SAXSdb — 6y9z

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

Gag-Pol polyprotein

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Peptidyl-prolyl cis-trans isomerase A × 1 （P62937）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1LW
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 133–352 Author chain B； PDBConstruct 1–220； UniProt 133–352 Author chain C； PDBConstruct 1–220； UniProt 133–352 Author chain D； PDBConstruct 1–220； UniProt 133–352 Author chain G； PDBConstruct 1–220； UniProt 133–352 Author chain H； PDBConstruct 1–220； UniProt 133–352 Author chain N； PDBConstruct 1–220； UniProt 133–352 Author chain Y； PDBConstruct 1–220； UniProt 133–352 Author chain d； PDBConstruct 1–220； UniProt 133–352 Author chain e； PDBConstruct 1–220； UniProt 133–352 Author chain j； PDBConstruct 1–220； UniProt 133–352 Author chain k； PDBConstruct 1–220； UniProt 133–352

Peptidyl-prolyl cis-trans isomerase A

Homo sapiens

UniProt P62937

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 13	Gag-Pol polyprotein × 12 （P0C6F2）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPIA_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain J； PDBConstruct 1–164； UniProt 2–165

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	6y9z
Deposition date deposition_date	2020-03-10
Structure title title	Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9)
Keywords keywords	HIV, capsid, hexamer, helical assembly, curvature, 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.

6y9z__assembly_1__model_1

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

Download this curve (.dat)

6y9z__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6y9z__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.72 Å
Rg (electron density)	48.25 Å
Total Rg	48.48 Å
Atom count	18418
Residues	2364
Excluded volume	328100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6y9z__assembly_1__model_1`	tridecameric （13）	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	Gag-Pol polyprotein
Molecular weight formula_weight	24531.1 kDa
EC 编号 ec_number	3.4.23.16,2.7.7.49,2.7.7.7,3.1.26.13,3.1.13.2,2.7.7.-,3.1.-.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,G,H,N,Y,d,e,j,k
Atom count atom_count	18418

PIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPAATLEEMMTACQG

Source Source

Source organism organism	Human immunodeficiency virus 1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptidyl-prolyl cis-trans isomerase A
Molecular weight formula_weight	17905.3 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

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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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	4.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	80520

Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9)

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

Gag-Pol polyprotein

State in the Current Structure

Other States of the Same Protein in the Database

Peptidyl-prolyl cis-trans isomerase A

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

6y9z__assembly_1__model_1

6y9z__assembly_1__model_1 | I(q)

6y9z__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)

Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9)

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

Gag-Pol 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

Peptidyl-prolyl cis-trans isomerase A

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

6y9z__assembly_1__model_1

6y9z__assembly_1__model_1 | I(q)

6y9z__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

7. Citations (1)