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- PDB-1dsq: STRUCTURE OF THE MMTV NUCLEOCAPSID PROTEIN (ZINC FINGER 1) -

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Basic information

Entry
Database: PDB / ID: 1dsq
TitleSTRUCTURE OF THE MMTV NUCLEOCAPSID PROTEIN (ZINC FINGER 1)
ComponentsNUCLEIC ACID BINDING PROTEIN P14
KeywordsVIRAL PROTEIN / CCHC TYPE ZINC FINGER / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleotide binding / DNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesMouse mammary tumor virus
MethodSOLUTION NMR
AuthorsKlein, D.J. / Johnson, P.E. / Zollars, E.S. / De Guzman, R.N. / Summers, M.F.
CitationJournal: Biochemistry / Year: 2000
Title: The NMR structure of the nucleocapsid protein from the mouse mammary tumor virus reveals unusual folding of the C-terminal zinc knuckle.
Authors: Klein, D.J. / Johnson, P.E. / Zollars, E.S. / De Guzman, R.N. / Summers, M.F.
History
DepositionJan 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 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_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.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: NUCLEIC ACID BINDING PROTEIN P14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,3942
Polymers2,3291
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)20 / 100target function
RepresentativeModel #1lowest target function

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Components

#1: Protein/peptide NUCLEIC ACID BINDING PROTEIN P14


Mass: 2328.733 Da / Num. of mol.: 1 / Fragment: ZINC FINGER 1 OF NUCLEOCAPSID PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mouse mammary tumor virus / Genus: Betaretrovirus / Plasmid: PET-3D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSE / References: UniProt: P11284
#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

DetailsContents: 1 MM UNLABELLED MMTV NC, 25 MM ACETATE (D3), PH 7.0, 20 MM NACL, 0.1 MM ZNCL2, 0.1 MM BME
Sample conditionsIonic strength: ~50 mM / pH: 7.0 / Pressure: AMBIENT / Temperature: 25 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
GE PSGGEPSG6002

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5GUNTERTrefinement
NMRPipe1.7DELAGLIOprocessing
NMRView3JOHNSONdata analysis
RefinementSoftware ordinal: 1
Details: DATA WAS COLLECTED ON THE INTACT NUCLEOCAPSID PROTEIN BUT THE STRUCTURES OF THE N- AND C-TERMINAL ZINC FINGERS WERE CALCULATED INDEPENDENTLY. THESE TWO DOMAINS DO NOT INTERACT WITH EACH OTHER
NMR representativeSelection criteria: lowest target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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