SAXSdb — 7n9x

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

Capsid protein

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 18	Nanobody × 2 Nanobody × 2 Nanobody × 2 Peptidyl-prolyl cis-trans isomerase A × 6 （P62937）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B6DRA0_9HIV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 1–222； UniProt 133–354 Author chain BBB； PDBConstruct 1–222； UniProt 133–354 Author chain CCC； PDBConstruct 1–222； UniProt 133–354

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 18	Capsid protein × 6 （B6DRA0） Nanobody × 2 Nanobody × 2 Nanobody × 2	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	5
Chains and sequence ranges	Author chain GGG； PDBConstruct 1–165； UniProt 1–165 Author chain HHH； PDBConstruct 1–165； UniProt 1–165 Author chain III； PDBConstruct 1–165； UniProt 1–165

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	7n9x
Deposition date deposition_date	2021-06-18
Structure title title	CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions
Keywords keywords	HIV-1, hexamer, nanobody, CypA, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

7n9x__assembly_1__model_1

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

Download this curve (.dat)

7n9x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7n9x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	52.25 Å
Rg (electron density)	51.88 Å
Total Rg	51.91 Å
Atom count	22916
Residues	2980
Excluded volume	406880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7n9x__assembly_1__model_1`	octadecameric （18）	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 (5)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	24542.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	BBB,CCC,AAA
Atom count atom_count	11458

PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVG

Source Source

Source organism organism	Human immunodeficiency virus 1
Common name common_name	HIV-1
NCBI taxonomy ID ncbi_taxonomy_id	11676
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Nanobody
Molecular weight formula_weight	12373.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	FFF

DVQLQESGGGLVQAGGSLRLSCAASGSISRFNAMGWWRQAPGKEREFVARIVKGFDPVLADSVKGRFTISIDSAENTLALQMNRLKPEDTAVYYCFAALDTXXAYWGQGTQVTVS

Source Source

Source organism organism	Lama glama
Common name common_name	Llama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Nanobody
Molecular weight formula_weight	12116.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	EEE

DVQLQESGGGLVQAGGSLRLSCAASGSISRFNAMGWWRQAPGKEREFVARIVKGFDPVLADSVKGRFTISIDSAENTLALQMNRLKPEDTAVYYCFAALDTAYWGQGTQVTV

Source Source

Source organism organism	Lama glama
Common name common_name	Llama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Nanobody
Molecular weight formula_weight	12284.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	DDD

VQLQESGGGLVQAGGSLRLSCAASGSISRFNAMGWWRQAPGKEREFVARIVKGFDPVLADSVKGRFTISIDSAENTLALQRNRLKPEDTAVYYCFAALDTXXAYWGQGTQVTVS

Source Source

Source organism organism	Lama glama
Common name common_name	Llama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	Peptidyl-prolyl cis-trans isomerase A
Molecular weight formula_weight	18036.5 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	GGG,HHH,III

MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE

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 BL21(DE3)

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Unit-cell length a length_a	127.950 Å
Unit-cell length b length_b	137.850 Å
Unit-cell length c length_c	313.832 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	24

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.511 Å
Low-resolution limit resolution_low	49.581 Å
R factor r_factor	—
R_work r_work	0.2449
R_free r_free	0.2699

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

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

Capsid protein

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

7n9x__assembly_1__model_1

7n9x__assembly_1__model_1 | I(q)

7n9x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

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

Capsid protein

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

7n9x__assembly_1__model_1

7n9x__assembly_1__model_1 | I(q)

7n9x__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

7. Citations (1)