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1f6u

NMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition

Method: SOLUTION NMR Dmax: 59.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

HIV-1 NUCLEOCAPSID PROTEIN

Human immunodeficiency virus 1

UniProt P35962

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts Chain A； UniProt 378–432 Non-standard monomer：Yes (specific site not provided by mmCIF) HIV-1 STEM-LOOP SL2 FROM PSI-RNA PACKAGING × 1 ZN ZINC ION × 2 SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 25mM NaCl；Pressure ambient NMR measurement conditions：pH 6.5；278 K；Ionic strength (raw mmCIF value) 25mM NaCl；Pressure ambient NMR sample composition：0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural abundance, 15N or 13C/15N isotopic labeled | 25mM Acetate buffer NMR sample composition：0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural 15N isotopic labeled NMR sample composition：0.6-1.2 mM complex of Nucleocapsid protein and SL2 RNA; natural a13C/15N isotopic labeled Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1F6U Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2R05 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain Deposited 2007-08-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 482–492（11 aa） Fragment：UNP residues 482-492
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K
Resolution 2.55 Å R-free 0.280

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAG_HV1Y2
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–55； UniProt 378–432

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1f6u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1f6u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1f6u
Deposition date deposition_date2000-06-23
Structure title titleNMR structure of the HIV-1 nucleocapsid protein bound to stem-loop sl2 of the psi-RNA packaging signal. Implications for genome recognition
Keywords keywordsHIV-1, RNA, PROTEIN-RNA COMPLEX, PACKAGING SIGNAL, STRUCTURAL PROTEIN-RNA COMPLEX; STRUCTURAL PROTEIN/RNA
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.83 Å
Radius of gyration Rg (electron density) rg_electron15.11 Å
Forward intensity I(0) i01924330000.00
Molecular weight molecular_weight255080.0 kDa
Excluded volume excluded_volume271250 ų
Envelope volume envelope_volume34488 ų
Hydration-shell volume shell_volume16160 ų
Envelope diameter envelope_diameter64.7 Å
Shell Rg shell_rg24.55 Å
Envelope Rg envelope_rg19.58 Å
Shape Rg shape_rg15.04 Å
Total Rg total_rg15.37 Å
Total atoms total_atoms29940
Residues n_residues1460
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax59.9 Å
Rg (real space) rg_real14.95 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real1.9240e+09
I(0) uncertainty (real space) i0_real_error2.2990e+07
Rg (reciprocal space) rg_reciprocal14.94 Å
I(0) (reciprocal space) i0_reciprocal1924000000.0000
Solution quality estimate total_estimate0.7486
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary15.9 Å
Skewness Skewness skewness0.624
Kurtosis Kurtosis kurtosis0.334
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha446300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.435; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.432; Smooth: 0.992
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1f6ua_
Class classg — Small proteins
Fold Fold foldg.40 — Retrovirus zinc finger-like domains
Superfamily Superfamily superfamilyg.40.1 — Retrovirus zinc finger-like domains
Family Family familyg.40.1.1 — Retrovirus zinc finger-like domains

CATH v4.4 (1 domains)

Domain ID domain_id1f6uA00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily10 — Zinc finger, CCHC-type
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8. Citations (1)

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9. Files and Curves (10)