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- PDB-8qpx: Crystal structure of Geodia cydonium Immunoglobulin-like domain o... -

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Basic information

Entry
Database: PDB / ID: 8qpx
TitleCrystal structure of Geodia cydonium Immunoglobulin-like domain of Receptor Tyrosine Kinase
ComponentsReceptor tyrosine kinase (Fragment)
KeywordsIMMUNE SYSTEM / Ig-like / porifera / evolution
Function / homology
Function and homology information


kinase activity / membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...: / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / 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
Receptor tyrosine kinase
Similarity search - Component
Biological speciesGeodia cydonium (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLopez-Sagaseta, J. / Urdiciain, A.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesMargarita Salas Spain
Spanish Ministry of Science, Innovation, and UniversitiesRYC-2017-21683 Spain
Citation
Journal: Commun Biol / Year: 2025
Title: Unusual traits shape the architecture of the Ig ancestor molecule.
Authors: Urdiciain, A. / Madej, T. / Wang, J. / Song, J. / Erausquin, E. / Youkharibache, P. / Lopez-Sagaseta, J.
#1: Journal: Sci Rep / Year: 2025
Title: Severe deviation in protein fold prediction by advanced AI: a case study.
Authors: Lopez-Sagaseta, J. / Urdiciain, A.
History
DepositionOct 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Apr 2, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Receptor tyrosine kinase (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,40410
Polymers24,6231
Non-polymers1,7819
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel filtration assay supports the monomeric state for this protein
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint16 kcal/mol
Surface area11090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.910, 32.730, 92.050
Angle α, β, γ (deg.)90.000, 90.820, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Receptor tyrosine kinase (Fragment)


Mass: 24623.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Remaining N-terminal GP motif from 3C site / Source: (gene. exp.) Geodia cydonium (invertebrata) / Gene: TK_2L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O18431

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: 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

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Non-polymers , 3 types, 105 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium sulfate, 26% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2023
RadiationMonochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.1→40.91 Å / Num. obs: 47524 / % possible obs: 98.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Rpim(I) all: 0.023 / Χ2: 0.9 / Net I/σ(I): 17.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 5 / Num. unique obs: 3990 / CC1/2: 0.947 / Rpim(I) all: 0.157 / Χ2: 1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless1.12.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40.91 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2503 689 4.79 %
Rwork0.2218 13693 -
obs0.2232 14382 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 115 98 1675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211600
X-RAY DIFFRACTIONf_angle_d0.49382176
X-RAY DIFFRACTIONf_chiral_restr0.0463277
X-RAY DIFFRACTIONf_plane_restr0.0025263
X-RAY DIFFRACTIONf_dihedral_angle_d4.7067273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.260.30441160.24552721X-RAY DIFFRACTION98.47
2.26-2.490.27441490.24612705X-RAY DIFFRACTION98.55
2.49-2.850.32021410.24432695X-RAY DIFFRACTION98.51
2.85-3.590.24041460.23442733X-RAY DIFFRACTION98.39
3.59-40.910.22611370.19912839X-RAY DIFFRACTION98.45
Refinement TLS params.Method: refined / Origin x: 9.31014388062 Å / Origin y: -9.79483222786 Å / Origin z: 6.9598198259 Å
111213212223313233
T0.229140543504 Å20.0204110317137 Å2-0.00815150925861 Å2-0.18552635165 Å20.0456994240931 Å2--0.301054612214 Å2
L1.92959501557 °2-0.351316551078 °2-2.10044387351 °2-0.993084261331 °21.56202104029 °2--8.53224428696 °2
S-0.119424114931 Å °-0.176259656685 Å °-0.0677227114585 Å °0.0638562980651 Å °0.0295905565269 Å °0.0938740332172 Å °0.0534235450837 Å °-0.267439173478 Å °0.0919454673605 Å °
Refinement TLS groupSelection details: (chain A and resseq 134:407)

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