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- PDB-2muq: Solution Structure of the Human FAAP20 UBZ -

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Basic information

Entry
Database: PDB / ID: 2muq
TitleSolution Structure of the Human FAAP20 UBZ
ComponentsFanconi anemia-associated protein of 20 kDa
KeywordsUbiquitin Binding Protein / UBZ / FAAP20 / zinc finger / ubiquitin-binding / Fanconi Anemia
Function / homology
Function and homology information


Fanconi anaemia nuclear complex / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / translesion synthesis / interstrand cross-link repair / ubiquitin binding / Fanconi Anemia Pathway / PKR-mediated signaling / cell junction ...Fanconi anaemia nuclear complex / ubiquitin-modified protein reader activity / K63-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / translesion synthesis / interstrand cross-link repair / ubiquitin binding / Fanconi Anemia Pathway / PKR-mediated signaling / cell junction / chromosome / nuclear body / DNA damage response / chromatin / nucleoplasm / metal ion binding / cytosol
Similarity search - Function
FAAP20, zinc finger UBZ2-type / FAAP20, FANCA interaction domain / Ubiquitin-binding zinc-finger / FAAP20 FANCA interaction domain / Zinc finger UBZ2-type profile.
Similarity search - Domain/homology
Fanconi anemia core complex-associated protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsWojtaszek, J.L. / Wang, S. / Zhou, P.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Ubiquitin recognition by FAAP20 expands the complex interface beyond the canonical UBZ domain.
Authors: Wojtaszek, J.L. / Wang, S. / Kim, H. / Wu, Q. / D'Andrea, A.D. / Zhou, P.
History
DepositionSep 16, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Jun 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 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

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Assembly

Deposited unit
A: Fanconi anemia-associated protein of 20 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9192
Polymers4,8531
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Fanconi anemia-associated protein of 20 kDa


Mass: 4853.492 Da / Num. of mol.: 1 / Fragment: UBZ, UNP residues 140-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C1orf86, FAAP20, FP7162 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NZ36
#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
1112D 1H-15N HSQC
1223D sparse-sampled HNCO
1323D sparse-sampled HNCA
1423D sparse-sampled HN(CO)CA
1523D sparse-sampled HN(CA)CB
1623D sparse-sampled HN(CO)CACB
1723D sparse-sampled HACANH
1823D sparse-sampled (HA)CA(CO)NH
1924D sparse-sampled (H)CC(CO)NH TOCSY
11013D 1H-15N NOESY
11134D sparse-sampled (H)CCH TOCSY
11234D sparse-sampled CHCH NOESY
11324D sparse-sampled CHNH NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM [U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21.5 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 0.05 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31.5 mM [U-100% 13C; U-100% 15N] protein, 25 mM sodium phosphate, 100 mM potassium chloride, 10 mM DTT, 0.05 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMprotein-1[U-100% 15N]1
25 mMsodium phosphate-21
100 mMpotassium chloride-31
10 mMDTT-41
0.05 %sodium azide-51
1.5 mMprotein-6[U-100% 13C; U-100% 15N]2
25 mMsodium phosphate-72
100 mMpotassium chloride-82
10 mMDTT-92
0.05 %sodium azide-102
1.5 mMprotein-11[U-100% 13C; U-100% 15N]3
25 mMsodium phosphate-123
100 mMpotassium chloride-133
10 mMDTT-143
0.05 %sodium azide-153
Sample conditionsIonic strength: 0.1-0.125 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
XEASYBartels et al.data analysis
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddarddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SCRUBCoggins and Zhouprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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