug Administration-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the seven-transmembrane-helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its complementarity-determining region H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal modes of G-protein-coupled receptor oligomerization. We show that CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function.
#1: 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
DepositionSep 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
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Revision 1.1Oct 2, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: REGN7663 Fab light chain
H: REGN7663 Fab heavy chain
R: C-X-C chemokine receptor type 4
F: REGN7663 Fab light chain
G: REGN7663 Fab heavy chain
I: C-X-C chemokine receptor type 4
O: REGN7663 Fab light chain
P: REGN7663 Fab heavy chain
Q: C-X-C chemokine receptor type 4
Y: REGN7663 Fab light chain
Z: REGN7663 Fab heavy chain
AA: C-X-C chemokine receptor type 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)493,08432
Polymers484,19812
Non-polymers8,88620
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "W"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "CA"
d_5ens_1chain "D"
d_6ens_1chain "E"
d_7ens_1chain "K"
d_8ens_1chain "M"
d_9ens_1chain "N"
d_10ens_1chain "V"
d_11ens_1chain "A"
d_12ens_1chain "X"
d_1ens_2chain "AA"
d_2ens_2chain "I"
d_3ens_2chain "Q"
d_4ens_2chain "R"
d_1ens_3chain "T"
d_2ens_3chain "J"
d_3ens_3chain "BA"
d_4ens_3chain "S"
d_1ens_4chain "Y"
d_2ens_4chain "L"
d_3ens_4chain "O"
d_4ens_4chain "F"
d_1ens_5chain "Z"
d_2ens_5chain "H"
d_3ens_5chain "P"
d_4ens_5chain "G"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1CLRCLRCLRCLRAABA701
d_21ens_1CLRCLRCLRCLRRQ705
d_31ens_1CLRCLRCLRCLRRN702
d_41ens_1CLRCLRCLRCLRAAFA705
d_51ens_1CLRCLRCLRCLRIR701
d_61ens_1CLRCLRCLRCLRIS702
d_71ens_1CLRCLRCLRCLRIV705
d_81ens_1CLRCLRCLRCLRQW701
d_91ens_1CLRCLRCLRCLRQX702
d_101ens_1CLRCLRCLRCLRQAA705
d_111ens_1CLRCLRCLRCLRRM701
d_121ens_1CLRCLRCLRCLRAACA702
d_11ens_2METMETGLYGLYAAL24 - 30642 - 324
d_21ens_2METMETGLYGLYIF24 - 30642 - 324
d_31ens_2METMETGLYGLYQI24 - 30642 - 324
d_41ens_2METMETGLYGLYRC24 - 30642 - 324
d_11ens_3CLRCLRCLRCLRQY703
d_12ens_3D21D21D21D21QZ704
d_21ens_3CLRCLRCLRCLRIT703
d_22ens_3D21D21D21D21IU704
d_31ens_3CLRCLRCLRCLRAADA703
d_32ens_3D21D21D21D21AAEA704
d_41ens_3CLRCLRCLRCLRRO703
d_42ens_3D21D21D21D21RP704
d_11ens_4ASPASPLYSLYSYJ1 - 1121 - 112
d_21ens_4ASPASPLYSLYSLA1 - 1121 - 112
d_31ens_4ASPASPLYSLYSOG1 - 1121 - 112
d_41ens_4ASPASPLYSLYSFD1 - 1121 - 112
d_11ens_5GLNGLNSERSERZK1 - 1251 - 125
d_21ens_5GLNGLNSERSERHB1 - 1251 - 125
d_31ens_5GLNGLNSERSERPH1 - 1251 - 125
d_41ens_5GLNGLNSERSERGE1 - 1251 - 125

