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9q85

PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system

Method: ELECTRON MICROSCOPY D_max: 174.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q85
deposition_date	2025-02-22
title	PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system
keywords	CIRSPR-Cas, spacer acquisition, Csn2, Cas1, Cas2, CRISPR integrase, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	52.38 Å
rg_electron	51.66 Å
i0	1928670000.00
molecular_weight	330020.0 kDa
excluded_volume	397370 Å³
envelope_volume	632820 Å³
shell_volume	101680 Å³
envelope_diameter	173.8 Å
shell_rg	55.39 Å
envelope_rg	50.64 Å
shape_rg	51.68 Å
total_rg	51.71 Å
total_atoms	23106
n_residues	2886
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	174.0 Å
rg_real	52.30 Å
rg_real_error	1.30 Å
i0_real	1.9290e+09
i0_real_error	3.5380e+07
rg_reciprocal	52.43 Å
i0_reciprocal	1929000000.0000
total_estimate	0.8902
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.0 Å
skewness	0.233
kurtosis	-0.566
angular_range	— – 0.1500 Å⁻¹
current_alpha	0.0001
highest_alpha	204400000.0000
n_real_points	31
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.883

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	CRISPR-associated endonuclease Cas9
formula_weight	162498.5 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	23106

MTKPYSIGLDIGTNSVGWAVITDNYKVPSKKMKVLGNTSKKYIKKNLLGVLLFDSGITAEGRRLKRTARRRYTRRRNRILYLQEIFSTEMATLDDAFFQRLDDSFLVPDDKRDSKYPIFGNLVEEKVYHDEFPTIYHLRKYLADSTKKADLRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDLSLENSKQLEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQADFRKCFNLDEKASLHFSKESYDEDLETLLGYIGDDYSDVFLKAKKLYDAILLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTYNEVFKDDTKNGYAGYIDGKTNQEDFYVYLKNLLAEFEGADYFLEKIDREDFLRKQRTFDNGSIPYQIHLQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPYYVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKESSAEAFINRMTSFDLYLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVRLYFKDKRKVTDKDIIEYLHAIYGYDGIELKGIEKQFNSSLSTYHDLLNIINDKEFLDDSSNEAIIEEIIHTLTIFEDREMIKQRLSKFENIFDKSVLKKLSRRHYTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIHDDALSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVKVMGGRKPESIVVEMARENQYTNQGKSNSQQRLKRLEKSLKELGSKILKENIPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDDLDIDRLSNYDIDHIIPQAFLKDNSIDNKVLVSSASNRGKSDDFPSLEVVKKRKTFWYQLLKSKLISQRKFDNLTKAERGGLLPEDKAGFIQRQLVETRQITKHVARLLDEKFNNKKDENNRAVRTVKIITLKSTLVSQFRKDFELYKVREINDFHHAHDAYLNAVIASALLKKYPKLEPEFVYGDYPKYNSFRERKSATEKVYFYSNIMNIFKKSISLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEEQNHGLDRGKPKGLFNANLSSKPKPNSNENLVGAKEYLDPKKYGGYAGISNSFAVLVKGTIEKGAKKKITNVLEFQGISILDRINYRKDKLNFLLEKGYKDIELIIELPKYSLFELSDGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVKLLYHAKRISNTINENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKLLNSAFQSWQNHSIDELCSSFIGPTGSERKGLFELTSRGSAADFEFLGVKIPRYRDYTPSSLLKDATLIHQSVTGLYETRIDLAKLGEGLEGHHHHHH

Source

organism	Streptococcus thermophilus DGCC 7710
ncbi_taxonomy_id	1268061
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	crRNA
formula_weight	13609.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

CGCUAAAGAGGAAGAGGACAGUUUUAGAGCUGUGUUGUUUCG

Entity 3 polymer

description	tracrRNA
formula_weight	24119.4 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

CGAAACAACACAGCGAGUUAAAAUAAGGCUUAGUCCGUACUCAACUUGAAAAGGUGGCACCGAUUCGGUGUUUUU

Entity 4 polymer

description	DNA (43-MER)
formula_weight	15003.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GATGTCTTCCAATTTACTACTCGTTCTGGTGTTTCTCGAGGCGTCAGCC

Entity 5 polymer

description	DNA (43-MER)
formula_weight	15182.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	E

GGCTGACGCCTCGAGAAACACCAGAACGAGTAGTAAATTGGAAGACATC

Entity 6 polymer

description	CRISPR-associated endonuclease Cas1
formula_weight	34854.9 kDa
ec_number	3.1.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,G

MAGWRTVVVNIHSKLSYKNNHLIFRNSYKTEMIHLSEIDILLLETTDIVLTTMLVKRLVDENILVIFCDDKRLPTAFLTPYYARHDSSLQIARQIAWKENVKCEVWTAIIAQKILNQSYYLGECSFFEKSQSIMELYHGLERFDPSNREGHSARIYFNTLFGNDFTRESDNDINAALDYGYTLLLSMFAREVVVCGCMTQIGLKHANQFNQFNLASDIMEPFRPIIDRIVYQNRHNNFVKIKKELFSIFSETYLYNGKEMYLSNIVSDYTKKVIKALNQLGEEIPEFRMSGHHHHHH

Source

organism	Streptococcus thermophilus DGCC 7710
ncbi_taxonomy_id	1268061
host_organism	Escherichia coli BL21(DE3)

Entity 7 polymer

description	CRISPR-associated endoribonuclease Cas2
formula_weight	13431.6 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MSYRYMRMILMFDMPTDTAEERKAYRKFRKFLLSEGFIMHQFSVYSKLLLNHTANTAMVGRLKANNPKKGNITILTVTEKQFARMIYLYGDKNTSIANSEERLVFLGDNYCDED

Source

organism	Streptococcus thermophilus DGCC 7710
ncbi_taxonomy_id	1268061
host_organism	Escherichia coli BL21(DE3)

Entity 8 polymer

description	CRISPR-associated protein Csn2
formula_weight	27459.6 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	O,L,N,M

MGHHHHHHENLYFQGGMKINFSLLDEPMEVNLGTVLVIEDVSVFAQLVKEFYQYDEQSNLTIFDSKIRSIRSSELLLITDILGYDINTSQVLKLLHTDIVSQLNDKPEVRSEIDSLVSLITDIIMAECIENELDIEYDEITLLELIKALGVRIETKSCTVFEKIFEILQIFKYLVKKRILVFVNSLSYFSKDEIYQILEYTKLSQADVLFLEPRQIEGIQQFILDKDYILMPYNN

Source

organism	Streptococcus thermophilus DGCC 7710
ncbi_taxonomy_id	1268061
host_organism	Escherichia coli BL21(DE3)

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	1

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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	triclinic

resolution	3.62 Å
resolution_method	—
num_particles	24394

fit	/app/data/saxs_computation/q8/9q85/9q85.fit
pddf	/app/data/pr_computation/q8/9q85/9q85.pr.out
profile	/app/data/saxs_computation/q8/9q85/9q85.dat

PAM-bound Cas9-Cas1-Cas2-Csn2 supercomplex in the locked conformation, Streptococcus thermophilus DGCC 7710 CRISPR3 system

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 (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)