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- PDB-5z7l: Crystal structure of NDP52 SKICH region in complex with NAP1 -

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Basic information

Entry
Database: PDB / ID: 5z7l
TitleCrystal structure of NDP52 SKICH region in complex with NAP1
Components
  • 5-azacytidine-induced protein 2
  • Calcium-binding and coiled-coil domain-containing protein 2
KeywordsSIGNALING PROTEIN / NDP52 / NAP1 / SKICH / Autophagy
Function / homology
Function and homology information


dendritic cell differentiation / xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / positive regulation of autophagosome maturation / type I interferon-mediated signaling pathway / response to type II interferon / autophagosome membrane / autophagosome / canonical NF-kappaB signal transduction ...dendritic cell differentiation / xenophagy / serine/threonine protein kinase complex / dendritic cell proliferation / positive regulation of autophagosome maturation / type I interferon-mediated signaling pathway / response to type II interferon / autophagosome membrane / autophagosome / canonical NF-kappaB signal transduction / negative regulation of canonical NF-kappaB signal transduction / T cell activation / viral process / PML body / mitotic cell cycle / cytoplasmic vesicle / defense response to virus / cytoskeleton / intracellular membrane-bounded organelle / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Immunoglobulin-like - #2840 / Tbk1/Ikki binding domain / TBD domain / SKICH domain / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2 / 5-azacytidine-induced protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsFu, T. / Pan, L.F.
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 29, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
C: 5-azacytidine-induced protein 2
D: 5-azacytidine-induced protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5188
Polymers38,1494
Non-polymers3684
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-39 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.639, 45.026, 86.679
Angle α, β, γ (deg.)90.00, 123.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Calcium-binding and coiled-coil domain-containing protein 2


Mass: 14015.854 Da / Num. of mol.: 2 / Fragment: UNP residues 10-126
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q13137
#2: Protein/peptide 5-azacytidine-induced protein 2


Mass: 5058.892 Da / Num. of mol.: 2 / Fragment: UNP residues 33-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZI2
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q9H6S1
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: PEG3350,sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97914 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Jan 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.02→72.05 Å / Num. obs: 24065 / % possible obs: 99.5 % / Redundancy: 3.7 % / Net I/σ(I): 10.6
Reflection shellResolution: 2.02→2.07 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→40.645 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2216 1150 4.85 %
Rwork0.1703 --
obs0.1727 23688 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→40.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2577 0 24 272 2873
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072680
X-RAY DIFFRACTIONf_angle_d0.8523613
X-RAY DIFFRACTIONf_dihedral_angle_d8.6641669
X-RAY DIFFRACTIONf_chiral_restr0.054371
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.1120.33041510.26392796X-RAY DIFFRACTION98
2.112-2.22330.27671570.22472773X-RAY DIFFRACTION98
2.2233-2.36260.24611600.19792809X-RAY DIFFRACTION99
2.3626-2.5450.23241300.18512837X-RAY DIFFRACTION99
2.545-2.80110.23651480.17312820X-RAY DIFFRACTION99
2.8011-3.20620.21291350.15242835X-RAY DIFFRACTION98
3.2062-4.03890.18681430.14172807X-RAY DIFFRACTION97
4.0389-40.6530.19741260.15942861X-RAY DIFFRACTION96
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)
14.9641-0.0457-1.39016.2351-1.3513.8371-0.176-0.0853-0.3061-0.185-0.12530.14560.2328-0.17120.2590.16350.0308-0.00320.2366-0.01660.2839206.7373-23.84492.6725
24.8316-0.6841-0.25096.32430.44645.5258-0.00820.4946-0.5066-0.27640.0756-0.34870.4092-0.1791-0.03220.1597-0.0262-0.02110.3041-0.07850.26205.0814-24.512382.2136
34.8549-1.1119-0.58224.72540.2285.11310.32180.1428-0.4352-0.4582-0.38470.23270.4237-0.1273-0.10450.2118-0.0277-0.02850.2112-0.06180.2565212.0026-25.237583.0449
44.6679-0.2811-0.63071.7924-0.70443.05890.0764-0.0372-0.05880.0363-0.15930.01770.0966-0.00430.05310.1499-0.0021-0.00240.1713-0.05220.2639208.1857-19.761189.093
51.69280.1220.47184.2691-1.8925.0505-0.0007-0.15440.14550.19970.0658-0.0502-0.13750.107-0.04480.1440.0336-0.01330.1323-0.03690.1263176.7507-4.024991.2166
64.90181.3336-1.37964.9406-0.4915.9521-0.04270.11920.525-0.36040.09210.6698-0.496-0.1486-0.07460.2090.0654-0.0080.16410.05350.1598171.9705-1.111276.6839
72.234-1.49961.6813.06421.77858.3252-0.0753-0.0611-0.3056-0.07720.22830.02020.24550.3105-0.11610.143-0.01690.02290.13020.03260.2001178.6081-15.769586.5969
85.556-2.12212.83876.4492-4.2174.69220.04120.2335-0.2597-0.1312-0.06810.24590.28-0.01890.08960.161-0.0218-0.04710.1649-0.00550.1511171.6035-16.481485.6524
97.2322-2.83982.8893.05911.7235.4357-0.35860.19650.6831-0.68780.1062-0.331-0.58880.37630.22370.3085-0.02830.02850.25920.0120.2504167.8015.44580.1511
102.9173-0.42810.92413.2463-1.13493.086-0.0751-0.165-0.19770.17150.07860.03350.05710.01530.02710.13230.02460.0150.1383-0.01750.1253174.8551-10.869791.3113
111.2040.10170.43410.81141.53633.17670.0690.1726-0.11030.1262-0.12710.01230.2791-0.77910.11770.20750.0030.00790.2118-0.01760.2296191.6983-14.2994107.3096
121.5320.71042.43380.62751.59918.3603-0.00510.1733-0.0372-0.05740.1892-0.0353-0.37750.2951-0.21250.20530.0183-0.01360.1858-0.02320.2402194.4992-7.2547105.8401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 65 )
3X-RAY DIFFRACTION3chain 'A' and (resid 66 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 126 )
5X-RAY DIFFRACTION5chain 'B' and (resid 17 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 74 )
9X-RAY DIFFRACTION9chain 'B' and (resid 75 through 87 )
10X-RAY DIFFRACTION10chain 'B' and (resid 88 through 126 )
11X-RAY DIFFRACTION11chain 'C' and (resid 33 through 75 )
12X-RAY DIFFRACTION12chain 'D' and (resid 33 through 75 )

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