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- PDB-8pih: Structure of Api m1 in complex with two nanobodies -

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Basic information

Entry
Database: PDB / ID: 8pih
TitleStructure of Api m1 in complex with two nanobodies
Components
  • Phospholipase A2
  • nanobdoy AM1-1
  • nanobody AM1-4
KeywordsALLERGEN / antibody / nanobody
Function / homology
Function and homology information


phospholipase A2 activity / phospholipase A2 / arachidonate secretion / lipid catabolic process / phospholipid metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 domain superfamily
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Apis mellifera (honey bee)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsAagaard, J.B. / Gandini, R. / Spillner, E. / Miehe, M. / Andersen, G.R.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish Council for Independent Research0135-00061B Denmark
CitationJournal: To be published
Title: Nanobody-based IgG formats as blocking antibodies of the major honeybee venom allergen Api m 1
Authors: Aagaard, J.B.
History
DepositionJun 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: Phospholipase A2
B: nanobody AM1-4
C: nanobdoy AM1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6934
Polymers41,6573
Non-polymers351
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-19 kcal/mol
Surface area17020 Å2
Unit cell
Length a, b, c (Å)133.960, 51.330, 73.250
Angle α, β, γ (deg.)90.000, 120.780, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

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Components

#1: Protein Phospholipase A2 / bvPLA2 / Allergen Api m I / Phosphatidylcholine 2-acylhydrolase


Mass: 15161.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: P00630, phospholipase A2
#2: Antibody nanobody AM1-4


Mass: 13606.994 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)
#3: Antibody nanobdoy AM1-1


Mass: 12889.257 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)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 0.2 M NaCl, 0.1 M Phosphate/citrate pH 4.2, 20% w/v polyethylene glycol (PEG) 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.76→42.02 Å / Num. obs: 42066 / % possible obs: 98.64 % / Redundancy: 4.4 % / Biso Wilson estimate: 27.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0778 / Net I/σ(I): 12.71
Reflection shellResolution: 1.76→1.823 Å / Redundancy: 4.6 % / Num. unique obs: 4105 / CC1/2: 0.68 / % possible all: 97.34

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→42.02 Å / SU ML: 0.2209 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.8915
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2019 1990 4.73 %
Rwork0.1711 40064 -
obs0.1725 42054 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.92 Å2
Refinement stepCycle: LAST / Resolution: 1.76→42.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 1 200 2991
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732878
X-RAY DIFFRACTIONf_angle_d0.98923893
X-RAY DIFFRACTIONf_chiral_restr0.0512419
X-RAY DIFFRACTIONf_plane_restr0.008500
X-RAY DIFFRACTIONf_dihedral_angle_d5.8381412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80.43911250.38832744X-RAY DIFFRACTION95.67
1.8-1.850.30661460.32422820X-RAY DIFFRACTION97.69
1.85-1.910.26131300.26422820X-RAY DIFFRACTION97.91
1.91-1.970.25691440.2172825X-RAY DIFFRACTION97.92
1.97-2.040.21311390.19422858X-RAY DIFFRACTION98.2
2.04-2.120.21171420.17662832X-RAY DIFFRACTION98.54
2.12-2.220.221410.16982856X-RAY DIFFRACTION98.75
2.22-2.330.16361500.1612868X-RAY DIFFRACTION98.98
2.33-2.480.21451430.16142871X-RAY DIFFRACTION98.92
2.48-2.670.23621390.17112867X-RAY DIFFRACTION99.21
2.67-2.940.19361470.17192883X-RAY DIFFRACTION99.21
2.94-3.360.20251430.16042907X-RAY DIFFRACTION99.22
3.36-4.240.16711450.14752918X-RAY DIFFRACTION99.51
4.24-42.020.18951560.15432995X-RAY DIFFRACTION99.62
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)
11.498344092580.2692558015770.3807228166312.09000660828-0.4436006322851.93309002587-0.0257595349465-0.0662073030997-0.217111382420.07037254359040.07991971022470.1525714998360.156053449798-0.0294430918756-0.04647381612260.2146990074450.04015004967010.02910190684040.2177415442850.006884273190830.259447811192-8.47892388576-32.06546342815.1443016398
21.399543442170.0162330989161-0.06066408494711.746808384220.4141462847252.767044298950.095859448267-0.08798528501140.03649260347580.0652080650884-0.1757158708880.0142467650364-0.08311858080370.1022980502180.06616945889130.233115700699-0.0362005340081-0.0004751287714280.2979268900950.01103903797070.245734037852-6.04832590979-26.949933656941.7976784607
32.80440990177-0.4993696072030.1737861819210.817139566401-0.124178595952.973689969480.02716546112470.274907468637-0.0275544108915-0.039074236533-0.06531755814250.03663744947120.0508123983742-0.1021537534210.03398524632560.2381562466690.0140033661828-0.004405834443360.237758717841-0.007063099459630.221918597326-16.3662879401-26.1690892822-8.87754653702
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA6 - 1341 - 116
22chain BBB2 - 1281 - 127
33chain CCC2 - 1191 - 118

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