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- PDB-2md7: NMR structure of human Sp140 PHD finger trans conformer -

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Basic information

Entry
Database: PDB / ID: 2md7
TitleNMR structure of human Sp140 PHD finger trans conformer
ComponentsNuclear body protein SP140Nuclear bodies
KeywordsTRANSCRIPTION / PHD finger
Function / homology
Function and homology information


defense response / PML body / fibrillar center / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / metal ion binding / nucleus
Similarity search - Function
Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily ...Nuclear body protein Sp140 / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nuclear body protein SP140
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, distance geometry
Model detailslowest energy, model1
AuthorsZucchelli, C. / Quilici, G. / Musco, G.
CitationJournal: Febs J. / Year: 2014
Title: Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1.
Authors: Zucchelli, C. / Tamburri, S. / Quilici, G. / Palagano, E. / Berardi, A. / Saare, M. / Peterson, P. / Bachi, A. / Musco, G.
History
DepositionSep 2, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: 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_nmr_spectrometer / 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_nmr_spectrometer.model / _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_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Nuclear body protein SP140
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5673
Polymers6,4361
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Nuclear body protein SP140 / Nuclear bodies / Lymphoid-restricted homolog of Sp100 / LYSp100 / Nuclear autoantigen Sp-140 / Speckled 140 kDa


Mass: 6436.365 Da / Num. of mol.: 1 / Fragment: UNP residues 687-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP140, LYSP100 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13342
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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
1212D 1H-13C HSQC
1342D 1H-1H TOCSY
1452D 1H-1H TOCSY
1542D 1H-1H NOESY
1652D 1H-1H NOESY
1713D CBCA(CO)NH
1813D C(CO)NH
1913D HNCO
11013D HNCA
11113D HN(CA)CB
11213D H(CCO)NH
11323D (H)CCH-TOCSY
11433D HNHA
11532D 1H-15N HSQC
11633D 1H-15N NOESY
11732D 1H-15N HSQC
11822D 1H-13C HSQC
11923D 1H-13C NOESY aliphatic
12023D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Sp140 PHD finger trans conformer, 50 uM ZINC ION, 0.3 mM DSS, 5 mM DTT, 20 mM sodium phosphate pH 6.3, 150 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] Sp140 PHD finger trans conformer, 50 uM ZINC ION, 0.3 mM DSS, 5 mM DTT, 20 mM sodium phosphate pH 6.3, 150 mM NaCl, 100% D2O100% D2O
30.8 mM [U-100% 15N] Sp140 PHD finger trans conformer, 50 uM ZINC ION, 0.3 mM DSS, 5 mM DTT, 20 mM sodium phosphate pH 6.3, 150 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
41 mM Sp140 PHD finger trans conformer, 50 uM ZINC ION, 0.3 mM DSS, 5 mM DTT, 20 mM sodium phosphate pH 6.3, 150 mM NaCl, 100% D2O100% D2O
51 mM Sp140 PHD finger trans conformer, 50 uM ZINC ION, 0.3 mM DSS, 5 mM DTT, 20 mM sodium phosphate pH 6.3, 150 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSp140 PHD finger trans conformer-1[U-100% 13C; U-100% 15N]1
50 uMZINC ION-21
0.3 mMDSS-31
5 mMDTT-41
20 mMsodium phosphate pH 6.3-51
150 mMNaCl-61
1 mMSp140 PHD finger trans conformer-7[U-100% 13C; U-100% 15N]2
50 uMZINC ION-82
0.3 mMDSS-92
5 mMDTT-102
20 mMsodium phosphate pH 6.3-112
150 mMNaCl-122
0.8 mMSp140 PHD finger trans conformer-13[U-100% 15N]3
50 uMZINC ION-143
0.3 mMDSS-153
5 mMDTT-163
20 mMsodium phosphate pH 6.3-173
150 mMNaCl-183
1 mMSp140 PHD finger trans conformer-194
50 uMZINC ION-204
0.3 mMDSS-214
5 mMDTT-224
20 mMsodium phosphate pH 6.3-234
150 mMNaCl-244
1 mMSp140 PHD finger trans conformer-255
50 uMZINC ION-265
0.3 mMDSS-275
5 mMDTT-285
20 mMsodium phosphate pH 6.3-295
150 mMNaCl-305
Sample conditionspH: 6.3 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
ProcheckNMRLaskowski and MacArthurrefinement
RefinementMethod: simulated annealing, distance geometry / Software ordinal: 1
NMR constraintsNOE constraints total: 884 / NOE intraresidue total count: 435 / NOE long range total count: 76 / NOE medium range total count: 131 / NOE sequential total count: 233 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 23 / Protein psi angle constraints total count: 23
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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