8fnl

Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound

Method: ELECTRON MICROSCOPY

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

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

Human immunodeficiency virus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 8 DNA 4	DNA (27-MER) × 2 DNA (25-MER) × 2 MAGNESIUM ION × 4 ZINC ION × 2 ;(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide ; × 2 water × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POL_HV1N5
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 77–364； UniProt 1148–1435 Author chain B； PDBConstruct 77–364； UniProt 1148–1435 Author chain C； PDBConstruct 77–364； UniProt 1148–1435 Author chain D； PDBConstruct 77–364； UniProt 1148–1435 Author chain G； PDBConstruct 77–364； UniProt 1148–1435 Author chain H； PDBConstruct 77–364； UniProt 1148–1435 Author chain I； PDBConstruct 77–364； UniProt 1148–1435 Author chain J； PDBConstruct 77–364； UniProt 1148–1435

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

Human immunodeficiency virus 1

UniProt P42166

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 8 DNA 4	DNA (27-MER) × 2 DNA (25-MER) × 2 MAGNESIUM ION × 4 ZINC ION × 2 ;(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide ; × 2 water × 12	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LAP2A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 23–73； UniProt 50–100 Author chain B； PDBConstruct 23–73； UniProt 50–100 Author chain C； PDBConstruct 23–73； UniProt 50–100 Author chain D； PDBConstruct 23–73； UniProt 50–100 Author chain G； PDBConstruct 23–73； UniProt 50–100 Author chain H； PDBConstruct 23–73； UniProt 50–100 Author chain I； PDBConstruct 23–73； UniProt 50–100 Author chain J； PDBConstruct 23–73； UniProt 50–100

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	8fnl
Deposition date deposition_date	2022-12-27
Structure title title	Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound
Keywords keywords	Integrase, Nucleoprotein complex, Inhibitor, Drug resistance, VIRAL PROTEIN-DNA-INHIBITOR complex; VIRAL PROTEIN/DNA/INHIBITOR
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.

8fnl__assembly_1__model_1

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

Download this curve (.dat)

8fnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8fnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.43 Å
Rg (electron density)	38.02 Å
Total Rg	38.29 Å
Atom count	11304
Residues	1304
Excluded volume	198010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8fnl__assembly_1__model_1`	dodecameric （12）	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 (7)

Entity 1 Entity 1 polymer

Description description	Lamina-associated polypeptide 2, isoform alpha,Integrase chimera
Molecular weight formula_weight	39899.5 kDa
EC 编号 ec_number	2.7.7.-,3.1.-.-
Mutation mutation	E138K,Q148K
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,G,H,I,J
Atom count atom_count	11936

GSHMPKRGRPAATEVKIPKPRGRPPLPAGTNSKGPPDFSSDEEREPTPVLGSGAAAAGQSRAAVGRKATKKTDGGGFLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTDNGSNFTSTTVKAACWWAGIKQKFGIPYNPQSKGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED

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	DNA (27-MER)
Molecular weight formula_weight	8188.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,K

ACTGCTAGAGATTTTCCCGCCCACGCT

Entity 3 Entity 3 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7773.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,L

AGCGTGGGCGGGAAAATCTCTAGCA

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	;(4R,12aS)-N-(2,4-difluorobenzyl)-7-hydroxy-4-methyl-6,8-dioxo-3,4,6,8,12,12a-hexahydro-2H-pyrido[1',2':4,5]pyrazino[2,1-b][1,3]oxazine-9-carboxamide ;
Molecular weight formula_weight	419.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	590

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Resolution resolution	2.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	136589

Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound

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

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

State in the Current Structure

Other States of the Same Protein in the Database

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

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

8fnl__assembly_1__model_1

8fnl__assembly_1__model_1 | I(q)

8fnl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Structure of E138K/Q148K HIV-1 intasome with Dolutegravir bound

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

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lamina-associated polypeptide 2, isoform alpha,Integrase chimera

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

8fnl__assembly_1__model_1

8fnl__assembly_1__model_1 | I(q)

8fnl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)