8rd3

Crystal structure of Saccharomyces cerevisiae Nmd4 protein bound to Upf1 helicase domain

Method: X-RAY DIFFRACTION

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

ATP-dependent helicase NAM7

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Nonsense-mediated decay protein 4 × 1 （Q12129） 1,2-ETHANEDIOL × 9 SUCCINIC ACID × 1 FORMIC ACID × 1 MALONIC ACID × 1 water × 2	Consistent with protein count

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 4–634； UniProt 221–851

Nonsense-mediated decay protein 4

Saccharomyces cerevisiae S288C

UniProt Q12129

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ATP-dependent helicase NAM7 × 1 （P30771） 1,2-ETHANEDIOL × 9 SUCCINIC ACID × 1 FORMIC ACID × 1 MALONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NMD4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 5–221； UniProt 2–218

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	8rd3
Deposition date deposition_date	2023-12-07
Structure title title	Crystal structure of Saccharomyces cerevisiae Nmd4 protein bound to Upf1 helicase domain
Keywords keywords	Nonsense-mediated mRNA decay, PIN domain, Helicase, Protein complex, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

8rd3__assembly_1__model_1

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

Download this curve (.dat)

8rd3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rd3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.71 Å
Rg (electron density)	29.78 Å
Total Rg	30.51 Å
Atom count	6813
Residues	846
Excluded volume	121980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rd3__assembly_1__model_1`	dimeric （2）	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 (7)

Entity 1 Entity 1 polymer

Description description	ATP-dependent helicase NAM7
Molecular weight formula_weight	72303.0 kDa
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	6893

MASEQEAIPPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQLVRHHHHHH

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Nonsense-mediated decay protein 4
Molecular weight formula_weight	25560.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPGSTQYNFIIDASAFEKGLGNIKRWCSDCTEAVTLNFYIPTFTLNELDFLQQRRKSFAARESLKFIDRLDDSKFANLKVFIEFPEVLDIILWSDVMEHNDSSGKINIAKLPKRLKNLLKSCIYKCYLEGNEGLHWFLISEDPQIREMAMQCNIPSCSIVDVDSILSKDMNDKSFRESEKFNNMMLKNGTKEESENGREIIRTNFNKTVYASRGTGELWSP

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 non-polymer

Description description	SUCCINIC ACID
Molecular weight formula_weight	118.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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Unit-cell length a length_a	119.350 Å
Unit-cell length b length_b	131.160 Å
Unit-cell length c length_c	169.550 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.402 Å
Low-resolution limit resolution_low	48.800 Å
R factor r_factor	0.2029
R_work r_work	0.2019
R_free r_free	0.2222

Crystal structure of Saccharomyces cerevisiae Nmd4 protein bound to Upf1 helicase domain

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 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

8rd3__assembly_1__model_1

8rd3__assembly_1__model_1 | I(q)

8rd3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)

Crystal structure of Saccharomyces cerevisiae Nmd4 protein bound to Upf1 helicase domain

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 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

8rd3__assembly_1__model_1

8rd3__assembly_1__model_1 | I(q)

8rd3__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Citations (1)