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- PDB-7p2d: Structure of alphaMbeta2/Cd11bCD18 headpiece in complex with a na... -

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Basic information

Entry
Database: PDB / ID: 7p2d
TitleStructure of alphaMbeta2/Cd11bCD18 headpiece in complex with a nanobody
Components
  • Integrin beta
  • Isoform 2 of Integrin alpha-M
  • hCD11bNb1 nanobody
KeywordsIMMUNE SYSTEM / integrin receptor / complement / adhesion / phagocytosis
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of neutrophil degranulation / cellular extravasation / 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 ...ectodermal cell differentiation / positive regulation of neutrophil degranulation / cellular extravasation / 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 / leukocyte migration involved in inflammatory response / complement receptor mediated signaling pathway / cargo receptor activity / integrin complex / heterotypic cell-cell adhesion / leukocyte 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 / phagocytosis / Integrin cell surface interactions / response to mechanical stimulus / endothelial cell migration / specific granule membrane / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / receptor-mediated endocytosis / response to ischemia / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / membrane raft / innate immune response / external side of plasma membrane / Neutrophil degranulation / protein-containing complex binding / cell surface / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Integrin domains. Chain A, domain 2 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin beta / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsJensen, R.K. / Andersen, G.R.
Funding support Denmark, 3items
OrganizationGrant numberCountry
LundbeckfondenR155-2015-2666 Denmark
Danish Council for Independent Research4181-00137 Denmark
Novo Nordisk FoundationNNF18OC0052105 Denmark
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Structural insights into the function-modulating effects of nanobody binding to the integrin receptor alpha M beta 2.
Authors: Jensen, R.K. / Pedersen, H. / Lorentzen, J. / Laursen, N.S. / Vorup-Jensen, T. / Andersen, G.R.
#1: Journal: J Immunol / Year: 2021
Title: Complement Receptor 3 Forms a Compact High-Affinity Complex with iC3b.
Authors: Jensen, R.K. / Bajic, G. / Sen, M. / Springer, T.A. / Vorup-Jensen, T. / Andersen, G.R.
History
DepositionJul 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Integrin alpha-M
B: Integrin beta
C: hCD11bNb1 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,83010
Polymers150,8313
Non-polymers1,9997
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6870 Å2
ΔGint2 kcal/mol
Surface area61360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.100, 114.100, 250.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Isoform 2 of 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: 84010.945 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: Homo sapiens (human) / References: UniProt: P11215
#2: Protein Integrin beta


Mass: 52692.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2 / Production host: Homo sapiens (human) / References: UniProt: A0A494C0X7

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Antibody / Non-polymers , 2 types, 3 molecules C

#3: Antibody hCD11bNb1 nanobody


Mass: 14127.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Sugars , 2 types, 5 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 1:1 ratio with reservoir containing 1.25 M sodium malonate, 76 mM HEPES pH 8.0, 24 mM HEPES pH 6.5, and 0.5% Jeffamine ED2001 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 EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3.2→46 Å / Num. obs: 31887 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 36 % / Biso Wilson estimate: 99.86 Å2 / CC1/2: 0.99 / Rsym value: 0.114 / Net I/σ(I): 20.7
Reflection shellResolution: 3.2→3.35 Å / Redundancy: 37 % / Num. unique obs: 4057 / CC1/2: 0.87 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NEH

