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- PDB-9gmu: Structure ofhuman aM ligand binding domain in complex with the aC... -

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Basic information

Entry
Database: PDB / ID: 9gmu
TitleStructure ofhuman aM ligand binding domain in complex with the aCR3 nanobody
Components
  • Integrin alpha-M
  • aCR VHH
KeywordsIMMUNE SYSTEM / integrin receptor / ligand binding domain / antibody / VHH
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / vertebrate eye-specific patterning / : / complement component C3b binding / complement-mediated synapse pruning ...ectodermal cell differentiation / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / vertebrate eye-specific patterning / : / complement component C3b binding / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / complement receptor mediated signaling pathway / cargo receptor activity / integrin complex / heterotypic cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / negative regulation of dopamine metabolic process / forebrain development / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / response to mechanical stimulus / specific granule membrane / positive regulation of superoxide anion generation / heat shock protein binding / receptor-mediated endocytosis / cell-matrix adhesion / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / innate immune response / external side of plasma membrane / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : ...: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / von Willebrand factor type A domain / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLorentzen, J. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Lundbeckfonden Denmark
CitationJournal: To be published
Title: Structure of ligand bound aMb2
Authors: Lorentzen, J. / Andersen, G.R.
History
DepositionAug 29, 2024Deposition site: PDBE / Processing site: PDBE
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
A: Integrin alpha-M
B: Integrin alpha-M
C: aCR VHH
D: aCR VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1108
Polymers73,8694
Non-polymers2414
Water724
1
A: Integrin alpha-M
D: aCR VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0554
Polymers36,9342
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin alpha-M
C: aCR VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0554
Polymers36,9342
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.564, 56.142, 137.444
Angle α, β, γ (deg.)90.000, 128.610, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"
d_1ens_2chain "C"
d_2ens_2chain "D"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1ASPASPLYSLYSAA132 - 3159 - 192
d_2ens_1ASPASPLYSLYSBB132 - 3159 - 192
d_1ens_2GLNGLNSERSERCC2 - 1231 - 122
d_2ens_2GLNGLNSERSERDD2 - 1231 - 122

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.227453731318, 0.00334771585195, 0.973783134434), (-0.00149693253419, -0.999991707111, 0.00378746647968), (0.97378773832, -0.00231916103822, -0.227446833765)-90.0254155608, 39.4228954263, 113.148515914
2given(0.217611850385, 0.00178377891007, 0.976033760023), (0.00598843454109, -0.999981947937, 0.000492393201414), (0.976017018921, 0.00573776368612, -0.217618604086)-89.9335776279, 39.5711366437, 112.201404516

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Components

#1: Protein Integrin alpha-M / CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit ...CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit alpha / Leukocyte adhesion receptor MO1 / Neutrophil adherence receptor


Mass: 22480.596 Da / Num. of mol.: 2 / Fragment: UNP residues 145-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli (E. coli) / References: UniProt: P11215
#2: Antibody aCR VHH


Mass: 14453.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.05 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES, pH 7.0, 1.5 M Li2S04.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.8→49.25 Å / Num. obs: 11989 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 131.32 Å2 / CC1/2: 0.997 / Rsym value: 0.1689 / Net I/σ(I): 7.48
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1194 / CC1/2: 0.701 / CC star: 0.908 / Rsym value: 1.352 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.8→49.25 Å / SU ML: 0.4702 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 30.5553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2976 780 6.52 %
Rwork0.2418 11190 -
obs0.2453 11989 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 186.28 Å2
Refinement stepCycle: LAST / Resolution: 3.8→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4858 0 16 0 4874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594968
X-RAY DIFFRACTIONf_angle_d0.83186696
X-RAY DIFFRACTIONf_chiral_restr0.0505718
X-RAY DIFFRACTIONf_plane_restr0.0065876
X-RAY DIFFRACTIONf_dihedral_angle_d11.92761844
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.18221007266
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.304163073648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-4.040.32631250.26631855X-RAY DIFFRACTION100
4.04-4.350.33141350.23641833X-RAY DIFFRACTION100
4.35-4.790.24161310.19741840X-RAY DIFFRACTION99.6
4.79-5.480.29991310.22351859X-RAY DIFFRACTION100
5.48-6.90.31341270.2861878X-RAY DIFFRACTION99.65
6.9-49.250.2961310.24231925X-RAY DIFFRACTION99.32
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)
19.54185891109-0.112432070355-2.671914935194.75463568828-0.2480715511064.312936067590.08555842486470.151342328242-0.14977759722-2.33355982938-0.478657092677-1.24456464816-0.2380849013131.031272642920.4703966664573.3617896952-0.02208073223570.4985446435871.184980952170.08623051657691.3772396135118.034207586730.313308379354.3225969687
26.160346473680.438760870825-0.06774493676974.45557847315-0.2571478929579.570567403930.272803215984-1.06178784-0.5978411233351.28455479085-0.5794751765572.0520718349-0.0521322911699-0.1584881884220.1260605046041.56130068888-0.01397313711870.6889547937081.030452343430.06491630338542.57631667997-32.92287966339.28787782921118.278939809
36.834943091022.07645615087-1.78000386179.328500407720.4022214379383.39684589052-0.14107376986-0.508215513608-0.2661237609730.489909473418-0.3378564997010.0292706262858-0.3590024107971.044561742580.5849397523341.13701178455-0.129613799007-0.410770434171.473504561060.1648844550281.00919671148-4.7444215835211.6482301076104.110444799
45.56830338368-0.731340261614-0.6548921208069.93605168135-2.968500463716.71742400380.432921729417-1.23116729658-0.244342958009-0.578346096503-0.61310529706-0.822691608476-0.6083267845510.6951342672060.1861883458411.19167695186-0.0916562766783-0.3026779111581.416788670780.1661569445560.92951594584710.669312357227.945318780184.9822251004
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA132 - 3151 - 184
22chain BBB132 - 3151 - 184
33chain CCC2 - 1231 - 122
44chain DDD2 - 1231 - 122

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