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- PDB-6rhv: Crystal structure of mouse CD11b I-domain (CD11b-I) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6rhv
TitleCrystal structure of mouse CD11b I-domain (CD11b-I) in complex with Staphylococcus aureus octameric bi-component leukocidin LukGH (LukH K319A mutant)
Components
  • (Beta-channel forming ...) x 2
  • Integrin alpha-M
KeywordsTOXIN / LEUKOCIDIN / PORE-FORMING TOXIN / OCTAMER / receptor / complex
Function / homology
Function and homology information


positive regulation of mast cell differentiation / positive regulation of hippocampal neuron apoptotic process / : / : / leukocyte adhesion to vascular endothelial cell / Toll Like Receptor 4 (TLR4) Cascade / : / cellular extravasation / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation ...positive regulation of mast cell differentiation / positive regulation of hippocampal neuron apoptotic process / : / : / leukocyte adhesion to vascular endothelial cell / Toll Like Receptor 4 (TLR4) Cascade / : / cellular extravasation / positive regulation of prostaglandin-E synthase activity / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / positive regulation of microglial cell mediated cytotoxicity / opsonin binding / neutrophil apoptotic process / Integrin cell surface interactions / Cell surface interactions at the vascular wall / complement component C3b binding / cytolysis in another organism / vertebrate eye-specific patterning / complement-mediated synapse pruning / negative regulation of dopamine metabolic process / leukocyte migration involved in inflammatory response / activated T cell proliferation / microglia development / heparan sulfate proteoglycan binding / cargo receptor activity / leukocyte cell-cell adhesion / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / positive regulation of protein targeting to membrane / phagocytosis / forebrain development / heat shock protein binding / Neutrophil degranulation / neutrophil chemotaxis / receptor-mediated endocytosis / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / apoptotic signaling pathway / microglial cell activation / cell-cell adhesion / heparin binding / membrane => GO:0016020 / cell adhesion / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / nucleus / metal ion binding / plasma membrane
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 ...Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Integrin alpha cytoplasmic region / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / 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 / Distorted Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-channel forming cytolysin / Beta-channel forming cytolysin / Integrin alpha-M / Uncharacterized leukocidin-like protein 2 / Uncharacterized leukocidin-like protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsTrstenjak, N. / Milic, D. / Djinovic-Carugo, K. / Badarau, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Christian Doppler ForschungsgesellschaftCD-Laboratory for High-Content Structural Biology and Biotechnology Austria
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular mechanism of leukocidin GH-integrin CD11b/CD18 recognition and species specificity.
Authors: Trstenjak, N. / Milic, D. / Graewert, M.A. / Rouha, H. / Svergun, D. / Djinovic-Carugo, K. / Nagy, E. / Badarau, A.
History
DepositionApr 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Beta-channel forming cytolysin
H: Beta-channel forming cytolysin
C: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,88610
Polymers95,3933
Non-polymers4937
Water6,413356
1
G: Beta-channel forming cytolysin
H: Beta-channel forming cytolysin
C: Integrin alpha-M
hetero molecules

G: Beta-channel forming cytolysin
H: Beta-channel forming cytolysin
C: Integrin alpha-M
hetero molecules

G: Beta-channel forming cytolysin
H: Beta-channel forming cytolysin
C: Integrin alpha-M
hetero molecules

G: Beta-channel forming cytolysin
H: Beta-channel forming cytolysin
C: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,54440
Polymers381,57212
Non-polymers1,97228
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)130.494, 130.494, 109.051
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Space group name HallP4ab2ab
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z
#3: y+1/2,-x+1/2,z
#4: x+1/2,-y+1/2,-z
#5: -x+1/2,y+1/2,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11H-582-

HOH

21H-649-

HOH

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Components

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Beta-channel forming ... , 2 types, 2 molecules GH

#1: Protein Beta-channel forming cytolysin / Bi-component leukocidin LukGH subunit G / Gamma-hemolysin component B / Gamma-hemolysin subunit B


Mass: 35625.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: lukG, ELQ85_15505, EP54_11070, EQ90_09460, HMPREF3211_02235, NCTC10654_02179, NCTC10702_03203, NCTC13131_01350, RK64_10675
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A0D6HCK9, UniProt: Q2FWP0*PLUS
#2: Protein Beta-channel forming cytolysin / Bi-component leukocidin LukGH subunit H / Leukocidin S subunit / Succinyl-diaminopimelate desuccinylase


Mass: 37624.578 Da / Num. of mol.: 1 / Mutation: K319A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: lukH, BTN44_11630, EP54_11065, EQ90_09455, HMPREF3211_02234, NCTC10654_02180, NCTC10702_03204, NCTC13131_01351, NCTC13196_01958, RK64_10680
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: A0A0D6HC73, UniProt: Q2FWN9*PLUS

