SAXSdb — 7d7s

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

Protein Nef

Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–209	Not recorded	Tyrosine-protein kinase Fyn × 1 （E5RFS5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000	Resolution 3.32 Å R-free 0.300
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–209	Not recorded	Tyrosine-protein kinase Fyn × 1 （E5RFS5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000	Resolution 3.32 Å R-free 0.300

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 7D7S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3RBB HIV-1 NEF protein in complex with engineered HCK SH3 domain Deposited 2011-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.245
3RBB HIV-1 NEF protein in complex with engineered HCK SH3 domain Deposited 2011-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes, 8% ethylene glycol, 22% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.35 Å R-free 0.245
3REA HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.00 Å R-free 0.205
3REA HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 2.00 Å R-free 0.205
3REB HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Hepes, 0.05 M sodium citrate, 15% isopropanol, 30% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.45 Å R-free 0.243
3REB HIV-1 Nef protein in complex with engineered Hck-SH3 domain Deposited 2011-04-04	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 45–210（166 aa）	Mutation：I47M, T48A, C59S, C210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；100 mM Hepes, 0.05 M sodium citrate, 15% isopropanol, 30% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K	Resolution 3.45 Å R-free 0.243
4ORZ HIV-1 Nef protein in complex with single domain antibody sdAb19 and an engineered Hck SH3 domain Deposited 2014-02-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 45–210（166 aa） Fragment：Nef protein, UNP residues 45-210	Mutation：I47M, T48A, C59S, C210A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；About 0.1 micro L of protein solution at 10 mg/ml concentration was mixed with 0.1 micro L of reservoir solution from a 70 L reservoir in 96-well Hampton 3553 crystallization plates. Initial crystals of NefSF2 sdAb19 SH3B6 could be obtained in 0.2 M potassium formate and 20% polyethylene glycol (PEG) 3350. Crystal conditions were optimized to 0.2 M potassium formate, 17.5% polyethylene glycol (PEG) 3350 and 0.35 M ammonium chloride grown by hanging-drop vapor diffusion in Linbro crystallization plates. , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.236
4U5W Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains Deposited 2014-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 62–209（148 aa） Fragment：UNP residues 62-209 Chain C 62–209（148 aa） Fragment：UNP residues 62-209	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 IOD IODIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.15 K；0.09 M ADA, pH 6.5, 10.8% (v/v) 2-methyl-2,4-pentanediol, 100 mM NaI	Resolution 1.86 Å R-free 0.195
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 57–207（151 aa） Fragment：UNP residues 57-207 Chain B 57–207（151 aa） Fragment：UNP residues 57-207	Not recorded	BOG octyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol	Resolution 3.20 Å R-free 0.251
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 57–207（151 aa） Fragment：UNP residues 57-207 Chain E 57–207（151 aa） Fragment：UNP residues 57-207	Not recorded	BOG octyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol	Resolution 3.20 Å R-free 0.251
6B72 A novel HIV-1 Nef dimer interface induced by a single octyl-glucoside molecule Deposited 2017-10-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 57–207（151 aa） Fragment：UNP residues 57-207 Chain F 57–207（151 aa） Fragment：UNP residues 57-207	Not recorded	BOG octyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；18%-20% PEG5000 MME, 0.1 M Bis-Tris propane, pH 8.0, 5% glycerol	Resolution 3.20 Å R-free 0.251
8F2P Nef SF2 dimerization mutant bound to Hck SH3 Deposited 2022-11-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 62–209（148 aa） Fragment：Nef SF2 core domain (UNP residues 62-209)	Mutation：L116D	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium chloride, 0.1 M sodium acetate, pH 4.6, 12% v/v MPD	Resolution 2.63 Å R-free 0.252

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

View Construct and Data Evidence

UniProt name	NEF_HV1A2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 1–209 Author chain B； PDBConstruct 1–209； UniProt 1–209