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5

NCS oper:
IDCodeMatrixVector
1given(-0.716630915866, -0.330933900981, -0.613940456076), (0.67006786711, -0.570923443203, -0.474400121699), (-0.193517916205, -0.751351565635, 0.630889563177)405.366152124, 176.716852991, 176.249385601
2given(-0.251747513308, -0.892696649504, -0.373785876549), (-0.967361856082, 0.220583039657, 0.124716326174), (-0.0288830216839, 0.392983224298, -0.919091919494)372.954581062, 261.718487604, 188.12956411
3given(0.670067867219, -0.570923443109, -0.474400121658), (0.716630915786, 0.330933901097, 0.613940456107), (-0.193517916123, -0.751351565656, 0.630889563178)176.715852955, -99.3651521313, 176.249385591
4given(-1), (-1), (1)305.999, 306.001
5given(0.967361856081, -0.220583039657, -0.124716326174), (-0.251747513309, -0.892696649504, -0.373785876549), (-0.0288830216842, 0.392983224299, -0.919091919494)44.281512396, 372.954581062, 188.12956411
6given(-0.67006786722, 0.570923443112, 0.474400121654), (-0.716630915784, -0.330933901097, -0.613940456109), (-0.193517916127, -0.751351565653, 0.630889563179)129.283147046, 405.366152131, 176.249385591
7given(3.10396153225E-12, 1, -4.79868914082E-12), (-1, 3.10396153225E-12, -7.0682546781E-12), (-7.06825467808E-12, 4.79868914084E-12, 1)-0.000999999939722, 305.999, 4.33431068814E-10
8given(0.251747513308, 0.892696649504, 0.373785876549), (0.967361856082, -0.220583039657, -0.124716326174), (-0.0288830216842, 0.392983224299, -0.919091919494)-66.9545810619, 44.2815123959, 188.12956411
9given(0.716630915784, 0.330933901097, 0.613940456108), (-0.670067867219, 0.570923443112, 0.474400121654), (-0.193517916127, -0.751351565653, 0.630889563179)-99.3661521313, 129.283147045, 176.249385591
10given(3.09441361424E-12, -1, -4.8012819066E-12), (1, 3.09441361424E-12, -7.07276532046E-12), (7.07276532047E-12, -4.80128190658E-12, 1)306.001, 0.00100000037094, -4.33772129327E-10
11given(-0.967361856082, 0.220583039657, 0.124716326174), (0.251747513308, 0.892696649504, 0.373785876549), (-0.0288830216843, 0.392983224298, -0.919091919494)261.717487604, -66.9535810619, 188.12956411
12given(-1), (-1), (1)305.999, 306.001
13given(2.22044604925E-16, 1), (-1, 2.22044604925E-16), (1)-0.00100000000006, 305.999
14given(-2.22044604925E-16, -1), (1, -2.22044604925E-16), (1)306.001, 0.00099999999992
15given(3.5527136788E-15, 1, -6.3255416134E-15), (-1, 3.5527136788E-15, -4.15828195894E-16), (-4.15828195894E-16, 6.3255416134E-15, 1)3.12638803734E-13, 306, -8.24229573482E-13
16given(4.81414907938E-12, -1, -6.48621946459E-12), (1, 4.81414907938E-12, 2.09991876019E-13), (-2.09991875988E-13, -6.48621946459E-12, 1)305.999, 0.00099999925996, 9.89146542452E-10
17given(-1), (-1), (1)306, 306
18given(2.22044604925E-16, -1), (1, 2.22044604925E-16), (1)306.001, 0.00100000000026
19given(-2.22044604925E-16, 1), (-1, -2.22044604925E-16), (1)-0.00100000000022, 305.999
20given(-1), (-1), (1)305.999, 306.001
21given(2.22044604925E-16, -1), (1, 2.22044604925E-16), (1)306.001, 0.000999999999749
22given(2.22044604925E-16, 1), (-1, 2.22044604925E-16), (1)-0.001, 305.999
23given(-1), (-1), (1)305.999, 306.001

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Components

#1: Antibody
REGN7663 Fab light chain


Mass: 24185.904 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody
REGN7663 Fab heavy chain


Mass: 25799.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein
C-X-C chemokine receptor type 4


Mass: 71063.609 Da / Num. of mol.: 4
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
#4: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C27H46O
#5: Chemical
ChemComp-D21 / (2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate


Mass: 674.929 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H71O8P
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetrameric CXCR4 in complex with REGN7663 Fab / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 31775 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 74.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003617436
ELECTRON MICROSCOPYf_angle_d0.702123768
ELECTRON MICROSCOPYf_chiral_restr0.04412708
ELECTRON MICROSCOPYf_plane_restr0.00622852
ELECTRON MICROSCOPYf_dihedral_angle_d7.36572472
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAAAELECTRON MICROSCOPYNCS constraints0.000663739204293
ens_1d_3BAAAELECTRON MICROSCOPYNCS constraints0.000642142585803
ens_1d_4BAAAELECTRON MICROSCOPYNCS constraints0.000663739204286
ens_1d_5BAAAELECTRON MICROSCOPYNCS constraints8.2862810229E-14
ens_1d_6BAAAELECTRON MICROSCOPYNCS constraints0.000642142585804
ens_1d_7BAAAELECTRON MICROSCOPYNCS constraints0.000663739204291
ens_1d_8BAAAELECTRON MICROSCOPYNCS constraints4.38822772758E-11
ens_1d_9BAAAELECTRON MICROSCOPYNCS constraints0.000642142585809
ens_1d_10BAAAELECTRON MICROSCOPYNCS constraints0.000663739204289
ens_1d_11BAAAELECTRON MICROSCOPYNCS constraints4.38813261206E-11
ens_1d_12BAAAELECTRON MICROSCOPYNCS constraints0.000642142585807
ens_2d_2LAAELECTRON MICROSCOPYNCS constraints2.52406072743E-13
ens_2d_3LAAELECTRON MICROSCOPYNCS constraints1.76352069246E-13
ens_2d_4LAAELECTRON MICROSCOPYNCS constraints1.59473020693E-13
ens_3d_2YQELECTRON MICROSCOPYNCS constraints7.64452849159E-14
ens_3d_3YQELECTRON MICROSCOPYNCS constraints3.89594464438E-11
ens_3d_4YQELECTRON MICROSCOPYNCS constraints3.46275695933E-14
ens_4d_2JYELECTRON MICROSCOPYNCS constraints2.66857759286E-13
ens_4d_3JYELECTRON MICROSCOPYNCS constraints3.52836598698E-13
ens_4d_4JYELECTRON MICROSCOPYNCS constraints3.06300044434E-13
ens_5d_2KZELECTRON MICROSCOPYNCS constraints4.46294801971E-13
ens_5d_3KZELECTRON MICROSCOPYNCS constraints6.04406535245E-14
ens_5d_4KZELECTRON MICROSCOPYNCS constraints3.86684612376E-13

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