SAXSdb — 9z3q

▼

1. Structure Basics

entry_id	9z3q
deposition_date	2025-11-07
title	Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs
keywords	KSHV, glycoprotein, Antibody, IMMUNE SYSTEM; IMMUNE SYSTEM
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	38.71 Å
rg_electron	38.47 Å
i0	269249000.00
molecular_weight	133950.0 kDa
excluded_volume	167770 Å³
envelope_volume	218890 Å³
shell_volume	48437 Å³
envelope_diameter	144.2 Å
shell_rg	43.04 Å
envelope_rg	38.61 Å
shape_rg	38.45 Å
total_rg	38.80 Å
total_atoms	9433
n_residues	1192
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

▼

3. P(r) Analysis (GNOM)

dmax	129.7 Å
rg_real	38.79 Å
rg_real_error	1.14 Å
i0_real	2.6920e+08
i0_real_error	4.9430e+06
rg_reciprocal	38.74 Å
i0_reciprocal	269200000.0000
total_estimate	0.8887
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	41.1 Å
skewness	0.334
kurtosis	-0.484
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	51000000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.898

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	MLKH10 Light chain FV
formula_weight	12427.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	9433

DIVMTQSPDSLSVSLGERATINCKSSQSVLYSSNNKNYLAWYQQKPGQPPKLLIYWASTRGSGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCQQYYNSPRFGGWTKVEIK

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 polymer

description	MLKH10 Heavy chain FV
formula_weight	13144.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

EVQLLESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQSPGKGLEWVSGINWNGGSLSYADSIQGRFTISRDNAENSLYLQMHSLRAEDTALYYCARVQGSGSYNNFDYWGQGTLVTVSS

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 3 polymer

description	MLKH3 Light chain FV
formula_weight	11538.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

DIQLTQSPSSVSASVGDRVTISCRASQGISSWLVWYQQKPGKAPKPLIYAASSLQNGVPARFSGSGSGTDFTLTINSLQPEDFATYYCQQANSFPYTFGQGTKLEIK

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 4 polymer

description	MLKH3 Heavy chain FV
formula_weight	13088.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

EVQLVQSGPEVKKPGSSVKVSCKASGDSFSSNTISWVRQAPGQGLEWMGRLITILGTANYAQKFQGRVTITADETATTAYMELSSLRSEDTAIYYCAISEGGYTYDSGSYIWGQGTLVTVSS

Source

organism	Mus musculus
common_name	mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 5 polymer

description	Envelope glycoprotein H
formula_weight	80917.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MDAMKRGLCCVLLLCGAVFVSPSASATGALPTTATTITRSATQLINGRTNLSIELEFNGTSFFLNWQNLLNVITEPALTELWTSAEVAEDLRVTLKKRQSLFFPNKTVVISGDGHRYTCEVPTSSQTYNITKGFNYSALPGHLGGFGINARLVLGDIFASKWSLFARDTPEYRVFYPMNVMAVKFSISIGNNESGVALYGVVSEDFVVVTLHNRSKEANETASHLLFGLPDSLPSLKGHATYDELTFARNAKYALVAILPKDSYQTLLTENYTRIFLNMTESTPLEFTRTIQTRIVSIEARRACAAQEAAPDIFLVLFQMLVAHFLVARGIAEHRFVEVDCVCRQYAELYFLRRISRLCMPTFTTVGYNHTTLGAVAATQIARVSATKLASLPRSSQETVLAMVQLGARDGAVPSSILEGIAMVVEHMYTAYTYVYTLGDTERKLMLDIHTVLTDSCPPKDSGVSEKLLRTYLMFTSMCTNIELGEMIARFSKPDSLNIYRAFSPCFLGLRYDLHPAKLRAEAPQSSALTRTAVARGTSGFAELLHALHLDSLNLIPAINCSKITADKIIATVPLPHVTYIISSEALSNAVVYEVSEIFLKSAMFISAIKPDCSGFNFSQIDRHIPIVYNISTPRRGCPLCDSVIMSYDESDGLQSLMYVTNERVQTNLFLDKSPFFDNNNLHIHYLWLRDNGTVVEIRGMYGSGSGHHHHHHGLNDIFEAQKIEWHE

Source

organism	Human gammaherpesvirus 8
ncbi_taxonomy_id	37296
host_organism	Homo sapiens

Entity 6 polymer

description	Envelope glycoprotein L
formula_weight	18815.8 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MDAMKRGLCCVLLLCGAVFVSPSASDGIQYVALPCCAIQASAASTLPLFFAVHSIHFADPNHCNGVCIAKLRSKTGDITVETCVNGFNLRSFLVAVVRRLGSWASQENLRLLWYLQRSLTAYTVGFNATTADSSIHNVNIIIISVGKAMNRTGSVSGSQTRAKSSSRRAHAGQKGK

Source

organism	Human gammaherpesvirus 8
ncbi_taxonomy_id	37296
host_organism	Homo sapiens

▶

6. Citations (1)

▶

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	3.51 Å
resolution_method	—
num_particles	75257

fit	/app/data/saxs_computation/z3/9z3q/9z3q.fit
pddf	/app/data/pr_computation/z3/9z3q/9z3q.pr.out
profile	/app/data/saxs_computation/z3/9z3q/9z3q.dat

Cryo-EM structure of KSHV glycoprotein gHgL in complex with MLKH3 and MLKH10 FABs

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)