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- PDB-4han: Crystal structure of Galectin 8 with NDP52 peptide -

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Basic information

Entry
Database: PDB / ID: 4han
TitleCrystal structure of Galectin 8 with NDP52 peptide
Components
  • Calcium-binding and coiled-coil domain-containing protein 2
  • Galectin-8
KeywordsSUGAR BINDING PROTEIN / Autophagy / innate immunity / carbohydrate recognition domain (CRD) / autophagy adapter molecule / NAD binding / NDP52 peoptide binding / Cytosol
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 / PML body / cellular response to virus / integrin binding ...lymphatic endothelial cell migration / xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / PML body / cellular response to virus / integrin binding / cytoplasmic vesicle / carbohydrate binding / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / membrane / metal ion binding / nucleus / cytosol / cytoplasm
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Galectin-8 / Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.551 Å
AuthorsKim, B.-W. / Hong, S.B. / Kim, J.H. / Kwon, D.H. / Song, H.K.
CitationJournal: Nat Commun / Year: 2013
Title: Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8.
Authors: Kim, B.W. / Hong, S.B. / Kim, J.H. / Kwon, D.H. / Song, H.K.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Galectin-8
C: Calcium-binding and coiled-coil domain-containing protein 2
D: Calcium-binding and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0219
Polymers69,3764
Non-polymers1,6455
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-8 kcal/mol
Surface area27240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.884, 71.884, 314.493
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112

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Components

#1: Protein Galectin-8 /


Mass: 33222.207 Da / Num. of mol.: 2 / Fragment: UNP residues 1-155. 184-317
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Protein/peptide 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: 1465.564 Da / Num. of mol.: 2 / Fragment: UNP residues 372-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13137
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 3.38 Å3/Da / Density % sol: 63.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-Hcl pH8.5, 30~34% (v/w) PEG400, 200mM LiSO4, and 10mM Nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.55→40.1 Å / Num. obs: 30888 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.551→40.096 Å / SU ML: 0.23 / σ(F): 0 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2138 1977 6.49 %Random
Rwork0.1913 ---
obs0.1928 30450 98.4 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.551→40.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4781 0 109 351 5241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085031
X-RAY DIFFRACTIONf_angle_d1.5326824
X-RAY DIFFRACTIONf_dihedral_angle_d15.4751845
X-RAY DIFFRACTIONf_chiral_restr0.139746
X-RAY DIFFRACTIONf_plane_restr0.004874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5507-2.61450.30091320.25141955X-RAY DIFFRACTION95
2.6145-2.68510.25831320.24261966X-RAY DIFFRACTION96
2.6851-2.76410.30371400.23292004X-RAY DIFFRACTION96
2.7641-2.85330.26011330.22681943X-RAY DIFFRACTION97
2.8533-2.95530.2551390.2231992X-RAY DIFFRACTION98
2.9553-3.07360.21551390.22272015X-RAY DIFFRACTION98
3.0736-3.21340.24281350.21332035X-RAY DIFFRACTION99
3.2134-3.38270.26041410.20242050X-RAY DIFFRACTION100
3.3827-3.59450.19671450.18212082X-RAY DIFFRACTION100
3.5945-3.87190.23641430.17762037X-RAY DIFFRACTION100
3.8719-4.26110.18511450.162074X-RAY DIFFRACTION100
4.2611-4.87680.16191490.14442059X-RAY DIFFRACTION100
4.8768-6.14070.19661510.18712108X-RAY DIFFRACTION100
6.1407-40.10080.19431530.20582153X-RAY DIFFRACTION99
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)
16.3648-0.0978-1.64920.6302-1.50763.7103-0.0761-0.3093-0.08660.04570.1414-0.03560.22170.0757-0.0280.3220.0507-0.02240.3222-0.12020.414723.1528-6.0774336.6088
21.39530.24510.73472.7024-0.69952.61760.0677-0.20550.1759-0.08360.00670.1311-0.3301-0.0618-0.06160.34940.11460.04680.3786-0.13480.431626.18221.9484323.4845
34.206-0.3559-0.46913.12150.25432.80890.08040.3922-0.3308-0.0801-0.14740.21110.1492-0.74350.06510.2771-0.01670.05360.6094-0.0630.3587-5.6022-9.8489347.2401
41.64050.58670.71541.24950.21272.51970.119-0.029-0.0304-0.1515-0.0211-0.1139-0.1170.1652-0.07770.25270.07860.1210.42670.02150.417723.63491.8234355.9302
53.5675-1.0117-0.60883.23130.60613.0882-0.218-0.2244-0.37320.21370.11970.15650.73840.22810.05580.55480.12180.07810.3346-0.00160.374330.2312-30.5188334.067
61.3878-2.4205-1.80564.90014.16783.8071-0.15040.16180.3412-0.10.3177-0.0317-0.3908-0.318-0.16680.65010.29970.07830.8410.07330.3309-2.6750.114334.6043
70.11460.1811-0.17840.86450.43013.76660.04710.41310.01340.11590.1812-0.1514-0.22460.1090.11650.47920.1249-0.19711.1741-0.12580.176237.268-22.9752346.7688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 155 )
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 291 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 155 )
5X-RAY DIFFRACTION5chain 'B' and (resid 156 through 291 )
6X-RAY DIFFRACTION6chain 'C' and (resid 372 through 380 )
7X-RAY DIFFRACTION7chain 'D' and (resid 372 through 380 )

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