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9vz8

Local refinement region of HPV45 in complex with antibody 10G2

Method: ELECTRON MICROSCOPY D_max: 108.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vz8
deposition_date	2025-07-22
title	Local refinement region of HPV45 in complex with antibody 10G2
keywords	Human papillomavirus, Cryo-EM, structural protein, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
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	33.94 Å
rg_electron	33.34 Å
i0	186149000.00
molecular_weight	107790.0 kDa
excluded_volume	133930 Å³
envelope_volume	180720 Å³
shell_volume	45231 Å³
envelope_diameter	111.8 Å
shell_rg	40.07 Å
envelope_rg	33.50 Å
shape_rg	33.35 Å
total_rg	33.85 Å
total_atoms	7601
n_residues	1015
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	108.5 Å
rg_real	33.88 Å
rg_real_error	0.83 Å
i0_real	1.8610e+08
i0_real_error	3.2700e+06
rg_reciprocal	33.92 Å
i0_reciprocal	186200000.0000
total_estimate	0.9018
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	41.5 Å
skewness	0.244
kurtosis	-0.510
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	58400000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.915

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Major capsid protein L1
formula_weight	57379.9 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,D,E
atom_count	7601

MALWRPSDSTVYLPPPSVARVVSTDDYVSRTSIFYHAGSSRLLTVGNPYFRVVPNGAGNKQAVPKVSAYQYRVFRVALPDPNKFGLPDSTIYNPETQRLVWACVGMEIGRGQPLGIGLSGHPFYNKLDDTESAHAATAVITQDVRDNVSVDYKQTQLCILGCVPAIGEHWAKGTLCKPAQLQPGDCPPLELKNTIIEDGDMVDTGYGAMDFSTLQDTKCEVPLDICQSICKYPDYLQMSADPYGDSMFFCLRREQLFARHFWNRAGVMGDTVPTDLYIKGTSANMRETPGSCVYSPSPSGSIITSDSQLFNKPYWLHKAQGHNNGICWHNQLFVTVVDTTRSTNLTLCASTQNPVPSTYDPTKFKQYSRHVEEYDLQFIFQLCTITLTAEVMSYIHSMNSSILENWNFGVPPPPTTSLVDTYRFVQSVAVTCQKDTTPPEKQDPYDKLKFWTVDLKEKFSSDLDQYPLGRKFLVQAGLRRRPTIGPRKRPAASTSTASTASRPAKRVRIRSKK

Source

organism	human papillomavirus 45
ncbi_taxonomy_id	10593
host_organism	Escherichia coli

Entity 2 polymer

description	10G2 Fab light chain
formula_weight	12215.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIVLTQSPASLSVSLGQRATISCRASQSVSTSSYSYMHWYQQKPGQPPKLLIKYASNLDSGVPARFSGSGSGTDFTLNIHPVEEEDTAKYYCQHSWEIPWTFGGGTKLEIK

Entity 3 polymer

description	10G2 Fab heavy chain
formula_weight	13365.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLQQPGAELVKPGASVKLSCKASGYSFTSYWMHWVKQRPGQGLEWIGEIDPSNSNTNYNQKFKGKATLTVDKSSSTAYMQLSSLTSEDSAVYYCARFYGTNYYAMDYWGQGTSVTSLS

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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	3.810 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.81 Å
resolution_method	—
num_particles	993420

fit	/app/data/saxs_computation/vz/9vz8/9vz8.fit
pddf	/app/data/pr_computation/vz/9vz8/9vz8.pr.out
profile	/app/data/saxs_computation/vz/9vz8/9vz8.dat

Local refinement region of HPV45 in complex with antibody 10G2

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)