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9vbk

Cryo-EM structure of human PLD4 bound to ssDNA (poly(T))

Method: ELECTRON MICROSCOPY D_max: 120.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vbk
deposition_date	2025-06-04
title	Cryo-EM structure of human PLD4 bound to ssDNA (poly(T))
keywords	Exonuclease, IMMUNE SYSTEM; IMMUNE SYSTEM
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	39.81 Å
rg_electron	38.68 Å
i0	535839000.00
molecular_weight	188740.0 kDa
excluded_volume	235960 Å³
envelope_volume	317350 Å³
shell_volume	66618 Å³
envelope_diameter	127.4 Å
shell_rg	46.31 Å
envelope_rg	37.88 Å
shape_rg	38.66 Å
total_rg	39.20 Å
total_atoms	13309
n_residues	1661
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	120.4 Å
rg_real	39.47 Å
rg_real_error	0.83 Å
i0_real	5.3580e+08
i0_real_error	8.2070e+06
rg_reciprocal	39.68 Å
i0_reciprocal	536000000.0000
total_estimate	0.9046
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	57.2 Å
skewness	-0.010
kurtosis	-0.697
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	253800000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.938; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.957

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	;5'-3' exonuclease PLD4 ;
formula_weight	46287.3 kDa
ec_number	3.1.16.1,3.1.4.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13309

RDSCQLVLVESIPQDLPSAAGSPSAQPLGQAWLQLLDTAQESVHVASYYWSLTGPDIGVNDSSSQLGEALLQKLQQLLGRNISLAVATSSPTLARTSTDLQVLAARGAHVRQVPMGRLTRGVLHSKFWVVDGRHIYMGSANMDWRSLTQVKELGAVIYNCSHLAQDLEKTFQTYWVLGVPKAVLPKTWPQNFSSHFNRFQPFHGLFDGVPTTAYFSASPPALCPQGRTRDLEALLAVMGSAQEFIYASVMEYFPTTRFSHPPRYWPVLDNALRAAAFGKGVRVRLLVGCGLNTDPTMFPYLRSLQALSNPAANVSVDVKVFIVPVGNHSNIPFSRVNHSKFMVTEKAAYIGTSNWSEDYFSSTAGVGLVVTQSPGAQPAGATVQEQLRQLFERDWSSRYAVGLDGQAPGQDCVWQGLEVLFQ

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	;DNA (5'-D(TPTP*T)-3') ;
formula_weight	14860.5 kDa
src_method	syn
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	F,G

TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

Entity 3 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	8

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	syn
entity_count	15

Entity 5 non-polymer

description	THYMIDINE-3'-PHOSPHATE
formula_weight	322.2 kDa
src_method	syn
entity_count	1

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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	triclinic

resolution	3.06 Å
resolution_method	—
num_particles	65742

fit	/app/data/saxs_computation/vb/9vbk/9vbk.fit
pddf	/app/data/pr_computation/vb/9vbk/9vbk.pr.out
profile	/app/data/saxs_computation/vb/9vbk/9vbk.dat

Cryo-EM structure of human PLD4 bound to ssDNA (poly(T))

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)