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- PDB-2mxp: Solution structure of NDP52 ubiquitin-binding zinc finger -

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Basic information

Entry
Database: PDB / ID: 2mxp
TitleSolution structure of NDP52 ubiquitin-binding zinc finger
ComponentsCalcium-binding and coiled-coil domain-containing protein 2
KeywordsMETAL BINDING PROTEIN / zinc finger / NDP52 / ubiquitin-binding / C2H2-type
Function / homology
Function and homology information


xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / viral process / autophagosome / PML body / cytoplasmic vesicle / cytoskeleton / intracellular membrane-bounded organelle ...xenophagy / positive regulation of autophagosome maturation / response to type II interferon / autophagosome membrane / viral process / autophagosome / 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
SKICH domain / : / SKICH domain / CALCOCO1/2, zinc finger UBZ1-type / Zinc finger UBZ1-type profile.
Similarity search - Domain/homology
Calcium-binding and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsPan, L. / Xie, X.
CitationJournal: Autophagy / Year: 2015
Title: Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2
Authors: Xie, X. / Li, F. / Wang, Y. / Wang, Y. / Lin, Z. / Cheng, X. / Liu, J. / Chen, C. / Pan, L.
History
DepositionJan 12, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9532
Polymers3,8881
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: 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: 3887.546 Da / Num. of mol.: 1 / Fragment: C-terminal, UNP residues 414-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALCOCO2, NDP52 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q13137
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HN(CA)CB
1313D 1H-15N NOESY
1412D 1H-13C HSQC
2523D (H)CCH-TOCSY
2623D 1H-13C NOESY aliphatic
2732D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] entity_1-1, 1 mM [U-100% 15N] entity_1-2, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] entity_1-3, 100% D2O100% D2O
31.2 mM entity_1-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-100% 13C; U-100% 15N]1
1 mMentity_1-2[U-100% 15N]1
1 mMentity_1-3[U-100% 13C; U-100% 15N]2
1.2 mMentity_1-43
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.16.5ambient atm298 K
20.16.5ambient atm298 K

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NMR measurement

NMR spectrometerType: Agilent INOVA / Manufacturer: Agilent / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettchemical shift assignment
PIPPGarrettdata analysis
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 793 / NOE intraresidue total count: 252 / NOE long range total count: 176 / NOE medium range total count: 159 / NOE sequential total count: 206 / Protein other angle constraints total count: 35 / Protein phi angle constraints total count: 17 / Protein psi angle constraints total count: 18
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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