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- PDB-8ce9: Crystal structure of human Cd11b I domain in C121 space group -

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Basic information

Entry
Database: PDB / ID: 8ce9
TitleCrystal structure of human Cd11b I domain in C121 space group
ComponentsIntegrin alpha-M
KeywordsCELL ADHESION / ITGAMA integrin leukocytes
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning ...ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / cell-matrix adhesion / receptor-mediated endocytosis / positive regulation of superoxide anion generation / 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 / external side of plasma membrane / innate immune response / 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 Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site ...: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / 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 / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKoekemoer, L. / Williams, E. / Ni, X. / Gao, Q. / Coker, J. / MacLean, E.M. / Wright, N.D. / Marsden, B. / Von Delft, F. / Schwenzer, A. / Midwood, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
University of Oxford, Medical Sciences Internal Fund (MSIF) United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human Cd11b I domain in C121 space group
Authors: Koekemoer, L. / Williams, E. / Ni, X. / Gao, Q. / Coker, J. / MacLean, E.M. / Wright, N.D. / Marsden, B. / Von Delft, F. / Schwenzer, A. / Midwood, K.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Integrin alpha-M
A: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,02027
Polymers49,2982
Non-polymers1,72225
Water1,49583
1
B: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,46213
Polymers24,6491
Non-polymers81312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,55814
Polymers24,6491
Non-polymers90913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.495, 51.494, 90.172
Angle α, β, γ (deg.)90.000, 132.961, 90.000
Int Tables number5
Space group name H-MC121

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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: 24648.975 Da / Num. of mol.: 2
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 25% PEG Smear Medium 0.1M cacodylate pH 5.5 0.2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.11→65.99 Å / Num. obs: 23208 / % possible obs: 92.5 % / Redundancy: 6.4 % / CC1/2: 0.981 / Net I/σ(I): 7.5
Reflection shellResolution: 2.11→2.15 Å / Num. unique obs: 728 / CC1/2: 0.298

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→65.989 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 6.435 / SU ML: 0.163 / Cross valid method: FREE R-VALUE / ESU R: 0.243 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2389 1085 4.675 %
Rwork0.1883 22123 -
all0.191 --
obs-23208 92.458 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.606 Å2
Baniso -1Baniso -2Baniso -3
1-1.069 Å2-0 Å21.006 Å2
2---2.663 Å20 Å2
3----0.102 Å2
Refinement stepCycle: LAST / Resolution: 2.11→65.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2974 0 105 83 3162
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133164
X-RAY DIFFRACTIONr_bond_other_d0.0020.0153023
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6584251
X-RAY DIFFRACTIONr_angle_other_deg1.2831.5766926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2955392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42422.426169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44315520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3131521
X-RAY DIFFRACTIONr_chiral_restr0.0740.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02746
X-RAY DIFFRACTIONr_nbd_refined0.210.2680
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.22892
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21506
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21466
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2127
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.215
X-RAY DIFFRACTIONr_nbd_other0.2110.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.210
X-RAY DIFFRACTIONr_mcbond_it2.3243.2281544
X-RAY DIFFRACTIONr_mcbond_other2.3213.2261542
X-RAY DIFFRACTIONr_mcangle_it3.2844.8371935
X-RAY DIFFRACTIONr_mcangle_other3.2814.8371935
X-RAY DIFFRACTIONr_scbond_it3.1563.5621620
X-RAY DIFFRACTIONr_scbond_other3.1553.5631621
X-RAY DIFFRACTIONr_scangle_it4.5575.1952313
X-RAY DIFFRACTIONr_scangle_other4.5565.1962314
X-RAY DIFFRACTIONr_lrange_it6.10139.0323394
X-RAY DIFFRACTIONr_lrange_other6.09738.9963387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.11-2.1650.261660.28710240.28518470.7660.7559.01460.279
2.165-2.2240.313700.26111500.26417970.760.81767.89090.248
2.224-2.2890.258610.24113130.24117490.840.85578.55920.224
2.289-2.3590.283700.22714520.22916960.8570.86689.74060.21
2.359-2.4360.28840.20715470.21116390.8740.8999.51190.186
2.436-2.5210.267750.21614940.21815710.8840.90399.87270.187
2.521-2.6170.249590.20414930.20615520.9060.911000.177
2.617-2.7230.278600.19114240.19414840.8940.9181000.166
2.723-2.8440.264710.18913400.19314110.8950.9221000.165
2.844-2.9830.266480.18113150.18413630.880.9231000.158
2.983-3.1440.251410.19212580.19312990.8890.9171000.168
3.144-3.3340.277640.18711530.19212170.8980.9291000.168
3.334-3.5630.19600.18110870.18211470.9380.9421000.165
3.563-3.8480.238380.16710480.16910860.9290.9571000.157
3.848-4.2140.184490.1539360.1549850.9540.9661000.143
4.214-4.7090.198800.1418430.1469230.9620.9731000.14
4.709-5.4330.198400.167490.1617890.9560.9651000.155
5.433-6.6420.291160.2026700.2046860.9270.9451000.189
6.642-9.3460.274170.1845210.1865380.9010.941000.179
9.346-65.9890.233160.2163050.2173210.9150.9131000.23

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