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- PDB-9pwn: Crystal structure of Fabs 7411 in complex with TREM2 peptide -

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Basic information

Entry
Database: PDB / ID: 9pwn
TitleCrystal structure of Fabs 7411 in complex with TREM2 peptide
Components
  • 7411 Fab Heavy Chain
  • 7411 Fab Light Chain
  • TREM-2 stalk peptide
KeywordsIMMUNE SYSTEM / Fab / antibody / complex
Function / homology
Function and homology information


positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of C-C chemokine receptor CCR7 signaling pathway / excitatory synapse pruning / positive regulation of CD40 signaling pathway ...positive regulation of high-density lipoprotein particle clearance / regulation of toll-like receptor 6 signaling pathway / positive regulation of complement activation, classical pathway / detection of lipoteichoic acid / regulation of macrophage inflammatory protein 1 alpha production / regulation of hippocampal neuron apoptotic process / regulation of plasma membrane bounded cell projection organization / positive regulation of C-C chemokine receptor CCR7 signaling pathway / excitatory synapse pruning / positive regulation of CD40 signaling pathway / negative regulation of triglyceride storage / negative regulation of cell activation / detection of peptidoglycan / positive regulation of macrophage fusion / import into cell / sulfatide binding / negative regulation of macrophage colony-stimulating factor signaling pathway / positive regulation of antigen processing and presentation of peptide antigen via MHC class II / negative regulation of fat cell proliferation / lipoteichoic acid binding / positive regulation of engulfment of apoptotic cell / positive regulation of establishment of protein localization / positive regulation of synapse pruning / microglial cell activation involved in immune response / negative regulation of toll-like receptor 2 signaling pathway / negative regulation of autophagic cell death / respiratory burst after phagocytosis / negative regulation of astrocyte activation / positive regulation of CAMKK-AMPK signaling cascade / semaphorin receptor binding / positive regulation of low-density lipoprotein particle clearance / positive regulation of microglial cell migration / apolipoprotein A-I binding / detection of lipopolysaccharide / Other semaphorin interactions / T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / CXCL12-activated CXCR4 signaling pathway / negative regulation of toll-like receptor 4 signaling pathway / negative regulation of neuroinflammatory response / high-density lipoprotein particle binding / negative regulation of p38MAPK cascade / very-low-density lipoprotein particle binding / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of glial cell apoptotic process / complement-mediated synapse pruning / dendritic cell differentiation / microglial cell proliferation / semaphorin receptor complex / positive regulation of microglial cell activation / phagocytosis, recognition / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / negative regulation of NLRP3 inflammasome complex assembly / cellular response to lipoprotein particle stimulus / regulation of TOR signaling / regulation of resting membrane potential / positive regulation of phagocytosis, engulfment / cellular response to peptidoglycan / peptidoglycan binding / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of chemotaxis / positive regulation of amyloid-beta clearance / positive regulation of potassium ion transport / semaphorin receptor activity / phosphatidylethanolamine binding / positive regulation of proteasomal protein catabolic process / positive regulation of osteoclast differentiation / negative regulation of amyloid fibril formation / cellular response to lipid / kinase activator activity / regulation of interleukin-6 production / apoptotic cell clearance / dendritic spine maintenance / negative regulation of interleukin-1 beta production / phagocytosis, engulfment / regulation of innate immune response / phosphatidylserine binding / negative regulation of cholesterol storage / pyroptotic inflammatory response / regulation of cytokine production involved in inflammatory response / lipid homeostasis / cellular response to lipoteichoic acid / amyloid-beta clearance / positive regulation of ATP biosynthetic process / lipoprotein particle binding / positive regulation of intracellular signal transduction / humoral immune response / regulation of lipid metabolic process / positive regulation of interleukin-10 production / apolipoprotein binding / plasma membrane raft / negative regulation of tumor necrosis factor production / positive regulation of cholesterol efflux / social behavior / positive regulation of TOR signaling / response to axon injury / negative regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production involved in inflammatory response / astrocyte activation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction
Similarity search - Function
: / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Triggering receptor expressed on myeloid cells 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsArndt, J.W. / Chao, Q. / Cooke, H.A. / Almeida, A.D.S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Mabs / Year: 2025
Title: Building a potent TREM2 agonistic, biparatopic, common light chain antibody.
Authors: da Silva Almeida, A. / Geddie, M.L. / Bhate, A. / Quan, C. / Arndt, J.W. / Jiao, Y. / Santoro, J.C. / Noiman, L. / Vijayakumar, R. / Sanchez-Salazar, J. / Datta, A. / Antognetti, G. / ...Authors: da Silva Almeida, A. / Geddie, M.L. / Bhate, A. / Quan, C. / Arndt, J.W. / Jiao, Y. / Santoro, J.C. / Noiman, L. / Vijayakumar, R. / Sanchez-Salazar, J. / Datta, A. / Antognetti, G. / Hartana, C.A. / Wang, X.F. / Smith, B.A. / Bartlett, D. / Duncan, D. / Liu, C.C. / Otero Gutierrez, K. / Cameron, T.O. / Koirala, S. / Cooke, H.A.
History
DepositionAug 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: 7411 Fab Heavy Chain
L: 7411 Fab Light Chain
A: TREM-2 stalk peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89719
Polymers48,4983
Non-polymers1,39916
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7980 Å2
ΔGint-130 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.650, 71.760, 105.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide TREM-2 stalk peptide


