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- PDB-1a1t: STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-... -

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Basic information

Entry
Database: PDB / ID: 1a1t
TitleSTRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES
Components
  • NUCLEOCAPSID PROTEINVirus
  • SL3 STEM-LOOP RNA
KeywordsViral protein/RNA / NUCLEOCAPSID PROTEIN / COMPLEX (NUCLEOCAPSID PROTEIN-RNA) / STEM-LOOP RNA / Viral protein-RNA COMPLEX
Function / homology
Function and homology information


nucleic acid binding / zinc ion binding
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Gag protein p6 / Gag protein p6 / Few Secondary Structures / Irregular / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
RNA / RNA (> 10) / Gag polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodSOLUTION NMR / distance geometry
AuthorsDe Guzman, R.N. / Wu, Z.R. / Stalling, C.C. / Pappalardo, L. / Borer, P.N. / Summers, M.F.
CitationJournal: Science / Year: 1998
Title: Structure of the HIV-1 nucleocapsid protein bound to the SL3 psi-RNA recognition element.
Authors: De Guzman, R.N. / Wu, Z.R. / Stalling, C.C. / Pappalardo, L. / Borer, P.N. / Summers, M.F.
History
DepositionDec 15, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: 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_struct_assembly / pdbx_struct_conn_angle / 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_database_status.process_site / _pdbx_nmr_software.name / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: SL3 STEM-LOOP RNA
A: NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9954
Polymers12,8642
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)25 / 800LEAST TOTAL PENALTY
Representative

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Components

#1: RNA chain SL3 STEM-LOOP RNA


Mass: 6477.919 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein NUCLEOCAPSID PROTEIN / Virus


Mass: 6386.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: NL4-3 / Cell line: BL21 / Gene: NC / Plasmid: PRD2 / Gene (production host): NC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: Q75677
#3: 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
111NOESY
121TOCSY
131TRIPLE-RESONANCE

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX600BrukerDMX6006001
GE DRX800GEDRX8008002
GE GE OMEGA PSG 600GEGE OMEGA PSG 6008003

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Processing

NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
NMRViewstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: THE COORDINATES FOR THE 25 MODELS WHICH WERE SUBMITTED TO SCIENCE REPRESENT THE BEST-FIT SUPERPOSITION OF THE BACKBONE C, CA AND N ATOMS OF HIV-1 NUCLEOCAPSID PROTEIN (FROM LYS 3 - GLU 51) ...Details: THE COORDINATES FOR THE 25 MODELS WHICH WERE SUBMITTED TO SCIENCE REPRESENT THE BEST-FIT SUPERPOSITION OF THE BACKBONE C, CA AND N ATOMS OF HIV-1 NUCLEOCAPSID PROTEIN (FROM LYS 3 - GLU 51) AND ALL HEAVY ATOMS OF SL3 RNA RECOGNITION ELEMENT (FROM C 4 - G17). THE STRUCTURES WERE GENERATED WITH A TOTAL OF 719 EXPERIMENTAL DISTANCE RESTRAINTS WITH THE USE OF THE PROGRAM DYANA. HYDROGEN BOND RESTRAINTS WERE USED TO IMPROVE CONVERGENCE OF THE STRUCTURES, BUT NOT ALTER THE GLOBAL FOLD.
NMR ensembleConformer selection criteria: LEAST TOTAL PENALTY / Conformers calculated total number: 800 / Conformers submitted total number: 25

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