1a1t

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES

Method: SOLUTION NMR D_max: 66.0 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

NUCLEOCAPSID PROTEIN

Human immunodeficiency virus 1

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	Not recorded	SL3 STEM-LOOP RNA × 1 ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K	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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q75677_9HIV1
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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a1t
Deposition date deposition_date	1997-12-15
Structure title title	STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES
Keywords keywords	NUCLEOCAPSID PROTEIN, COMPLEX (NUCLEOCAPSID PROTEIN-RNA), STEM-LOOP RNA, Viral protein-RNA COMPLEX; Viral protein/RNA
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	15.97 Å
Radius of gyration Rg (electron density) rg_electron	16.28 Å
Forward intensity I(0) i0	3160500000.00
Molecular weight molecular_weight	325930.0 kDa
Excluded volume excluded_volume	345330 Å³
Envelope volume envelope_volume	30549 Å³
Hydration-shell volume shell_volume	14537 Å³
Envelope diameter envelope_diameter	70.4 Å
Shell Rg shell_rg	24.24 Å
Envelope Rg envelope_rg	19.82 Å
Shape Rg shape_rg	16.21 Å
Total Rg total_rg	16.51 Å
Total atoms total_atoms	37900
Residues n_residues	1875
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.0 Å
Rg (real space) rg_real	16.22 Å
Rg uncertainty (real space) rg_real_error	0.86 Å
I(0) (real space) i0_real	3.1610e+09
I(0) uncertainty (real space) i0_real_error	4.5060e+07
Rg (reciprocal space) rg_reciprocal	16.19 Å
I(0) (reciprocal space) i0_reciprocal	3160000000.0000
Solution quality estimate total_estimate	0.6913
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.702
Kurtosis Kurtosis kurtosis	0.138
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	467100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.294; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.102; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	SL3 STEM-LOOP RNA
Molecular weight formula_weight	6477.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	37900

GGACUAGCGGAGGCUAGUCC

Entity 2 Entity 2 polymer

Description description	NUCLEOCAPSID PROTEIN
Molecular weight formula_weight	6386.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN

来源 Source

来源生物 organism	Human immunodeficiency virus 1
NCBI Class编号 ncbi_taxonomy_id	11676
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a1ta_
Class class	g — Small proteins
Fold Fold fold	g.40 — Retrovirus zinc finger-like domains
Superfamily Superfamily superfamily	g.40.1 — Retrovirus zinc finger-like domains
Family Family family	g.40.1.1 — Retrovirus zinc finger-like domains

CATH v4.4 (1 domains)

Domain ID domain_id	1a1tA00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

fit	/app/data/saxs_computation/a1/1a1t/1a1t.fit
pddf	/app/data/pr_computation/a1/1a1t/1a1t.pr.out
profile	/app/data/saxs_computation/a1/1a1t/1a1t.dat

STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES

1. Protein Identity and Related Structures Protein Identity & Related Structures

NUCLEOCAPSID PROTEIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)