Mass: 2058.123 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NZC2

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Antibody , 2 types, 2 molecules HL

#1: Antibody 7411 Fab Heavy Chain


Mass: 23308.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 7411 Fab Light Chain


Mass: 23131.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 194 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 11% w/v PEG 8000, 240 mM ammonium sulfate, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00007 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 174028 / % possible obs: 99.8 % / Redundancy: 5.2 % / CC1/2: 0.998 / Net I/σ(I): 8.52
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.7 % / Num. unique obs: 10755 / CC1/2: 0.565 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38.96 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.736 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21786 1766 5 %RANDOM
Rwork0.17772 ---
obs0.17974 33550 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å2-0 Å20 Å2
2---0.11 Å2-0 Å2
3----0.69 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 81 178 3611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163191
X-RAY DIFFRACTIONr_angle_refined_deg1.2991.7914779
X-RAY DIFFRACTIONr_angle_other_deg0.4541.7297398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5585447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.963513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34610544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02764
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1572.1361791
X-RAY DIFFRACTIONr_mcbond_other2.1532.1351791
X-RAY DIFFRACTIONr_mcangle_it3.0533.8222237
X-RAY DIFFRACTIONr_mcangle_other3.0523.8222238
X-RAY DIFFRACTIONr_scbond_it3.3722.5061727
X-RAY DIFFRACTIONr_scbond_other3.3712.5081728
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9334.4152543
X-RAY DIFFRACTIONr_long_range_B_refined6.79424.493697
X-RAY DIFFRACTIONr_long_range_B_other6.762243667
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 132 -
Rwork0.274 2515 -
obs--98.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.01431.1676-0.41411.6656-0.18530.28880.0976-0.13860.19730.0798-0.0417-0.0824-0.09560.0747-0.05590.0353-0.02280.010.0208-0.0230.0787-8.5179-39.63064.6768
20.79921.30340.082.16780.12810.00920.0679-0.06380.03960.0684-0.08270.00010.0017-0.00670.01480.0846-0.01640.03680.035-0.02680.1121-16.0926-26.859215.7602
311.0170.98431.45954.8827-0.67277.0958-0.0204-0.763-0.27330.42980.0267-0.30840.50790.2565-0.00630.1050.0285-0.0170.0870.00410.0295-29.6557-59.675514.6694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 221
2X-RAY DIFFRACTION2L1 - 212
3X-RAY DIFFRACTION3A131 - 147

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