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- PDB-9hll: murine aM I-domain in complex with nanobody aCR3 -

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Basic information

Entry
Database: PDB / ID: 9hll
Titlemurine aM I-domain in complex with nanobody aCR3
Components
  • Integrin alpha-M
  • aCR3 nanobody
KeywordsIMMUNE SYSTEM / antibody / integrin receptor / complement / phagocytosis
Function / homology
Function and homology information


positive regulation of mast cell differentiation / leukocyte adhesion to vascular endothelial cell / Toll Like Receptor 4 (TLR4) Cascade / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of microglial cell mediated cytotoxicity / neutrophil apoptotic process / opsonin binding / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...positive regulation of mast cell differentiation / leukocyte adhesion to vascular endothelial cell / Toll Like Receptor 4 (TLR4) Cascade / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of microglial cell mediated cytotoxicity / neutrophil apoptotic process / opsonin binding / Integrin cell surface interactions / Cell surface interactions at the vascular wall / vertebrate eye-specific patterning / complement component C3b binding / complement-mediated synapse pruning / leukocyte migration involved in inflammatory response / complement receptor mediated signaling pathway / activated T cell proliferation / heparan sulfate proteoglycan binding / microglia development / cargo receptor activity / phagocytosis, engulfment / leukocyte cell-cell adhesion / negative regulation of dopamine metabolic process / forebrain development / amyloid-beta clearance / positive regulation of protein targeting to membrane / phagocytosis / positive regulation of superoxide anion generation / neutrophil chemotaxis / Neutrophil degranulation / receptor-mediated endocytosis / integrin-mediated signaling pathway / microglial cell activation / cell-cell adhesion / heparin binding / cell adhesion / membrane raft / external side of plasma membrane / cell surface / metal ion binding / nucleus / membrane / 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 domain superfamily / Integrin alpha, N-terminal / 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 speciesMus musculus (house mouse)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsFruergaard, M.U. / Andersen, G.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Other privateLeo LF-OC-22-001076
Other privateAlexion Discovery RN7049 Denmark
Other governmentFNU 3103-00009B Denmark
CitationJournal: To Be Published
Title: murine aM I-domain in complex with nanobody aCR3
Authors: Fruergaard, M.U. / Andersen, G.R.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 17, 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: aCR3 nanobody
C: aCR3 nanobody
D: aCR3 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9807
Polymers65,6924
Non-polymers2883
Water1,820101
1
A: Integrin alpha-M
C: aCR3 nanobody


Theoretical massNumber of molelcules
Total (without water)36,7842
Polymers36,7842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.402, 127.444, 125.855
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "B" and ((resid 2 and (name N or name...
d_2ens_1(chain "C" and ((resid 2 and (name N or name...
d_3ens_1(chain "D" and ((resid 2 and (name N or name...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 2 - 123 / Label seq-ID: 1 - 122

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2CC
d_3DD

NCS oper:
IDCodeMatrixVector
1given(0.222815286782, 0.442511044296, -0.868641078727), (-0.648970368051, -0.597577721931, -0.470890993377), (-0.72745502223, 0.668644032298, 0.154027103796)18.0605174113, -38.460724444, -4.01403320353
2given(0.329754009379, 0.79529435423, 0.508693604666), (0.766934009318, -0.539882188903, 0.346899765721), (0.550522041929, 0.275742837142, -0.787966604061)13.2445366715, -58.5694941757, 53.101505385

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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


Mass: 22330.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgam / Production host: Escherichia coli (E. coli) / References: UniProt: P05555
#2: Antibody aCR3 nanobody


Mass: 14453.850 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Sep 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.17→35.04 Å / Num. obs: 33520 / % possible obs: 99.58 % / Redundancy: 13.6 % / Biso Wilson estimate: 46.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.0708 / Net I/σ(I): 20.64
Reflection shellResolution: 2.17→2.23 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.8807 / Num. unique obs: 2314 / CC1/2: 0.969 / CC star: 0.992 / % possible all: 97.2

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→35.04 Å / SU ML: 0.3109 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.0889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2594 2002 5.99 %
Rwork0.2024 31421 -
obs0.2057 33423 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.19 Å2
Refinement stepCycle: LAST / Resolution: 2.17→35.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4291 0 15 101 4407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114394
X-RAY DIFFRACTIONf_angle_d1.22255936
X-RAY DIFFRACTIONf_chiral_restr0.062623
X-RAY DIFFRACTIONf_plane_restr0.0122777
X-RAY DIFFRACTIONf_dihedral_angle_d14.20531583
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBX-RAY DIFFRACTIONTorsion NCS1.72559704419
ens_1d_3BBX-RAY DIFFRACTIONTorsion NCS1.26652085454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.230.32841410.25472154X-RAY DIFFRACTION97.2
2.23-2.290.30431330.26282225X-RAY DIFFRACTION99.2
2.29-2.350.3381380.25782228X-RAY DIFFRACTION99.66
2.36-2.430.35621480.25642206X-RAY DIFFRACTION99.37
2.43-2.520.34671410.2772230X-RAY DIFFRACTION99.66
2.52-2.620.29791470.25892208X-RAY DIFFRACTION99.83
2.62-2.740.3121280.23382248X-RAY DIFFRACTION99.87
2.74-2.880.25531550.22212232X-RAY DIFFRACTION99.87
2.88-3.060.28631420.23652238X-RAY DIFFRACTION99.96
3.06-3.30.26271440.21872237X-RAY DIFFRACTION99.92
3.3-3.630.27031450.18942250X-RAY DIFFRACTION99.87
3.63-4.160.22451410.18042304X-RAY DIFFRACTION100
4.16-5.230.19891420.15612285X-RAY DIFFRACTION100
5.23-35.040.26491570.19712376X-RAY DIFFRACTION99.61
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)
11.18566191422-0.405628200952-0.03538696534615.43402823763-0.9218344172383.63235401380.128276926744-0.147215621357-0.0460773141212-0.031923255299-0.2797206383890.5000552276060.05190552414990.003104283262190.1411214850630.223169664086-0.05896005919970.002370967584630.442198373313-0.05024695097080.375834020241-19.1446959107-17.3288647305-0.211016035664
22.145535171430.940467434423-0.9777045293952.79774080911-0.7951255619361.12461879364-0.8319070017840.382247283368-0.298247460117-0.8357103639260.347680953742-0.2963493277381.337254206430.08699036641460.372630550521.28980485165-0.03363848532170.2287323797360.683753533993-0.01500261576160.468192156201-17.6793932911-55.22910462219.96401690882
31.21544414568-0.301380649532-0.02621242882613.811924575110.006638327552093.28318901282-0.02422728038670.1507389082290.179907071581-0.988910676383-0.1352104109360.41481563023-0.700734438313-0.4343701733940.07231181162060.9449564370960.219172773204-0.2393927546150.563720409127-0.05672416902730.422865980311-18.97290128561.31976602924-26.5482602944
43.91513490848-1.075201029120.7762839503731.40364388983-0.3542112128763.16366728357-0.330092970330.2330097314020.311217629457-0.03861146614560.192015493352-0.1049522640.02862309251530.1399502150340.1139822142920.579296510101-0.0799296200157-0.02961341382160.4278139404270.03935780238760.373628657679-32.0034434961-38.549029422319.8631847889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA148 - 3281 - 181
22chain BBB2 - 1231 - 122
33chain CCC2 - 1231 - 122
44chain DDD2 - 1261 - 125

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