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- PDB-9fww: Human NKp30 in complex with a VHH variant -

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Basic information

Entry
Database: PDB / ID: 9fww
TitleHuman NKp30 in complex with a VHH variant
Components
  • Natural cytotoxicity triggering receptor 3
  • VHH
KeywordsIMMUNE SYSTEM / Natural killer cells / NKp30 / VHHs / humanization / molecular dynamics / Hallmark / framework residues / antigen recognition
Function / homology
Function and homology information


cell recognition / immune receptor activity / immune response-activating cell surface receptor signaling pathway / NK T cell activation / positive regulation of natural killer cell mediated cytotoxicity / natural killer cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / immune response / inflammatory response / identical protein binding / plasma membrane
Similarity search - Function
Natural cytotoxicity triggering receptor 3 / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Natural cytotoxicity triggering receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.844 Å
AuthorsMusil, D. / Freire, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: On the humanization of VHHs: Prospective case studies, experimental and computational characterization of structural determinants for functionality.
Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / ...Authors: Fernandez-Quintero, M.L. / Guarnera, E. / Musil, D. / Pekar, L. / Sellmann, C. / Freire, F. / Sousa, R.L. / Santos, S.P. / Freitas, M.C. / Bandeiras, T.M. / Silva, M.M.S. / Loeffler, J.R. / Ward, A.B. / Harwardt, J. / Zielonka, S. / Evers, A.
History
DepositionJul 1, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Natural cytotoxicity triggering receptor 3
B: VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3844
Polymers26,7962
Non-polymers5892
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint2 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.457, 156.457, 89.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-325-

HOH

31B-201-

HOH

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Components

#1: Protein Natural cytotoxicity triggering receptor 3 / Activating natural killer receptor p30 / Natural killer cell p30-related protein / NK-p30 / NKp30


Mass: 12325.925 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCR3, 1C7, LY117 / Production host: Homo sapiens (human) / References: UniProt: O14931
#2: Antibody VHH


Mass: 14469.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: 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
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (v/v) PEG 4000, 20% (v/v) Isopropanol, 0.1 M Sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.844→77.594 Å / Num. obs: 29007 / % possible obs: 91.3 % / Redundancy: 13.5 % / CC1/2: 0.983 / Rpim(I) all: 0.032 / Rrim(I) all: 0.117 / Net I/σ(I): 15.4
Reflection shellResolution: 1.844→2.046 Å / Num. unique obs: 1450 / CC1/2: 0.785 / Rpim(I) all: 0.462

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (23-JAN-2024)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.844→77.59 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.147 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1521 5.24 %RANDOM
Rwork0.1991 ---
obs0.1996 29007 60.7 %-
Displacement parametersBiso mean: 35.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.5144 Å20 Å20 Å2
2--2.5144 Å20 Å2
3----5.0288 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: 1 / Resolution: 1.844→77.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1802 0 38 208 2048
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.982677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d702SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes353HARMONIC5
X-RAY DIFFRACTIONt_it1962HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion15.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion254SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1704SEMIHARMONIC4
LS refinement shellResolution: 1.844→1.97 Å
RfactorNum. reflection% reflection
Rfree0.2966 -4.65 %
Rwork0.2629 554 -
obs--6.7 %
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)
12.5049-1.2731.16952.04860.0123.50290.02990.07370.0722-0.07040.0381-0.08550.30350.405-0.0679-0.00620.17480.00850.02440.0235-0.1361-45.4911-23.075-8.1894
20.5596-0.5139-0.65821.25210.52643.13970.0614-0.0585-0.01570.0496-0.02520.0644-0.04790.173-0.03620.00280.01960.01420.00690.0427-0.0787-58.7162-9.48029.171
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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