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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 / 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 / C-C chemokine receptor activity / endothelial tube morphogenesis / endothelial cell differentiation / C-C chemokine binding / Signaling by ROBO receptors / regulation of chemotaxis / cellular response to organonitrogen compound / positive regulation of chemotaxis / Formation of definitive endoderm / positive regulation of dendrite extension / anchoring junction / Chemokine receptors bind chemokines / dendritic cell chemotaxis / positive regulation of oligodendrocyte differentiation / epithelial cell development / cell leading edge / cellular response to cytokine stimulus / small molecule binding / detection of temperature stimulus involved in sensory perception of pain / regulation of calcium ion transport / Binding and entry of HIV virion / coreceptor activity / detection of mechanical stimulus involved in sensory perception of pain / regulation of cell adhesion / cardiac muscle contraction / neurogenesis / cell chemotaxis / response to activity / ubiquitin binding / G protein-coupled receptor activity / calcium-mediated signaling / brain development / neuron migration / response to virus / cellular response to xenobiotic stimulus / late endosome / virus receptor activity / positive regulation of cold-induced thermogenesis / actin binding / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / cytoplasmic vesicle / lysosome / response to hypoxia / early endosome / positive regulation of cell migration / immune response / inflammatory 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
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
CitationJournal: 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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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
Water0
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 / 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

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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 FIELDBright-field microscopy / 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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