4neh


Resolution: 3.2→45.95 Å / SU ML: 0.5018 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.5214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Data was carried out against a data corrected for anisotropy by the STARANISO server
RfactorNum. reflection% reflection
Rfree0.2948 1131 4.28 %
Rwork0.2605 25291 -
obs0.2619 26422 82.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 127.62 Å2
Refinement stepCycle: LAST / Resolution: 3.2→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10291 0 128 0 10419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006110614
X-RAY DIFFRACTIONf_angle_d1.155714359
X-RAY DIFFRACTIONf_chiral_restr0.0721610
X-RAY DIFFRACTIONf_plane_restr0.01621895
X-RAY DIFFRACTIONf_dihedral_angle_d6.77111499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.350.3934550.34361248X-RAY DIFFRACTION33.12
3.35-3.520.3002720.29741751X-RAY DIFFRACTION46.78
3.52-3.740.36061420.3243022X-RAY DIFFRACTION80.53
3.74-4.030.32841750.29873796X-RAY DIFFRACTION99.95
4.03-4.440.30711600.26613783X-RAY DIFFRACTION99.95
4.44-5.080.26131700.23693806X-RAY DIFFRACTION99.92
5.08-6.390.32081760.27223860X-RAY DIFFRACTION100
6.4-45.950.26241810.23284025X-RAY DIFFRACTION99.88
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)
13.541415142940.783196968826-1.579046963494.35871386805-0.6263982324383.72306826357-0.333127503661-0.533119989715-0.2479661708990.1915827133080.324360489199-0.03162873900871.064497269340.267016770954-0.1035617336290.7343849904460.08241564905520.02304136589420.4737059435370.1160841111830.47565842899553.8565966954-29.3884792332-44.8852535073
23.844207573410.596504389224-1.458960727162.59137837991-0.2279382636450.706471126587-0.5214682251120.8527879943370.852385465313-0.1139378210220.343948365965-0.545613021073-1.489375819831.770553208930.1027977833181.08754141108-0.737111760724-0.2657330941192.016056358430.1028592575110.92750309319236.4648794564-65.434031854-13.6964467284
32.743324353-1.390145504450.8449886603737.12296656497-1.501718657432.76071809420.3272144359190.2878885409971.402508015520.274428847836-0.728708423714-1.07192429843-1.366701606920.5255325802630.4712559285351.31735216529-0.3543589727920.3704295514491.24064133351-0.06631778904991.6256559709175.138282664513.3185203728-62.8555742791
44.47491447256-0.4377511611461.524910530054.99701829441-0.6370216205083.86615784871-0.734730165775-0.8775708368931.30456118177-0.720652989599-0.193527795859-0.446830832791-1.74745827353-1.028870673370.7870641471352.218946875750.359185426932-0.3741454320221.43996754192-0.1433302710820.8644732182137.978025945926.6864938317-69.1179051415
55.11102246182.91987880917-3.161363200597.057849432-1.124346435262.1658281867-0.0905152049625-0.73605274641-0.231117984517-0.1070418559950.1983332458550.983431757225-0.00476752130684-1.32956671255-0.02336802748980.6160940379710.0969993909179-0.07076425081281.721827843880.3324535126790.79578116929821.660220029-2.26627441508-64.7377516285
62.854146394340.119805572262-0.6619960563540.7960561751760.1179314965491.15920521589-0.2040369458160.692213210711-0.734600714211-0.2295497530310.5077229367120.9608198799281.19895911093-1.5912019050.2463344754341.26085423832-1.240224685880.07743643145171.900307188970.6707744229991.0643238806722.57281985-36.5320795001-55.5772807637
76.263112828551.46750969931.114038270981.021850796510.8418587160270.6869190731540.181464348071-0.201919698176-0.256708229456-0.469367284111-0.139979832687-0.457480165403-0.5580078737380.980481220403-0.01069399987991.65156498117-0.0733480908374-0.1188717721981.389211472370.002055161537080.90126775153646.025241700825.5953787107-84.2692752669
84.75201083788-0.8429145480791.292031677952.78051995161-1.571889828981.398425770061.16724979681-0.104074277265-1.581860828360.897376960062-0.3625821898280.2143912163562.405105679570.622157855687-0.7459879067773.04332730464-0.052578187556-0.3803455354921.19968394772-0.04485044341241.0613270800131.0576908969-97.2501384644-2.37053626052
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and (resid 1:129 or resid 325:600 or resid 1001:1002 or resid 2001:2002 )AA - I1 - 20021
22chain A and (resid 130:324 or resid 2003 )AA130 - 324130 - 324
33chain A and (resid 601:755 or resid 1021:1022 )AA - G601 - 1022601
44chain B and (resid 1:59 )BJ1 - 591 - 59
55chain B and (resid 60:100 or resid 344:423 or resid 1031:1032 )BJ - B60 - 103260
66chain B and (resid 101:343 or resid 2011:2012 or resid 1041 )BJ - B101 - 1041101
77chain B and (resid 424:458)BJ424 - 458424 - 458
88chain CCC1 - 1211 - 121

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