SAXSdb — 9qdq

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent helicase NAM7

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	Nonsense-mediated mRNA decay factor EBS1 × 1 （Q03466） Nonsense-mediated decay protein 4 × 1 （Q12129） ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RENT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–971； UniProt 1–971

Nonsense-mediated mRNA decay factor EBS1

Saccharomyces cerevisiae

UniProt Q03466

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	ATP-dependent helicase NAM7 × 1 （P30771） Nonsense-mediated decay protein 4 × 1 （Q12129） ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EBS1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–884； UniProt 1–884

Nonsense-mediated decay protein 4

Saccharomyces cerevisiae

UniProt Q12129

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 3 RNA 1	ATP-dependent helicase NAM7 × 1 （P30771） Nonsense-mediated mRNA decay factor EBS1 × 1 （Q03466） ;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMD4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–218； UniProt 1–218

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9qdq
Deposition date deposition_date	2025-03-06
Last revision last_revision	2025-10-22
Structure title title	Cryo-EM structure of Upf1-Nmd4-Ebs1 in complex with RNA
Keywords keywords	helicase, Nonsense-mediated decay, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9qdq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9qdq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qdq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	46.22 Å
Rg (electron density)	46.59 Å
Total Rg	46.63 Å
Atom count	11382
Residues	1414
Excluded volume	203190 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qdq__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ATP-dependent helicase NAM7
Molecular weight formula_weight	109561.0 kDa
EC 编号 ec_number	3.6.4.12,3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	11382

MVGSGSHTPYDISNSPSDVNVQPATQLNSTLVEDDDVDNQLFEEAQVTETGFRSPSASDNSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDLGDTVLECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPCAQTKNANWDTDQWQPLIEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATINDIDAPEEQEAIPPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQLVRPQPRKTERPMNAQFNVESEMGDFPKFQDFDAQSMVSFSGQIGDFGNAFVDNTELSSYINNEYWNFENFKSAFSQKQNRNEIDDRNLYQEEASHLNSNFARELQREEQKHELSKDFSNLGI

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Nonsense-mediated mRNA decay factor EBS1
Molecular weight formula_weight	100102.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEPSNTQKEDLPTAFNGIKSQLNSILKSNQLFQDYALLNGFLAFVHSKLNAAILTSIESQCGKSFAADLDSFDQSSISSILDFSWESVHYPIFKWFQMWRNYILFEKENKKQQTKFIDFRKMNSKMLKFFKTVQNFYVNVINTVYKKYDISVLLPKRIIQDLKLSDIENTTNVGDILAVKTFNSSSPLAHLIPTLFHRCLLFLGTAYRYKTLLEEISNKYSISNFKKSLDFFRLASLVLPSAGETYSQAGAIFLQTGNLGIAVFNFVKGMMTKMPSPVSIKNFGALMVDNKSSLNRSLHTTIMNTYLQESKGPRTPAKEILEFYFLGLFGSVWSPTSWRDDTKPNQLNNGIKLRHLENALYETMSARYLNNIKTIFHNLIITIGGFHLLLKRRSDVSAKTLKDLRSNELDYLNFAFKYIAHILNDIVKESWSENPEVSEILGMVRIINCWIKANPMVLQYSQSNLEFVNALAYLINDIVKKKPSPSFSITEHIPKRTYWFEEDLMVKGLSFVNFQLSDFDDYEKILEMDHSLDRLIGNPPLCDKLSASSEMLLRLQAVVNISSQLLQNNNCGVEWSDNKSRYIFNKKIGFKETVKNSMKTSKQSNEKAKLQRKNKPSTTNGSISMADLERQMRSSSLDSFSPTMGYSGSSVPMAPDTFNVKPSGTITGNKVNVELLKIELSGQNADGAITNISPGYSNAAISSSNSTDESSFDLNNILSSMQQKHAEKSFAKSMQGVNEQIPANDVCHQAQRPMQGGLYSSQQPSSMSSLNSAYQNASMPPSASMVSYPYPFLNQQGQGVFPPYNAQNLQWQSEAYSLKSMNFANPTWLGDQYQTSAPSSAYAQAQRQMFQQPMQQDVGKYMQFPFDAQSNTDSMRGNSRNNMF

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Nonsense-mediated decay protein 4
Molecular weight formula_weight	25316.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MTQYNFIIDASAFEKGLGNIKRWCSDCTEAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSKFANLKVFIEFPEVLDIILWSDVMEHNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCSIVDVDSILSKDMNDKSFRESEKFNNMMLKNGTKEESENGREIIRTNFNKTVYASRGTGELWSP

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;brewer's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PUPUPUPUPUPUPUPUPUPU)-3') ;
Molecular weight formula_weight	9140.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	160049

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent helicase NAM7

State in the Current Structure

Other States of the Same Protein in the Database

Nonsense-mediated mRNA decay factor EBS1

State in the Current Structure

Other States of the Same Protein in the Database

Nonsense-mediated decay protein 4

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qdq__assembly_1__model_1

9qdq__assembly_1__model_1 | I(q)

9qdq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

ATP-dependent helicase NAM7

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nonsense-mediated mRNA decay factor EBS1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nonsense-mediated decay protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9qdq__assembly_1__model_1

9qdq__assembly_1__model_1 | I(q)

9qdq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

7. Citations (1)