SAXSdb — 9z3j

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1. Structure Basics

entry_id	9z3j
deposition_date	2025-11-06
title	;HCoV-NL63 S2' peptide bound to TMPRSS2 S441A (complexed with the H1H7 Fab and an anti-kappa-nanobody) ;
keywords	;TMPRSS2, NL63, S2prime, coronavirus, cleavage, SARS-CoV-2, spike, fusion, protease, entry, antiviral, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, SSGCID, VIRAL PROTEIN, 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	36.79 Å
rg_electron	36.52 Å
i0	138954000.00
molecular_weight	94675.0 kDa
excluded_volume	118110 Å³
envelope_volume	157220 Å³
shell_volume	37637 Å³
envelope_diameter	124.1 Å
shell_rg	40.97 Å
envelope_rg	35.81 Å
shape_rg	36.50 Å
total_rg	36.88 Å
total_atoms	6684
n_residues	895
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	122.2 Å
rg_real	37.00 Å
rg_real_error	1.47 Å
i0_real	1.3900e+08
i0_real_error	2.5630e+06
rg_reciprocal	36.87 Å
i0_reciprocal	138900000.0000
total_estimate	0.8597
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.377
kurtosis	-0.599
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	12040000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.790; Smooth: 0.739

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	;HCoV-NL63 S2' peptide ;
formula_weight	1679.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6773

RIAGRSALEDLLFSK

Source

organism	Human coronavirus NL63
ncbi_taxonomy_id	277944
host_organism	Homo sapiens

Entity 2 polymer

description	Inactive TMPRSS2 construct
formula_weight	57816.8 kDa
mutation	S441A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MTRLTVLALLAGLLASSRASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHRENDDDDKTTGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNDDDDKIVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDAGGPLVCSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGDDDDKSGHHHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 3 polymer

description	H1H7 heavy chain
formula_weight	24054.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQSPGKGLEWVAVIWNDGSYVYYADSVKGRFTISRDISKNTLFLQMNSLRAEDTAVYYCAREGEWVLYYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 4 polymer

description	H1H7 light chain
formula_weight	23510.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYSYTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source

organism	Homo sapiens
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

Entity 5 polymer

description	anti-kappa nanobody
formula_weight	17252.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	N

MKKTAIAIAVALAGFATVAQAAPMGSQVQLQESGGGLVQPGGSLRLSCAASGRTISRYAMSWFRQAPGKEREFVAVARRSGDGAFYADSVQGRFTVSRDDAKNTVYLQMNSLKPEDTAVYYCAIDSDTFYSGSYDYWGQGTQVTVSSHHHHHHHHEPEA

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 6 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	570.5 kDa
src_method	man
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	89

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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	2.800 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.80 Å
resolution_method	—
num_particles	270089

fit	/app/data/saxs_computation/z3/9z3j/9z3j.fit
pddf	/app/data/pr_computation/z3/9z3j/9z3j.pr.out
profile	/app/data/saxs_computation/z3/9z3j/9z3j.dat

;HCoV-NL63 S2' peptide bound to TMPRSS2 S441A (complexed with the H1H7 Fab and an anti-kappa-nanobody) ;

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 (7)

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 branched

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)