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

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Basic information

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


ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / cytolysis in another organism / vertebrate eye-specific patterning ...ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / cytolysis in another organism / 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 / receptor-mediated endocytosis / cell-matrix adhesion / positive regulation of superoxide anion generation / integrin-mediated signaling pathway / response to ischemia / 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 / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Integrin alpha cytoplasmic region / Integrin alpha-2 ...: / Integrin alpha-X-like, Ig-like domain 3 / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / 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 domain superfamily / Integrin alpha, N-terminal / 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)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)96,09510
Polymers95,6013
Non-polymers4937
Water362
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)384,37840
Polymers382,40612
Non-polymers1,97228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)122.107, 122.107, 133.697
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

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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: 37682.680 Da / Num. of mol.: 1
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 / Neutrophil adherence receptor


Mass: 22293.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): TUNER / References: UniProt: P11215

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Non-polymers , 3 types, 9 molecules

#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / 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 / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Crystallization drops were prepared by mixing 1.0 uL LukGH/huCD11b-I complex (5.2 mg/mL) in 25 mM HEPES (pH 7.5), 1 mM MgCl2 with 0.5 uL reservoir solution containing 30% (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: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.748→45.081 Å / Num. obs: 14539 / % possible obs: 53.8 % / Redundancy: 12.6 % / Biso Wilson estimate: 53.18 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.09 / Rrim(I) all: 0.347 / Net I/σ(I): 7.8
Reflection shellResolution: 2.748→2.994 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.668 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 902 / CC1/2: 0.627 / Rpim(I) all: 0.486 / Rrim(I) all: 1.739 / % possible all: 15

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3177refinement
XDSJanuary 26, 2018data reduction
STARANISO2.2.7 (8-Dec-2018)data scaling
Aimless0.7.3data scaling
PHASER2.7.17phasing
Coot0.8.9.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LukGH dimer from the structure of its complex with mouse CD11b I-domain (CD11b-I) and the modified huCD11b-I domain (PDB code 1IDO) lacking the C-terminal alpha-helix (residues 303-315)

1ido


Resolution: 2.75→45.08 Å / SU ML: 0.3789 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.8887
Details: The structure was refined against the diffraction data anisotropically scaled in STARANISO. The analyzed crystal diffracted to resolutions 2.75 angstrom along a* and b*, but only to 4.79 ...Details: The structure was refined against the diffraction data anisotropically scaled in STARANISO. The analyzed crystal diffracted to resolutions 2.75 angstrom along a* and b*, but only to 4.79 angstrom along c*. The reflection file contains two data blocks: 1. data processed with STARANISO and used in the final refinement; 2. scaled and merged intensities to which no restrictive resolution cut-off has been applied.
RfactorNum. reflection% reflectionSelection details
Rfree0.2812 658 4.53 %Random selection
Rwork0.2393 ---
obs0.2412 14518 53.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 61.12 Å2
Refinement stepCycle: LAST / Resolution: 2.75→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5730 0 25 2 5757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315872
X-RAY DIFFRACTIONf_angle_d0.78137934
X-RAY DIFFRACTIONf_chiral_restr0.0478858
X-RAY DIFFRACTIONf_plane_restr0.00431027
X-RAY DIFFRACTIONf_dihedral_angle_d12.42933517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.960.3209370.331703X-RAY DIFFRACTION13.99
2.96-3.260.3898690.31331483X-RAY DIFFRACTION29.3
3.26-3.730.33311200.26212437X-RAY DIFFRACTION47.93
3.73-4.690.23671820.22423841X-RAY DIFFRACTION74.17
4.69-45.090.28312500.23195396X-RAY DIFFRACTION99.65
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)
10.744049907456-0.2184117370780.264885119150.4700458941790.2579409758420.2836202120640.07266678915970.271853502401-0.738950667615-0.133028430559-0.08927528952920.2365376015770.072401430617-0.02412346691980.1243799816220.1627299499930.00136743300945-0.01983990663640.158244835886-0.131208519204-0.0633970914191-2.4837834210827.859732179434.1014747771
20.6062108323430.0986349357261-0.002909967946650.391399041206-0.1671724664090.22700211054-0.0502622240830.293705513457-0.544014945641-0.1940564176430.0369959098777-0.3828884691830.109466478321-0.0953678086822-0.04459982922620.1883828853340.08378946559420.04209682925220.1329843917430.006245982220280.18508708774522.787937815635.958366760335.3320059225
30.112433042635-0.0603519441385-0.01092738403350.0425204712866-0.002061950517580.0796191322889-0.11251455418-0.000327635914492-0.265992398048-0.0182181134870.228146280942-0.291965118920.2554053167690.1675182166780.02554992718850.3775021569270.0846050032280.1115606631260.315705596312-0.1301440236060.76599455605926.5611280193.2882399057336.3648250407
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'G' and resid 17 through 304)
2X-RAY DIFFRACTION2(chain 'H' and resid 45 through 324)
3X-RAY DIFFRACTION3(chain 'C' and resid 132 through 299)

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