SAXSdb — 5upw

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

Gag polyprotein

Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAG_HV1N5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 133–353 Author chain B； PDBConstruct 1–221； UniProt 133–353 Author chain C； PDBConstruct 1–221； UniProt 133–353 Author chain D； PDBConstruct 1–221； UniProt 133–353 Author chain E； PDBConstruct 1–221； UniProt 133–353 Author chain F； PDBConstruct 1–221； UniProt 133–353

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	5upw
Deposition date deposition_date	2017-02-04
Structure title title	CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations
Keywords keywords	Cryo-EM, HIV capsid, Chemical shift, Molecular Dynamics, hydrolase, viral protein; VIRAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

5upw__assembly_1__model_1

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

Download this curve (.dat)

5upw__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5upw__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	36.85 Å
Rg (electron density)	35.90 Å
Total Rg	36.41 Å
Atom count	10350
Residues	1326
Excluded volume	184510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5upw__assembly_1__model_1`	hexameric （6）	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 (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	—

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

Resolution resolution	5.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	38452

Description description	Gag polyprotein
Molecular weight formula_weight	24654.3 kDa
Mutation mutation	A92E
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10350

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

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

Gag polyprotein

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

5upw__assembly_1__model_1

5upw__assembly_1__model_1 | I(q)

5upw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)

Source organism organism	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
NCBI taxonomy ID ncbi_taxonomy_id	11698
Host organism host_organism	Escherichia coli

CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

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

Gag polyprotein

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

5upw__assembly_1__model_1

5upw__assembly_1__model_1 | I(q)

5upw__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

7. Citations (1)