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- PDB-1fre: XNF7 BBOX, DEVELOPMENTAL PROTEIN, PH 7.5, 30 C, WITH ZINC, NMR, 1... -

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Basic information

Entry
Database: PDB / ID: 1fre
TitleXNF7 BBOX, DEVELOPMENTAL PROTEIN, PH 7.5, 30 C, WITH ZINC, NMR, 1 STRUCTURE
ComponentsNUCLEAR FACTOR XNF7
KeywordsZINC-BINDING PROTEIN / XNF7 / BBOX / DEVELOPMENT / MID-BLASTULA-TRANSITION
Function / homology
Function and homology information


ubiquitin protein ligase activity / innate immune response / DNA binding / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
zinc finger of C3HC4-type, RING / B-box, C-terminal / B-Box C-terminal domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain ...zinc finger of C3HC4-type, RING / B-box, C-terminal / B-Box C-terminal domain / RNA binding activity-knot of a chromodomain / RNA binding activity-knot of a chromodomain / : / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / B-box zinc finger / B-Box-type zinc finger / B-box-type zinc finger / Zinc finger B-box type profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Nuclear factor 7, brain
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR
AuthorsBorden, K.L.B. / Freemont, P.S.
Citation
Journal: EMBO J. / Year: 1995
Title: Novel topology of a zinc-binding domain from a protein involved in regulating early Xenopus development.
Authors: Borden, K.L. / Lally, J.M. / Martin, S.R. / O'Reilly, N.J. / Etkin, L.D. / Freemont, P.S.
#1: Journal: Ann.N.Y.Acad.Sci. / Year: 1993
Title: The Ring Finger. A Novel Protein Sequence Motif Related to the Zinc Finger
Authors: Freemont, P.S.
#2: Journal: Dev.Biol. / Year: 1991
Title: The Cloning and Characterization of a Maternally Expressed Novel Zinc Finger Nuclear Phosphoprotein (Xnf7) in Xenopus Laevis
Authors: Reddy, B.A. / Kloc, M. / Etkin, L.
History
DepositionJan 31, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / 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.process_site / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEAR FACTOR XNF7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9472
Polymers4,8821
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)1 / -
Representative

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Components

#1: Protein/peptide NUCLEAR FACTOR XNF7


Mass: 4881.637 Da / Num. of mol.: 1 / Fragment: BBOX
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / References: UniProt: Q92021
#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

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Sample preparation

Sample conditionspH: 7.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR ensembleConformers submitted total number: 1

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