SAXSdb — 9qb3

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1. Structure Basics

entry_id	9qb3
deposition_date	2025-02-28
title	Dimer structure of H/ACA RNP lobe of human telomerase
keywords	telomerase, H/ACA, RNA-binding protein, RNA BINDING PROTEIN; RNA 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	59.80 Å
rg_electron	59.05 Å
i0	4848990000.00
molecular_weight	501510.0 kDa
excluded_volume	592260 Å³
envelope_volume	977820 Å³
shell_volume	133390 Å³
envelope_diameter	186.8 Å
shell_rg	65.66 Å
envelope_rg	57.09 Å
shape_rg	59.04 Å
total_rg	59.20 Å
total_atoms	34722
n_residues	3720
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	185.4 Å
rg_real	59.36 Å
rg_real_error	1.07 Å
i0_real	4.8490e+09
i0_real_error	9.0840e+07
rg_reciprocal	60.14 Å
i0_reciprocal	4855000000.0000
total_estimate	0.8628
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	85.6 Å
skewness	0.008
kurtosis	-0.493
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	306400000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.632

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	H/ACA ribonucleoprotein complex subunit DKC1
formula_weight	57779.2 kDa
ec_number	5.4.99.-
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,G,c,g
atom_count	34722

MADAEVIILPKKHKKKKERKSLPEEDVAEIQHAEEFLIKPESKVAKLDTSQWPLLLKNFDKLNVRTTHYTPLACGSNPLKREIGDYIRTGFINLDKPSNPSSHEVVAWIRRILRVEKTGHSGTLDPKVTGCLIVCIERATRLVKSQQSAGKEYVGIVRLHNAIEGGTQLSRALETLTGALFQRPPLIAAVKRQLRVRTIYESKMIEYDPERRLGIFWVSCEAGTYIRTLCVHLGLLLGVGGQMQELRRVRSGVMSEKDHMVTMHDVLDAQWLYDNHKDESYLRRVVYPLEKLLTSHKRLVMKDSAVNAICYGAKIMLPGVLRYEDGIEVNQEIVVITTKGEAICMAIALMTTAVISTCDHGIVAKIKRVIMERDTYPRKWGLGPKASQKKLMIKQGLLDKHGKPTDSTPATWKQEYVDYSESAKKEVVAEVVKAPQVVAEAAKTAKRKRESESESDETPPAAPQLIKKEKKKSKKDKKAKAGLESGAEPGDGDSDTTKKKKKKKKAKEVELVSE

Entity 2 polymer

description	H/ACA ribonucleoprotein complex subunit 1
formula_weight	22388.0 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	D,H,d,h

MSFRGGGRGGFNRGGGGGGFNRGGSSNHFRGGGGGGGGGNFRGGGRGGFGRGGGRGGFNKGQDQGPPERVVLLGEFLHPCEDDIVCKCTTDENKVPYFNAPVYLENKEQIGKVDEIFGQLRDFYFSVKLSENMKASSFKKLQKFYIDPYKLLPLQRFLPRPPGEKGPPRGGGRGGRGGGRGGGGRGGGRGGGFRGGRGGGGGGFRGGRGGGFRGRGH

Entity 3 polymer

description	H/ACA ribonucleoprotein complex subunit 2
formula_weight	17226.1 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	E,I,e,i

MTKIKADPDGPEAQAEACSGERTYQELLVNQNPIAQPLASRRLTRKLYKCIKKAVKQKQIRRGVKEVQKFVNKGEKGIMVLAGDTLPIEVYCHLPVMCEDRNLPYVYIPSKTDLGAAAGSKRPTCVIMVKPHEEYQEAYDECLEEVQSLPLPL

Entity 4 polymer

description	H/ACA ribonucleoprotein complex subunit 3
formula_weight	7720.0 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	F,J,f,j

MFLQYYLNEQGDRVYTLKKFDPMGQQTCSAHPARFSPDDKYSRHRITIKKRFKVLMTQQPRPVL

Entity 5 polymer

description	Telomerase Cajal body protein 1
formula_weight	59357.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,k

MKTLETQPLAPDCCPSDQDPAPAHPSPHASPMNKNADSELMPPPPERGDPPRLSPDPVAGSAVSQELREGDPVSLSTPLETEFGSPSELSPRIEEQELSENTSLPAEEANGSLSEEEANGPELGSGKAMEDTSGEPAAEDEGDTAWNYSFSQLPRFLSGSWSEFSTQPENFLKGCKWAPDGSCILTNSADNILRIYNLPPELYHEGEQVEYAEMVPVLRMVEGDTIYDYCWYSLMSSAQPDTSYVASSSRENPIHIWDAFTGELRASFRAYNHLDELTAAHSLCFSPDGSQLFCGFNRTVRVFSTARPGRDCEVRATFAKKQGQSGIISCIAFSPAQPLYACGSYGRSLGLYAWDDGSPLALLGGHQGGITHLCFHPDGNRFFSGARKDAELLCWDLRQSGYPLWSLGREVTTNQRIYFDLDPTGQFLVSGSTSGAVSVWDTDGPGNDGKPEPVLSFLPQKDCTNGVSLHPSLPLLATASGQRVFPEPTESGDEGEELGLPLLSTRHVHLECRLQLWWCGGAPDSSIPDDHQGEKGQGGTEGGVGELI

Entity 6 polymer

description	hTR, human telomerase RNA
formula_weight	145477.8 kDa
src_method	man
entity_count	2

Polymer

type	polyribonucleotide
strand_id	B,b

GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGACCUGCGGCGGGUCGCCUGCCCAGCCCCCGAACCCCGCCUGGAGGCCGCGGUCGGCCCGGGGCUUCUCCGGAGGCACCCACUGCCACCGCGAAGAGUUGGGCUCUGUCAGCCGCGGGUCUCUCGGGGGCGAGGGCGAGGUUCAGGCCUUUCAGGCCGCAGGAAGAGGAACGGAGCGAGUCCCCGCGCGCGGCGCGAUUCCCUGAGCUGUGGGACGUGCACCCAGGACUCGGCUCACACAUGC

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Homo sapiens

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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	3.900 Å
resolution_low	173.680 Å
r_factor	0.3260
r_work	0.3260
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	88419

fit	/app/data/saxs_computation/qb/9qb3/9qb3.fit
pddf	/app/data/pr_computation/qb/9qb3/9qb3.pr.out
profile	/app/data/saxs_computation/qb/9qb3/9qb3.dat

Dimer structure of H/ACA RNP lobe of human telomerase

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)