Tyrosine-protein kinase Fyn

Homo sapiens

UniProt E5RFS5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 82–144	Mutation：R96I	Protein Nef × 1 （P03407）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000	Resolution 3.32 Å R-free 0.300
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 82–144	Mutation：R96I	Protein Nef × 1 （P03407）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000 X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；0.10 M calcium acetate hydrate, 0.10 M sodium acetate buffer (pH 4.5), 10% w/v PEG 4000	Resolution 3.32 Å R-free 0.300

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 7D7S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7UD6 Designed Enzyme SH3-588 (Catechol O-methyltransferase catalytic domain and Src homology 3 binding domain fusion) Deposited 2022-03-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–141（56 aa）	Mutation：Q26V,N29R,E37L,R39V,R73E,Y74F,Q77L,N78V,T93Q,Q97Y,K98R	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；297 K；0.7 M magnesium formate, 0.1 M bis-tris propone pH 7.0.	Resolution 2.59 Å R-free 0.278

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

View Construct and Data Evidence

UniProt name	E5RFS5_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–64； UniProt 82–144 Author chain D； PDBConstruct 2–64； UniProt 82–144

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	7d7s
Deposition date deposition_date	2020-10-05
Structure title title	HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant
Keywords keywords	Complex, mutant, kinase, SH3, 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	25.14 Å
Radius of gyration Rg (electron density) rg_electron	24.75 Å
Forward intensity I(0) i0	22880700.00
Molecular weight molecular_weight	38468.0 kDa
Excluded volume excluded_volume	48799 Å³
Envelope volume envelope_volume	61332 Å³
Hydration-shell volume shell_volume	21734 Å³
Envelope diameter envelope_diameter	92.4 Å
Shell Rg shell_rg	30.16 Å
Envelope Rg envelope_rg	24.82 Å
Shape Rg shape_rg	24.72 Å
Total Rg total_rg	25.55 Å
Total atoms total_atoms	2737
Residues n_residues	328
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	89.3 Å
Rg (real space) rg_real	25.19 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	2.2880e+07
I(0) uncertainty (real space) i0_real_error	3.3050e+05
Rg (reciprocal space) rg_reciprocal	25.17 Å
I(0) (reciprocal space) i0_reciprocal	22880000.0000
Solution quality estimate total_estimate	0.6439
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.0 Å
Skewness Skewness skewness	0.359
Kurtosis Kurtosis kurtosis	-0.293
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7526000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.771; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.769; Smooth: 0.923

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein Nef
Molecular weight formula_weight	25585.8 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	2737

MGGKWSKRSMGGWSAIRERMRRAEPRAEPAADGVGAVSRDLEKHGAITSSNTAATNADCAWLEAQEEEEVGFPVRPQVPLRPMTYKAALDISHFLKEKGGLEGLIWSQRRQEILDLWIYHTQGYFPDWQNYTPGPGIRYPLTFGWCFKLVPVEPEKVEEANEGENNSLLHPMSLHGMEDAEKEVLVWRFDSKLAFHHMARELHPEYYKDSKLAAALEHHHHHH

来源 Source

来源生物 organism	Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)
通用名 common_name	HIV-1
NCBI Class编号 ncbi_taxonomy_id	11685
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tyrosine-protein kinase Fyn
Molecular weight formula_weight	8255.0 kDa
Mutation mutation	R96I
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MTGVTLFVALYDYEAITEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVDSILEHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Unit-cell length a length_a	122.110 Å
Unit-cell length b length_b	122.110 Å
Unit-cell length c length_c	145.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.320 Å
Low-resolution limit resolution_low	48.680 Å
R factor r_factor	0.2876
R_work r_work	0.2862
R_free r_free	0.2995

fit	/app/data/saxs_computation/d7/7d7s/7d7s.fit
pddf	/app/data/pr_computation/d7/7d7s/7d7s.pr.out
profile	/app/data/saxs_computation/d7/7d7s/7d7s.dat

HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant

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

Tyrosine-protein kinase Fyn

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)