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- PDB-4gxl: The crystal structure of Galectin-8 C-CRD in complex with NDP52 -

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Basic information

Entry
Database: PDB / ID: 4gxl
TitleThe crystal structure of Galectin-8 C-CRD in complex with NDP52
Components
  • Galectin-8
  • Peptide from Calcium-binding and coiled-coil domain-containing protein 2
KeywordsPROTEIN BINDING / protein-protein interaction / carbohydrate recognition / NDP52
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / cellular response to virus / PML body / integrin binding ...lymphatic endothelial cell migration / xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / cellular response to virus / PML body / integrin binding / cytoplasmic vesicle / carbohydrate binding / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. ...SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Galectin-8 / Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.023 Å
AuthorsLi, S. / Wandel, M.P. / Li, F. / Liu, Z. / He, C. / Wu, J. / Shi, Y. / Randow, F.
CitationJournal: Sci.Signal. / Year: 2013
Title: Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy
Authors: Li, S. / Wandel, M.P. / Li, F. / Liu, Z. / He, C. / Wu, J. / Shi, Y. / Randow, F.
History
DepositionSep 4, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-8
B: Peptide from Calcium-binding and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2264
Polymers19,0412
Non-polymers1842
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-7 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.087, 124.826, 43.737
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-575-

HOH

31A-581-

HOH

41A-585-

HOH

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Components

#1: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17532.883 Da / Num. of mol.: 1 / Fragment: UNP residues 186-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Protein/peptide Peptide from Calcium-binding and coiled-coil domain-containing protein 2 / Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 ...Antigen nuclear dot 52 kDa protein / Nuclear domain 10 protein NDP52 / Nuclear domain 10 protein 52 / Nuclear dot protein 52


Mass: 1508.615 Da / Num. of mol.: 1 / Fragment: UNP residues 368-381 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13137
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 2.73 Å3/Da / Density % sol: 54.89 % / Mosaicity: 0.465 °
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2% PEG 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 18, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 14009 / Num. obs: 13995 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Rmerge(I) obs: 0.085 / Χ2: 1.051 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.02-2.054.80.3336821.091100
2.05-2.095.20.2936891.107199.9
2.09-2.135.30.2666931.0861100
2.13-2.185.40.216951.0851100
2.18-2.225.30.1966811.0361100
2.22-2.275.40.1776931.0891100
2.27-2.335.30.1576751.0611100
2.33-2.395.40.1626931.0971100
2.39-2.475.40.1456811.0381100
2.47-2.545.40.1337091.0431100
2.54-2.645.30.1166861.0591100
2.64-2.745.40.0997021.0431100
2.74-2.875.40.0866861.0331100
2.87-3.025.30.0757101.0561100
3.02-3.215.30.0636951.0281100
3.21-3.455.30.0567081.021199.9
3.45-3.85.20.0687080.999199.9
3.8-4.355.20.0777171.049199.9
4.35-5.4850.0617221.065199.6
5.48-504.80.0437700.936199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.023→35.818 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8796 / SU ML: 0.13 / σ(F): 1.36 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 701 5.01 %RANDOM
Rwork0.1767 ---
obs0.1786 13992 99.76 %-
all-14009 --
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.844 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 66.32 Å2 / Biso mean: 22.8292 Å2 / Biso min: 10.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.063 Å2-0 Å2-0 Å2
2---0.4398 Å2-0 Å2
3---0.3768 Å2
Refinement stepCycle: LAST / Resolution: 2.023→35.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 12 119 1364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081287
X-RAY DIFFRACTIONf_angle_d1.2571740
X-RAY DIFFRACTIONf_chiral_restr0.092182
X-RAY DIFFRACTIONf_plane_restr0.005227
X-RAY DIFFRACTIONf_dihedral_angle_d12.73475
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0232-2.17940.21521420.17082602274499
2.1794-2.39860.21231550.163525862741100
2.3986-2.74560.20591420.170226422784100
2.7456-3.45870.21121230.169426802803100
3.4587-35.82340.22451390.189427812920100

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