SAXSdb — 1a6b

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

ZINC FINGER PROTEIN NCP10

OrganismNot specified

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–DNA Monomer Protein × 1 DNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 492–531	Fragment：CENTRAL DOMAIN RESIDUES 14-53	;DNA (5'-D(APCPGPCP*C)-3') ; × 1 ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；293 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.

Other PDB	Difference from Current Entry 1A6B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
1U6P NMR Structure of the MLV encapsidation signal bound to the Nucleocapsid protein Deposited 2004-07-30	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 479–534（56 aa） Fragment：Nucleoprotein p10	Not recorded	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
1WWD NMR structure determined for MLV NC complex with RNA sequence AACAGU Deposited 2005-01-05	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 B； PDBConstruct 1–40； UniProt 492–531

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1a6b
Deposition date deposition_date	1998-02-23
Structure title title	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
Keywords keywords	NUCLEOCAPSID PROTEIN, INTERCALATION, NUCLEIC ACID, RETROVIRUS, ZINC FINGER, Viral protein-DNA COMPLEX; Viral protein/DNA
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	12.78 Å
Radius of gyration Rg (electron density) rg_electron	13.19 Å
Forward intensity I(0) i0	352955000.00
Molecular weight molecular_weight	124340.0 kDa
Excluded volume excluded_volume	142250 Å³
Envelope volume envelope_volume	29355 Å³
Hydration-shell volume shell_volume	14086 Å³
Envelope diameter envelope_diameter	66.1 Å
Shell Rg shell_rg	23.94 Å
Envelope Rg envelope_rg	19.61 Å
Shape Rg shape_rg	13.23 Å
Total Rg total_rg	13.42 Å
Total atoms total_atoms	16140
Residues n_residues	900
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	34.8 Å
Rg (real space) rg_real	11.76 Å
Rg uncertainty (real space) rg_real_error	0.07 Å
I(0) (real space) i0_real	3.3650e+08
I(0) uncertainty (real space) i0_real_error	2.8280e+06
Rg (reciprocal space) rg_reciprocal	13.11 Å
I(0) (reciprocal space) i0_reciprocal	353000000.0000
Solution quality estimate total_estimate	0.6731
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	12.3 Å
Skewness Skewness skewness	0.476
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	2.8170
Highest regularization parameter α highest_alpha	114400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.007; Oscil: 0.958; Stabil: 0.979; Sysdev: 0.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.000

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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	;DNA (5'-D(APCPGPCP*C)-3') ;
Molecular weight formula_weight	1465.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	16140

ACGCC

Entity 2 Entity 2 polymer

Description description	ZINC FINGER PROTEIN NCP10
Molecular weight formula_weight	4706.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GERRRSQLDRDQCAYCKEKGHWAKDCPKKPRGPRGPRPQT

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	1

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1a6bb_
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	1a6bB00
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 (2)

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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/a6/1a6b/1a6b.fit
pddf	/app/data/pr_computation/a6/1a6b/1a6b.pr.out
profile	/app/data/saxs_computation/a6/1a6b/1a6b.dat

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

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

ZINC FINGER PROTEIN NCP10

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

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 (2)

9. Files and Curves (10)

Files (7)

Curves (3)