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1u6p

NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein

Method: SOLUTION NMR Dmax: 113.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Gag polyprotein

Moloney murine leukemia virus

UniProt P03332

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 479–534 Fragment：Nucleoprotein p10 101-MER × 1 ZN ZINC ION × 1 SOLUTION NMR NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR measurement conditions：pH 7；308 K；Ionic strength (raw mmCIF value) 10 mM Nacl；Pressure AMBIENT NMR sample composition：1.2MM PSI MONOMERIC RNA GUA-15N,13C;10MM TRIS, 100% D2O | 10MM TRIS, 100% D2O NMR sample composition：1.2MM PSI MONOMERIC RNA ADE-15N,13C; 10MM TRIS, 100% D2O | 10MM TRIS, 100% D2O NMR sample composition：1.2MM PSI MONOMERIC RNA CYT-15N,13C; 10MM TRIS, 100% D2O | 10MM TRIS, 100% D2O NMR sample composition：1.2MM PSI MONOMERIC RNA URA-15N,13C; 10MM TRIS, 100% D2O | 10MM TRIS, 100% D2O NMR sample composition：1.2MM PSI MONOMERIC RNA GUA-URA-CYT-2H, 10MM TRIS, 100% D2O; | 10MM TRIS, 100% D2O NMR sample composition：1.2MM PSI MONOMERIC RNA GUA-ADE-CYT-2H, 10MM TRIS, 100% D2O; | 10MM TRIS, 100% D2O 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 1U6P Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A6B NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES Deposited 1998-02-23 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 492–531（40 aa） Fragment：CENTRAL DOMAIN RESIDUES 14-53
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6.5；293 K
Resolution not provided
1MN8 Structure of Moloney Murine Leukaemia Virus Matrix Protein Deposited 2002-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–99（99 aa） Fragment：M-MuLV C-terminally truncated
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES-Na pH 7.5, 1.4M sodium citrate, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.00 Å R-free 0.169
1MN8 Structure of Moloney Murine Leukaemia Virus Matrix Protein Deposited 2002-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–99（99 aa） Fragment：M-MuLV C-terminally truncated
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES-Na pH 7.5, 1.4M sodium citrate, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.00 Å R-free 0.169
1MN8 Structure of Moloney Murine Leukaemia Virus Matrix Protein Deposited 2002-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–99（99 aa） Fragment：M-MuLV C-terminally truncated
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES-Na pH 7.5, 1.4M sodium citrate, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.00 Å R-free 0.169
1MN8 Structure of Moloney Murine Leukaemia Virus Matrix Protein Deposited 2002-09-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–99（99 aa） Fragment：M-MuLV C-terminally truncated
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M HEPES-Na pH 7.5, 1.4M sodium citrate, 100mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.00 Å R-free 0.169
1WWD NMR structure determined for MLV NC complex with RNA sequence AACAGU Deposited 2005-01-05 Different construct Different experimental conditions Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 479–534（56 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2；Pressure 1
NMR sample composition Unlabelled RNA, 1mM RNA Concentration, in 10mM NaCl, 10mM Tris-HCl, pH 7.0, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
NMR sample composition Unlabelled NC Protein, 1mM Protein Concentration, in 10mM NaCl, 10mM Tris-HCl, pH 7.0, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
Resolution not provided
1WWE NMR Structure Determined for MLV NC complex with RNA Sequence UUUUGCU Deposited 2005-01-05 Different construct Different experimental conditions Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 479–534（56 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2；Pressure 1
NMR sample composition Unlabelled RNA: 1mM RNA concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
NMR sample composition Unlabelled NC Protein: 1mM protein concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
Resolution not provided
1WWF NMR Structure Determined for MLV NC Complex with RNA Sequence CCUCCGU Deposited 2005-01-05 Different construct Different experimental conditions Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 479–534（56 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2；Pressure 1
NMR sample composition Unlabelled RNA: 1mM RNA concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
NMR sample composition Unlabelled NC Protein: 1mM protein concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
Resolution not provided
1WWG NMR Structure Determined for MLV NC Complex with RNA Sequence UAUCUG Deposited 2005-01-05 Different construct Different experimental conditions Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain A 479–534（56 aa）
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 7；288 K；Ionic strength (raw mmCIF value) 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2；Pressure 1
NMR sample composition Unlabelled RNA: 1mM RNA concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
NMR sample composition Unlabelled NC Protein: 1mM protein concentration, in 10mM Tris-HCl, pH 7.0, 10mM NaCl, 0.1mM ZnCl2, 0.1mM BME | 99.99% D2O
Resolution not provided

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GAG_MLVMO
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–56； UniProt 479–534

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 1u6p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1u6p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1u6p
Deposition date deposition_date2004-07-30
Structure title titleNMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein
Keywords keywords;MLV, A-MINOR K-TURN, STEM LOOP, BULGE, G-U MISMATCH, G-A MISMATCH, U-U MISMATCH, A-C MISMATCH, Zinc finger, NC, Viral protein-RNA COMPLEX ;; Viral 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_guinier33.50 Å
Radius of gyration Rg (electron density) rg_electron32.87 Å
Forward intensity I(0) i023745700000.00
Molecular weight molecular_weight785400.0 kDa
Excluded volume excluded_volume766210 ų
Envelope volume envelope_volume394940 ų
Hydration-shell volume shell_volume78503 ų
Envelope diameter envelope_diameter124.7 Å
Shell Rg shell_rg48.34 Å
Envelope Rg envelope_rg39.70 Å
Shape Rg shape_rg32.82 Å
Total Rg total_rg33.11 Å
Total atoms total_atoms82960
Residues n_residues3120
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 dmax113.9 Å
Rg (real space) rg_real33.58 Å
Rg uncertainty (real space) rg_real_error1.07 Å
I(0) (real space) i0_real2.3750e+10
I(0) uncertainty (real space) i0_real_error3.9290e+08
Rg (reciprocal space) rg_reciprocal33.53 Å
I(0) (reciprocal space) i0_reciprocal23740000000.0000
Solution quality estimate total_estimate0.8724
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.8 Å
Skewness Skewness skewness0.432
Kurtosis Kurtosis kurtosis-0.198
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19140000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.872
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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_idd1u6pa_
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_id1u6pA00
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)