SAXSdb — 9qdq

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1. Structure Basics

entry_id	9qdq
deposition_date	2025-03-06
last_revision	2025-10-22
title	Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA
keywords	helicase, Nonsense-mediated decay, 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	46.22 Å
rg_electron	46.59 Å
i0	379484000.00
molecular_weight	161800.0 kDa
excluded_volume	203190 Å³
envelope_volume	293710 Å³
shell_volume	54986 Å³
envelope_diameter	155.3 Å
shell_rg	47.76 Å
envelope_rg	46.24 Å
shape_rg	46.59 Å
total_rg	46.63 Å
total_atoms	11382
n_residues	1414
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	153.5 Å
rg_real	46.61 Å
rg_real_error	1.54 Å
i0_real	3.7950e+08
i0_real_error	6.8380e+06
rg_reciprocal	46.23 Å
i0_reciprocal	379300000.0000
total_estimate	0.8235
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	40.6 Å
skewness	0.439
kurtosis	-0.648
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	48290000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.888; Smooth: 0.453

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	ATP-dependent helicase NAM7
formula_weight	109561.0 kDa
ec_number	3.6.4.12,3.6.4.13
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	11382

MVGSGSHTPYDISNSPSDVNVQPATQLNSTLVEDDDVDNQLFEEAQVTETGFRSPSASDNSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDLGDTVLECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPCAQTKNANWDTDQWQPLIEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATINDIDAPEEQEAIPPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQLVRPQPRKTERPMNAQFNVESEMGDFPKFQDFDAQSMVSFSGQIGDFGNAFVDNTELSSYINNEYWNFENFKSAFSQKQNRNEIDDRNLYQEEASHLNSNFARELQREEQKHELSKDFSNLGI

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Trichoplusia ni

Entity 2 polymer

description	Nonsense-mediated mRNA decay factor EBS1
formula_weight	100102.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MEPSNTQKEDLPTAFNGIKSQLNSILKSNQLFQDYALLNGFLAFVHSKLNAAILTSIESQCGKSFAADLDSFDQSSISSILDFSWESVHYPIFKWFQMWRNYILFEKENKKQQTKFIDFRKMNSKMLKFFKTVQNFYVNVINTVYKKYDISVLLPKRIIQDLKLSDIENTTNVGDILAVKTFNSSSPLAHLIPTLFHRCLLFLGTAYRYKTLLEEISNKYSISNFKKSLDFFRLASLVLPSAGETYSQAGAIFLQTGNLGIAVFNFVKGMMTKMPSPVSIKNFGALMVDNKSSLNRSLHTTIMNTYLQESKGPRTPAKEILEFYFLGLFGSVWSPTSWRDDTKPNQLNNGIKLRHLENALYETMSARYLNNIKTIFHNLIITIGGFHLLLKRRSDVSAKTLKDLRSNELDYLNFAFKYIAHILNDIVKESWSENPEVSEILGMVRIINCWIKANPMVLQYSQSNLEFVNALAYLINDIVKKKPSPSFSITEHIPKRTYWFEEDLMVKGLSFVNFQLSDFDDYEKILEMDHSLDRLIGNPPLCDKLSASSEMLLRLQAVVNISSQLLQNNNCGVEWSDNKSRYIFNKKIGFKETVKNSMKTSKQSNEKAKLQRKNKPSTTNGSISMADLERQMRSSSLDSFSPTMGYSGSSVPMAPDTFNVKPSGTITGNKVNVELLKIELSGQNADGAITNISPGYSNAAISSSNSTDESSFDLNNILSSMQQKHAEKSFAKSMQGVNEQIPANDVCHQAQRPMQGGLYSSQQPSSMSSLNSAYQNASMPPSASMVSYPYPFLNQQGQGVFPPYNAQNLQWQSEAYSLKSMNFANPTWLGDQYQTSAPSSAYAQAQRQMFQQPMQQDVGKYMQFPFDAQSNTDSMRGNSRNNMF

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 3 polymer

description	Nonsense-mediated decay protein 4
formula_weight	25316.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MTQYNFIIDASAFEKGLGNIKRWCSDCTEAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSKFANLKVFIEFPEVLDIILWSDVMEHNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCSIVDVDSILSKDMNDKSFRESEKFNNMMLKNGTKEESENGREIIRTNFNKTVYASRGTGELWSP

Source

organism	Saccharomyces cerevisiae
common_name	;brewer's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 4 polymer

description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
formula_weight	9140.0 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	D

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

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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	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	160049

fit	/app/data/saxs_computation/qd/9qdq/9qdq.fit
pddf	/app/data/pr_computation/qd/9qdq/9qdq.pr.out
profile	/app/data/saxs_computation/qd/9qdq/9qdq.dat

Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)