SAXSdb — 5nui

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

Protein Nef

Simian immunodeficiency virus

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 87–235 Chain B； UniProt 87–235	Not recorded	SER-GLN-ILE-LYS-ARG-LEU-LEU-SER × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277 K；10% PEG 4000, 0.15 M ammonium sulfate, 0.1 M MES (pH 5.8)	Resolution 2.50 Å R-free 0.257

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 5NUI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3IK5 SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80) Deposited 2009-08-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 95–235（141 aa） Fragment：core domain Chain C 95–235（141 aa） Fragment：core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 3350, 0.2mM ammonmium fluoride, 0.1mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.184
3IK5 SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80) Deposited 2009-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 95–235（141 aa） Fragment：core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 3350, 0.2mM ammonmium fluoride, 0.1mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.184
3IK5 SIVmac239 Nef in complex with TCR zeta ITAM 1 polypeptide (A63-R80) Deposited 2009-08-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 95–235（141 aa） Fragment：core domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG 3350, 0.2mM ammonmium fluoride, 0.1mM hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.05 Å R-free 0.184
3IOZ SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93) Deposited 2009-08-15	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 95–235（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；277 K；15% PEG 3350, 0.15M KF, 0.1M hepes, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.70 Å R-free 0.329
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 165–173（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 165–173（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 165–175（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 165–175（11 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWF Rhesus macaque MHC class I molecule Mamu-B*17-QW9 Deposited 2011-05-09	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 199–207（9 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.246
3RWG Rhesus macaque MHC class I molecule Mamu-B*17-MW9 Deposited 2011-05-09	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 195–203（9 aa）	Not recorded	XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.237
5NUH Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain Deposited 2017-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 68–235（168 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 0.15 M tri-lithium-citrat, 1% 1.6 hexandiol	Resolution 2.78 Å R-free 0.229
5NUH Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain Deposited 2017-04-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 68–235（168 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；12% PEG 3350, 0.15 M tri-lithium-citrat, 1% 1.6 hexandiol	Resolution 2.78 Å R-free 0.229

7 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5QGG3_SIV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–151； UniProt 87–235 Author chain B； PDBConstruct 3–151； UniProt 87–235

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	5nui
Deposition date deposition_date	2017-04-30
Structure title title	Crystal structure of SIVmac239 Nef in an ExxxLM endocytic sorting motif bound state
Keywords keywords	SIV, Nef, endocytic sorting motif, ExxxLL, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.84 Å
Radius of gyration Rg (electron density) rg_electron	22.49 Å
Forward intensity I(0) i0	12746600.00
Molecular weight molecular_weight	28117.0 kDa
Excluded volume excluded_volume	35643 Å³
Envelope volume envelope_volume	43191 Å³
Hydration-shell volume shell_volume	17413 Å³
Envelope diameter envelope_diameter	76.6 Å
Shell Rg shell_rg	27.31 Å
Envelope Rg envelope_rg	22.38 Å
Shape Rg shape_rg	22.50 Å
Total Rg total_rg	23.17 Å
Total atoms total_atoms	2001
Residues n_residues	246
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	76.9 Å
Rg (real space) rg_real	22.99 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	1.2750e+07
I(0) uncertainty (real space) i0_real_error	1.6370e+05
Rg (reciprocal space) rg_reciprocal	22.96 Å
I(0) (reciprocal space) i0_reciprocal	12750000.0000
Solution quality estimate total_estimate	0.8576
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.0 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3343000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.824; Smooth: 0.953

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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	Protein Nef
Molecular weight formula_weight	17645.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2050

GAMDDIDEEDDDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFGS

来源 Source

来源生物 organism	Simian immunodeficiency virus
通用名 common_name	SIV
NCBI Class编号 ncbi_taxonomy_id	11723
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	SER-GLN-ILE-LYS-ARG-LEU-LEU-SER
Molecular weight formula_weight	1379.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

XXXXXXXXXXXXXXXX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5nuiA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

Domain ID domain_id	5nuiB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	62 — Nef Regulatory Factor
Homologous superfamily homologous superfamily	10 — Nef Regulatory Factor

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8. Citations (1)

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Unit-cell length a length_a	51.480 Å
Unit-cell length b length_b	140.730 Å
Unit-cell length c length_c	106.430 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	44.018 Å
R factor r_factor	0.1995
R_work r_work	0.1947
R_free r_free	0.2572

fit	/app/data/saxs_computation/nu/5nui/5nui.fit
pddf	/app/data/pr_computation/nu/5nui/5nui.pr.out
profile	/app/data/saxs_computation/nu/5nui/5nui.dat

Crystal structure of SIVmac239 Nef in an ExxxLM endocytic sorting motif bound state

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

Protein Nef

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)