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- PDB-7tds: Labrum-interacting protein from saliva LIPS-2 (34K-2) from Aedes ... -

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Basic information

Entry
Database: PDB / ID: 7tds
TitleLabrum-interacting protein from saliva LIPS-2 (34K-2) from Aedes albopictus, native data
Components34k2 salivary protein
KeywordsSIGNALING PROTEIN / mosquito / saliva / feeding behaviour / protein-protein interaction / proboscis / cuticle
Function / homologyextracellular region / NITRATE ION / Labrum-interacting protein from saliva LIPS-2
Function and homology information
Biological speciesAedes albopictus (Asian tiger mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGabrieli, P. / Forneris, F.
Funding support Italy, 5items
OrganizationGrant numberCountry
NATO Science for Peace and Security ProgramG5701 Italy
Ministero dell Universita e della RicercaPRIN 2017RPHBCW Italy
The Giovanni Armenise-Harvard FoundationCDA 2013 Italy
Fondazione CARIPLO2017-0798 Italy
Ministero dell Universita e della RicercaDipartimenti di Eccellenza 2018-2022 Italy
CitationJournal: Curr.Biol. / Year: 2022
Title: A salivary factor binds a cuticular protein and modulates biting by inducing morphological changes in the mosquito labrum.
Authors: Arnoldi, I. / Mancini, G. / Fumagalli, M. / Gastaldi, D. / D'Andrea, L. / Bandi, C. / Di Venere, M. / Iadarola, P. / Forneris, F. / Gabrieli, P.
History
DepositionJan 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 34k2 salivary protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4939
Polymers34,9001
Non-polymers5938
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.875, 109.875, 141.782
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein 34k2 salivary protein


Mass: 34899.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The construct was deprived of the signal sequence (uniprot residues 1-20) and cloning introduced an additional N-terminal GLY and three C-terminal ALA residues.
Source: (gene. exp.) Aedes albopictus (Asian tiger mosquito)
Tissue: Saliva / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): T7 SHUFFLE K12 / References: UniProt: Q5MIU2
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 6.13 Å3/Da / Density % sol: 79.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M (NH4)2SO4, 1 M LI2SO4, 0.1 M KNO3

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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 PILATUS 2M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.2→47.26 Å / Num. obs: 43932 / % possible obs: 98.5 % / Redundancy: 7.9 % / Biso Wilson estimate: 49.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Net I/σ(I): 14.2
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 8 % / Rmerge(I) obs: 1.426 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3689 / CC1/2: 0.616 / Rpim(I) all: 0.728 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
HKL2Mapphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→46.43 Å / SU ML: 0.2829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9181
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2079 2191 5 %
Rwork0.1863 41661 -
obs0.1874 43852 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.95 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2329 0 33 95 2457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072382
X-RAY DIFFRACTIONf_angle_d0.80553204
X-RAY DIFFRACTIONf_chiral_restr0.0466362
X-RAY DIFFRACTIONf_plane_restr0.0044415
X-RAY DIFFRACTIONf_dihedral_angle_d21.61981471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34081440.31552527X-RAY DIFFRACTION97.38
2.25-2.30.27391310.27672537X-RAY DIFFRACTION97.3
2.3-2.360.29861480.25082520X-RAY DIFFRACTION97.41
2.36-2.420.29261370.2492533X-RAY DIFFRACTION97.34
2.42-2.490.26561120.22912586X-RAY DIFFRACTION97.65
2.49-2.570.24881470.21462530X-RAY DIFFRACTION97.49
2.57-2.670.23411260.2172582X-RAY DIFFRACTION98.08
2.67-2.770.25051140.22512596X-RAY DIFFRACTION98.4
2.77-2.90.28661600.21442580X-RAY DIFFRACTION98.28
2.9-3.050.24661290.2172634X-RAY DIFFRACTION98.68
3.05-3.240.19721470.20612580X-RAY DIFFRACTION98.98
3.24-3.490.20021360.19882633X-RAY DIFFRACTION99.11
3.49-3.840.18891560.1642638X-RAY DIFFRACTION99.11
3.84-4.40.18011340.14772676X-RAY DIFFRACTION99.08
4.4-5.540.16421350.15722699X-RAY DIFFRACTION98.75
5.54-46.420.19051350.1732810X-RAY DIFFRACTION97.16
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)
11.972868064332.80949892191-0.6006168505225.16018397374-1.070717354530.206590881450.14101336759-0.3124358377280.0250288923250.163136324499-0.231135211068-0.200031864156-0.03187615866950.08664709898570.07809062471370.484982214997-0.06623443820590.002069373443130.508080967674-0.03115504153980.46143449752630.67001169681.014241134947.6744120931
22.20770643273-0.8386057485631.966533831963.15086928637-2.505863540156.760819304630.0854904362813-0.0757929129496-0.01026760511830.0724127287809-0.006494007837740.324912346605-0.0962273083045-0.371317046895-0.03215347107790.2777654398930.01680286212920.01224188439280.314814911229-0.02108854675250.3418290209863.2834522628960.874376073344.6848377301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 164 )
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 315 )

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