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- PDB-2d8q: Solution structure of the MYND domain of the human zinc finger MY... -

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Basic information

Entry
Database: PDB / ID: 2d8q
TitleSolution structure of the MYND domain of the human zinc finger MYND domain-containing protein 10
ComponentsZinc finger MYND domain containing protein 10
KeywordsMETAL BINDING PROTEIN / Zinc finger MYND domain containing protein 10 / BLu protein / ZMYND10 / zf-MYND / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of motile cilium assembly / inner dynein arm assembly / outer dynein arm assembly / cilium movement / motile cilium assembly / dynein axonemal particle / protein localization to cilium / centriolar satellite / protein folding chaperone / molecular adaptor activity ...positive regulation of motile cilium assembly / inner dynein arm assembly / outer dynein arm assembly / cilium movement / motile cilium assembly / dynein axonemal particle / protein localization to cilium / centriolar satellite / protein folding chaperone / molecular adaptor activity / apical plasma membrane / metal ion binding / cytoplasm
Similarity search - Function
Uncharacterised conserved protein UCP037948, zinc finger MYND-type / : / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile.
Similarity search - Domain/homology
Zinc finger MYND domain-containing protein 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMiyamoto, K. / Kigawa, T. / Tomizawa, T. / Tochio, N. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the MYND domain of the human zinc finger MYND domain-containing protein 10
Authors: Miyamoto, K. / Kigawa, T. / Tomizawa, T. / Tochio, N. / Sasagawa, A. / Koshiba, S. / Inoue, M. / Yokoyama, S.
History
DepositionDec 8, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger MYND domain containing protein 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6813
Polymers7,5501
Non-polymers1312
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 / 100target function,structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Zinc finger MYND domain containing protein 10 / BLu protein


Mass: 7550.459 Da / Num. of mol.: 1 / Fragment: zf-MYND
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ZMYND10 / Plasmid: P040816-10 / References: UniProt: O75800
#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
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 0.3mM zf-MYND U-13C,15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.1mM ZNCl2; 90% H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9321Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function,structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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