SAXSdb — 9v6r

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1. Structure Basics

entry_id	9v6r
deposition_date	2025-05-27
title	Hexameric RVFV GnGc-Fab140 complex
keywords	RVFV, complex, hexamer, antibody, VIRAL PROTEIN/IMMUNE SYSTEM, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/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	66.91 Å
rg_electron	66.62 Å
i0	6337740000.00
molecular_weight	651740.0 kDa
excluded_volume	805390 Å³
envelope_volume	1348600 Å³
shell_volume	162830 Å³
envelope_diameter	199.2 Å
shell_rg	76.32 Å
envelope_rg	62.70 Å
shape_rg	66.64 Å
total_rg	66.68 Å
total_atoms	45636
n_residues	5910
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	204.3 Å
rg_real	66.60 Å
rg_real_error	1.30 Å
i0_real	6.3380e+09
i0_real_error	1.3280e+08
rg_reciprocal	67.93 Å
i0_reciprocal	6353000000.0000
total_estimate	0.8485
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	97.7 Å
skewness	-0.090
kurtosis	-0.521
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.0001
highest_alpha	308700000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.489

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Envelopment polyprotein
formula_weight	116711.3 kDa
src_method	man
entity_count	12

Polymer

type	polypeptide(L)
strand_id	A,B,C,H,I,L,M,P,Q,T,V,Y
atom_count	45636

PHLRNRPGKGHNYIDGMTQEDATCKPVTYAGACSSFDVLLEKGKFPLFQSYAHHRTLLEAVHDTIIAKADPPSCDLQSAHGNPCMKEKLVMKTHCPNDYQSAHYLNNDGKMASVKCPPKYELTEDCNFCRQMTGASLKKGSYPLQDLFCQSSEDDGSKLKTKMKGVCEVGVQALKKCDGQLSTAHEVVPFAVFKNSKKVYLDKLDLKTEENLLPDSFVCFEHKGQYKGTMDSGQTKRELKSFDISQCPKIGGHGSKKCTGDAAFCSAYECTAQYANAYCSHANGSGIVQIQVSGVWKKPLCVGYERVVVKRELSAKPIQRVEPCTTCITKCEPHGLVVRSTGFKISSAVACASGVCVTGSQSPSTEITLKYPGISQSSGGDIGVHMAHDDQSVSSKIVAHCPPQDPCLVHGCIVCAHGLINYQCHTALSAFVVVFVFSSIAIICLAVLYRVLKCLKIAPRKVLNPLMWITAFIRWIYKKMVARVADNINQVNREIGWMEGGQLVLGNPAPIPRHAPIPRYSTYLMLLLIVSYASACSELIQASSRITTCSTEGVNTKCRLSGTALIRAGSVGAEACLMLKGVKEDQTKFLKIKTVSSELSCREGQSYWTGSFSPKCLSSRRCHLVGECHVNRCLSWRDNETSAEFSFVGESTTMRENKCFEQCGGWGCGCFNVNPSCLFVHTYLQSVRKEALRVFNCIDWVHKLTLEITDFDGSVSTIDLGASSSRFTNWGSVSLSLDAEGISGSNSFSFIESPGKGYAIVDEPFSEIPRQGFLGEIRCNSESSVLSAHESCLRAPNLISYKPMIDQLECTTNLIDPFVVFERGSLPQTRNDKTFAASKGNRGVQAFSKGSVQADLTLMFDNFEVDFVGAAVSCDAAFLNLTGCYSCNAGARVCLSITSTGTGSLSAHNKDGSLHIVLPSENGTKDQCQILHFTVPEVEEEFMYSCDGDERPLLVKGTLIAIDPFDDRREAGGESTVVNPKSGSWNFFDWFSGLMSWFGGPLKTILLICLYVALSIGLFFLLIYLGRTGLSKMWLAATKKASDYKDHDGDYKDHDIDYKDDDDK

Source

organism	Rift Valley fever virus
ncbi_taxonomy_id	11588
host_organism	Homo sapiens

Entity 2 polymer

description	Fab140 light chain
formula_weight	23582.0 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	D,F,J,N,R,W

QSALTQPASVSGSPGQSITISCTGTSSDIGAYNFVSWYQQHPGTAPKLLIYDVTNRPSGVSNRFSGSKSGNTASLTISGLQAEDEANYYCNSYTSSSHVVFGGGTKLTVLLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECSQPRFAAA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	Fab140 heavy chain
formula_weight	26554.4 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	E,G,K,O,S,X

STQSTWAGPGLVKPSQTLSLTCTVSGGSVSSGDYYWSWIRQPPGRGLEWIGYISYSGSTYYNPSLESRITMSGDTSKQQFSLKLSSVTVADTAVYYCATNYFHLHDFGDLYWYFDLWGRGTLVTVSSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGGGGSSAWSHPQFEK

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 branched

description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	627.6 kDa
src_method	man
entity_count	6

Entity 5 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	12

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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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	640793

fit	/app/data/saxs_computation/v6/9v6r/9v6r.fit
pddf	/app/data/pr_computation/v6/9v6r/9v6r.pr.out
profile	/app/data/saxs_computation/v6/9v6r/9v6r.dat

Hexameric RVFV GnGc-Fab140 complex

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 branched

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)