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- PDB-5z7a: Crystal structure of NDP52 SKICH region -

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Basic information

Entry
Database: PDB / ID: 5z7a
TitleCrystal structure of NDP52 SKICH region
ComponentsCalcium-binding and coiled-coil domain-containing protein 2
KeywordsSIGNALING PROTEIN / NDP52 / SKICH / Autophagy receptor / Selective autophagy
Function / homology
Function and homology information


xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle ...xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / autophagosome / viral process / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #2840 / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsPan, L.F. / Fu, T. / Liu, J.P. / Xie, X.Q.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470749 China
National Natural Science Foundation of China21621002 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Mechanistic insights into the interactions of NAP1 with the SKICH domains of NDP52 and TAX1BP1
Authors: Fu, T. / Liu, J. / Wang, Y. / Xie, X. / Hu, S. / Pan, L.
History
DepositionJan 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,5556
Polymers30,1162
Non-polymers4384
Water1,15364
1
A: Calcium-binding and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4004
Polymers15,0581
Non-polymers3423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-3 kcal/mol
Surface area6920 Å2
MethodPISA
2
B: Calcium-binding and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1542
Polymers15,0581
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-18 kcal/mol
Surface area6740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.502, 46.502, 99.561
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein 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: 15058.041 Da / Num. of mol.: 2 / Fragment: UNP residues 1-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q13137
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: PEG 3350, 0.2 M potassium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97946 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. obs: 9783 / % possible obs: 90.3 % / Redundancy: 3 % / Net I/σ(I): 12.49
Reflection shellResolution: 2.38→2.43 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vvv

3vvv


Resolution: 2.38→37.333 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 31.56
RfactorNum. reflection% reflection
Rfree0.2631 356 4.25 %
Rwork0.222 --
obs0.2238 8379 86.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.38→37.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 24 64 1889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031885
X-RAY DIFFRACTIONf_angle_d0.5892555
X-RAY DIFFRACTIONf_dihedral_angle_d3.2351057
X-RAY DIFFRACTIONf_chiral_restr0.047251
X-RAY DIFFRACTIONf_plane_restr0.004322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3803-2.72460.32031040.26862758X-RAY DIFFRACTION88
2.7246-3.43230.27811340.24522912X-RAY DIFFRACTION95
3.4323-37.3380.23881180.18972353X-RAY DIFFRACTION77

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