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9rmx

CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)

Method: ELECTRON MICROSCOPY D_max: 287.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rmx
deposition_date	2025-06-19
title	CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)
keywords	integrase, capsid, HIV-1, RNA, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	81.68 Å
rg_electron	81.43 Å
i0	15233200000.00
molecular_weight	1038400.0 kDa
excluded_volume	1295500 Å³
envelope_volume	2316700 Å³
shell_volume	233160 Å³
envelope_diameter	279.6 Å
shell_rg	82.54 Å
envelope_rg	79.06 Å
shape_rg	81.44 Å
total_rg	81.39 Å
total_atoms	72751
n_residues	9257
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	287.8 Å
rg_real	84.96 Å
rg_real_error	1.60 Å
i0_real	1.5230e+10
i0_real_error	3.2170e+08
rg_reciprocal	81.99 Å
i0_reciprocal	15250000000.0000
total_estimate	0.8858
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	106.0 Å
skewness	0.476
kurtosis	0.024
angular_range	— – 0.0950 Å⁻¹
current_alpha	1.1000
highest_alpha	1805000000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 0.887; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.415

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Integrase
formula_weight	32242.8 kDa
ec_number	2.7.7.-,3.1.-.-
mutation	D64N, D116N
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H,I,J,K,L
atom_count	72751

FLDGIDKAQEEHEKYHSNWRAMASDFNLPPVVAKEIVASCDKCQLKGEAMHGQVDCSPGIWQLNCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHTNNGSNFTSTTVKAACWWAGIKQEFGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNFKRKGGIGGYSAGERIVDIIATDIQTKELQKQITKIQNFRVYYRDSRDPVWKGPAKLLWKGEGAVVIQDNSDIKVVPRRKAKIIRDYGKQMAGDDCVASRQDED

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 2 polymer

description	Gag polyprotein
formula_weight	25630.4 kDa
src_method	man
entity_count	32

Polymer

type	polypeptide(L)
strand_id	U,V,W,X,Y,Z,a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t,u,v,w,x,y,z

PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Source

organism	Human immunodeficiency virus 1
ncbi_taxonomy_id	11676
host_organism	Homo sapiens

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	INOSITOL HEXAKISPHOSPHATE
formula_weight	660.0 kDa
src_method	syn
entity_count	8

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.630 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.63 Å
resolution_method	—
num_particles	58103

fit	/app/data/saxs_computation/rm/9rmx/9rmx.fit
pddf	/app/data/pr_computation/rm/9rmx/9rmx.pr.out
profile	/app/data/saxs_computation/rm/9rmx/9rmx.dat

CryoEM reconstruction of integrase filament at the lumen of native HIV-1 cores (box size 34.2 nm)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)