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Protein , 1 types, 1 molecules C

#3: 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: 22143.066 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 BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: P05555

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Non-polymers , 3 types, 363 molecules

#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystallization drops were prepared by mixing 1.0 uL LukGH/moCD11b-I complex (5 mg/mL) in 25 mM HEPES (pH 7.5), 50 mM NaCl and 1 mM MgCl2 with 1.0 uL reservoir solution containing 25% (v/v) ...Details: Crystallization drops were prepared by mixing 1.0 uL LukGH/moCD11b-I complex (5 mg/mL) in 25 mM HEPES (pH 7.5), 50 mM NaCl and 1 mM MgCl2 with 1.0 uL reservoir solution containing 25% (v/v) Jeffamine-600 and 10% (v/v) DMSO.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.287→46.942 Å / Num. obs: 42957 / % possible obs: 99.59 % / Redundancy: 5.57 % / Biso Wilson estimate: 44.45 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1867 / Rpim(I) all: 0.08582 / Rrim(I) all: 0.206 / Net I/σ(I): 7.45
Reflection shellResolution: 2.287→2.369 Å / Redundancy: 4.5 % / Rmerge(I) obs: 2.277 / Mean I/σ(I) obs: 0.64 / Num. unique obs: 4124 / CC1/2: 0.212 / Rpim(I) all: 1.158 / Rrim(I) all: 2.566 / % possible all: 97.63

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3177refinement
XDSJanuary 26, 2018data reduction
XSCALEJan 26, 2018 BUILT=20180126data scaling
PHASER2.7.17phasing
Coot0.8.9.1model building
BUCCANEERv1.5model building
ARP/wARP7.4, patch 2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chains A and C from the PDB entry 5k59

5k59


Resolution: 2.29→46.94 Å / SU ML: 0.3141 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.6861
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2100 4.89 %Random selection
Rwork0.1875 ---
obs0.1895 42957 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 54.23 Å2
Refinement stepCycle: LAST / Resolution: 2.29→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6021 0 25 356 6402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00236203
X-RAY DIFFRACTIONf_angle_d0.49018379
X-RAY DIFFRACTIONf_chiral_restr0.0423888
X-RAY DIFFRACTIONf_plane_restr0.00231088
X-RAY DIFFRACTIONf_dihedral_angle_d12.95943716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.340.3651320.3192566X-RAY DIFFRACTION95.71
2.34-2.40.35581380.2972701X-RAY DIFFRACTION99.72
2.4-2.460.33141390.292692X-RAY DIFFRACTION99.82
2.46-2.540.341370.27352679X-RAY DIFFRACTION99.96
2.54-2.620.33721390.25622693X-RAY DIFFRACTION99.96
2.62-2.710.23551380.22882682X-RAY DIFFRACTION100
2.71-2.820.2841380.22312702X-RAY DIFFRACTION99.96
2.82-2.950.24511400.20462720X-RAY DIFFRACTION99.97
2.95-3.10.28151390.19412703X-RAY DIFFRACTION99.44
3.1-3.30.22461400.16662722X-RAY DIFFRACTION100
3.3-3.550.17031400.15142727X-RAY DIFFRACTION99.93
3.55-3.910.21841410.1512742X-RAY DIFFRACTION99.93
3.91-4.470.18971430.13882779X-RAY DIFFRACTION99.97
4.47-5.640.15651430.1522792X-RAY DIFFRACTION99.8
5.64-46.950.23161530.21582957X-RAY DIFFRACTION99.71
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)
10.5921620669480.1756920196350.05754130318130.7244601922740.2397170621181.14137321884-0.00284265444970.0652814511644-0.0244942067905-0.115960000884-0.0200072765362-0.142757367804-0.1081257103260.03208915095570.03926337952960.3071139283860.02094286488240.04088876082080.252495479464-0.01508665816560.3579686249331.0363502758-70.703667989427.5284458744
20.367303513722-0.01711277787620.1083372056560.2696402282340.01955964163911.20249051223-0.001718260762210.06325471722160.0437934323155-0.000461794166425-0.0149395075413-0.0694383141392-0.007787442116980.00814804344140.01892498708260.2971748146940.0008860715690490.02858784440590.315227922356-0.001991189346510.37398023369925.6412159045-46.705618736329.5078835595
34.556456734140.463524710349-0.1516564665193.710272103840.3689188858774.6702095220.002453995412910.245876740783-0.2044442827-0.05926758364240.1480063841-0.305762608703-0.1124170729240.34671015661-0.1555934885450.340981085613-0.05752785104080.001780790024050.442669440384-0.02252125183050.41047944602458.8339363434-45.276411431930.0397741642
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 18 through 304)
2X-RAY DIFFRACTION2(chain 'H' and resid 37 through 324)
3X-RAY DIFFRACTION3(chain 'C' and resid 132 through 301)

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