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- PDB-2m9m: Solution Structure of ERCC4 domain of human FAAP24 -

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Basic information

Entry
Database: PDB / ID: 2m9m
TitleSolution Structure of ERCC4 domain of human FAAP24
ComponentsFanconi anemia-associated protein of 24 kDa
KeywordsDNA BINDING PROTEIN / Fanconi anemia / FAAP24 / ERCC4 domain
Function / homology
Function and homology information


FANCM-MHF complex / Fanconi anaemia nuclear complex / interstrand cross-link repair / Fanconi Anemia Pathway / PKR-mediated signaling / intracellular membrane-bounded organelle / chromatin binding / chromatin / DNA binding / nucleoplasm / cytosol
Similarity search - Function
Fanconi anemia-associated protein of 24kDa / Fanconi anemia core complex-associated protein 24, pseudonuclease domain / FANCM pseudonuclease domain / Rossmann fold - #10130 / DisA/LigA, helix-hairpin-helix motif / Helix-hairpin-helix motif / RuvA domain 2-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Fanconi anemia core complex-associated protein 24
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsWu, F. / Han, X. / Shi, C. / Gong, W. / Tian, C.
CitationJournal: Cell Res. / Year: 2013
Title: Structure analysis of FAAP24 reveals single-stranded DNA-binding activity and domain functions in DNA damage response.
Authors: Wang, Y. / Han, X. / Wu, F. / Leung, J.W. / Lowery, M.G. / Do, H. / Chen, J. / Shi, C. / Tian, C. / Li, L. / Gong, W.
History
DepositionJun 18, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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 24 kDa


Theoretical massNumber of molelcules
Total (without water)16,7511
Polymers16,7511
Non-polymers00
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 Fanconi anemia-associated protein of 24 kDa


Mass: 16751.336 Da / Num. of mol.: 1 / Fragment: ERCC4 domain, UNP residues 1-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAAP24, C19orf40 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BTP7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1413D HNCA
1513D HN(CO)CA
1613D HNCO
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D C(CO)NH
11023D (H)CCH-TOCSY
11123D (H)CCH-COSY
11213D 1H-15N NOESY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5-0.8 mM [U-100% 13C; U-100% 15N] FAAP24-ERCC4-1, 50 mM potassium phosphate-2, 50 mM sodium chloride-3, 1 mM beta-mercaptoethanol-4, 0.5 mM EDTA-5, 90% H2O/10% D2O90% H2O/10% D2O
20.5-0.8 mM [U-100% 13C; U-100% 15N] FAAP24-ERCC4-6, 50 mM potassium phosphate-7, 50 mM sodium chloride-8, 1 mM beta-mercaptoethanol-9, 0.5 mM EDTA-10, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMFAAP24-ERCC4-1[U-100% 13C; U-100% 15N]0.5-0.81
50 mMpotassium phosphate-21
50 mMsodium chloride-31
1 mMbeta-mercaptoethanol-41
0.5 mMEDTA-51
mMFAAP24-ERCC4-6[U-100% 13C; U-100% 15N]0.5-0.82
50 mMpotassium phosphate-72
50 mMsodium chloride-82
1 mMbeta-mercaptoethanol-92
0.5 mMEDTA-102
Sample conditionsIonic strength: 0.35 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8501
Varian INOVAVarianINOVA7002

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / 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 / Representative conformer: 1

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