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9xyb

Crystal structure of a ZIKV E glycoprotein DI-DIII vaccine candidate in complex with human neutralizing antibody MZ4

Method: X-RAY DIFFRACTION D_max: 103.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xyb
deposition_date	2025-08-25
title	Crystal structure of a ZIKV E glycoprotein DI-DIII vaccine candidate in complex with human neutralizing antibody MZ4
keywords	envelope protein, vaccine candidate, recombinant protein, Zika virus, human antibody, neutralizing antibody, VIRAL PROTEIN; VIRAL PROTEIN
method	X-RAY DIFFRACTION

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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	30.71 Å
rg_electron	30.49 Å
i0	82347000.00
molecular_weight	70263.0 kDa
excluded_volume	87373 Å³
envelope_volume	111900 Å³
shell_volume	32334 Å³
envelope_diameter	108.4 Å
shell_rg	35.77 Å
envelope_rg	30.51 Å
shape_rg	30.46 Å
total_rg	31.04 Å
total_atoms	4936
n_residues	641
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	103.9 Å
rg_real	30.93 Å
rg_real_error	0.79 Å
i0_real	8.2350e+07
i0_real_error	1.2160e+06
rg_reciprocal	30.84 Å
i0_reciprocal	82340000.0000
total_estimate	0.8503
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	32.0 Å
skewness	0.531
kurtosis	-0.240
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0001
highest_alpha	15260000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.863; Smooth: 0.780

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Human MZ4 Fab heavy chain
formula_weight	23371.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H
atom_count	4937

QVHLQESGPGLVRPSETLSLTCTVSDGSISSYYWSWIRQPPGKGLEWIGSIYYTGSTNYNPSLKSRVTMSVDTSKNQFSLRLNSVTAADTAMYYCAGLDRYSWNEGGDHWGQGILVSVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVE

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 2 polymer

description	Human MZ4 Fab light chain
formula_weight	22799.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

QPVLTQPPSASGTPGQRVSISCSGSRSNLGKNTVNWYQQLPGTAPKLLIYNHSRRPSGVPERFSGSKSGTSASLAISGLQSEDEADYFCAAWDDSLNGLYVFGTGTKVTVLRQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Envelope protein E
formula_weight	29375.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNGGGGGGGGLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLGGGGGGGGSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSGGGSGLNDIFEAQKIEWHEHHHHHHHH

Source

organism	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
ncbi_taxonomy_id	2043570
host_organism	Drosophila melanogaster

Entity 4 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1

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6. Citations (1)

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length_a	135.551 Å
length_b	57.257 Å
length_c	88.126 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.850 Å
resolution_low	32.900 Å
r_factor	0.2395
r_work	0.2354
r_free	0.3161

fit	/app/data/saxs_computation/xy/9xyb/9xyb.fit
pddf	/app/data/pr_computation/xy/9xyb/9xyb.pr.out
profile	/app/data/saxs_computation/xy/9xyb/9xyb.dat

Crystal structure of a ZIKV E glycoprotein DI-DIII vaccine candidate in complex with human neutralizing antibody MZ4

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

Diffraction

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)