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9pm6

Cryo-EM structure of modified Zika virus E protein dimer complexed with a neutralizing antibody OZ-D4 Fab

Method: ELECTRON MICROSCOPY D_max: 153.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pm6
deposition_date	2025-07-16
title	Cryo-EM structure of modified Zika virus E protein dimer complexed with a neutralizing antibody OZ-D4 Fab
keywords	neutralizing antibody, VIRAL PROTEIN, VIRAL PROTEIN-Immune System complex; 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	51.77 Å
rg_electron	52.49 Å
i0	262248000.00
molecular_weight	130540.0 kDa
excluded_volume	162020 Å³
envelope_volume	252910 Å³
shell_volume	43973 Å³
envelope_diameter	163.3 Å
shell_rg	48.22 Å
envelope_rg	51.14 Å
shape_rg	52.49 Å
total_rg	52.33 Å
total_atoms	9162
n_residues	1204
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	153.8 Å
rg_real	52.20 Å
rg_real_error	1.55 Å
i0_real	2.6220e+08
i0_real_error	5.2710e+06
rg_reciprocal	51.39 Å
i0_reciprocal	261900000.0000
total_estimate	0.7872
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	35.9 Å
skewness	0.407
kurtosis	-0.845
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0000
highest_alpha	10740000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.644; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Envelope protein E
formula_weight	47251.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9162

RSGSGEQKLISEEDLGGGGSIRCIGVSNRDFVEGMSGGTWVDIVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGCVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSGTGHHHHHH

Source

organism	Zika virus
ncbi_taxonomy_id	64320
host_organism	Drosophila

Entity 2 polymer

description	OZ-D4 Heavy chain
formula_weight	24403.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,C

QVQLQESGPGLVKPSETLSLTCTVSGGSISSYYWSWIRQPPGKGLEWIGYIYYSGSTNYNPSLKSRVTISVDTSKNQFSLKLSSVTAADTAVYYCARYSSGWSFSFDIWGQGTRVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKHHHHHHP

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	OZ-D4 Light chain
formula_weight	22528.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,D

QSALTQPASVAGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIHEGTKRPSGVSNRFSGSKSGNSASLTISGLQAEDEADYFCSSYAGGNTLVFGGGTNLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	3.45 Å
resolution_method	—
num_particles	710140

fit	/app/data/saxs_computation/pm/9pm6/9pm6.fit
pddf	/app/data/pr_computation/pm/9pm6/9pm6.pr.out
profile	/app/data/saxs_computation/pm/9pm6/9pm6.dat

Cryo-EM structure of modified Zika virus E protein dimer complexed with a neutralizing antibody OZ-D4 Fab

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)