SAXSdb — 3ioz

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	T-cell surface glycoprotein CD3 zeta chain × 1 （P20963）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5QGG3_SIVCZ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–143； UniProt 95–235

T-cell surface glycoprotein CD3 zeta chain

Homo sapiens

UniProt P20963

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Protein Nef × 1 （Q5QGG3）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CD3Z_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–45； UniProt 51–93

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	3ioz
Deposition date deposition_date	2009-08-15
Structure title title	SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)
Keywords keywords	;Protein-Protein complex, Cell membrane, Lipoprotein, Membrane, Myristate, Viral immunoevasion, Virulence, Disulfide bond, Host-virus interaction, Phosphoprotein, Receptor, Transmembrane, VIRAL PROTEIN-ANTIVIRAL PROTEIN COMPLEX, VIRAL PROTEIN-SIGNALING PROTEIN COMPLEX ;; VIRAL PROTEIN/SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ioz__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ioz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ioz__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.67 Å
Rg (electron density)	14.43 Å
Total Rg	15.66 Å
Atom count	1051
Residues	125
Excluded volume	18711 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ioz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein Nef
Molecular weight formula_weight	16698.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1051

GSDDLVGVSVRPKVPLRTMSYKLAIDMSHFIKEKGGLEGIYYSARRHRILDIYLEKEEGIIPDWQDYTSGPGIRYPKTFGWLWKLVPVNVSDEAQEDEEHYLMHPAQTSQWDDPWGEVLAWKFDPTLAYTYEAYVRYPEEFGS

Source Source

Source organism organism	Simian immunodeficiency virus
NCBI taxonomy ID ncbi_taxonomy_id	388909
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	T-cell surface glycoprotein CD3 zeta chain
Molecular weight formula_weight	5279.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSLRVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRD

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3iozA00
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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Unit-cell length a length_a	51.638 Å
Unit-cell length b length_b	51.638 Å
Unit-cell length c length_c	189.449 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.699 Å
Low-resolution limit resolution_low	35.854 Å
R factor r_factor	0.3020
R_work r_work	0.3010
R_free r_free	0.3290

SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)

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

T-cell surface glycoprotein CD3 zeta chain

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ioz__assembly_1__model_1

3ioz__assembly_1__model_1 | I(q)

3ioz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

SIVmac239 Nef in complex with a TCR zeta polypeptide DP1 (L51-D93)

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

T-cell surface glycoprotein CD3 zeta chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ioz__assembly_1__model_1

3ioz__assembly_1__model_1 | I(q)

3ioz__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)