SAXSdb — 2m88

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

Protein NRD1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 307–491	Fragment：UNP residues 307-491	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 8；293 K；Pressure ambient NMR measurement conditions：pH 8；293 K；Pressure ambient NMR measurement conditions：pH 8；293 K；Pressure ambient NMR sample composition：0.4 mM [U-13C; U-15N] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.4 mM [U-100% 13C; U-100% 15N; U-80% 2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.4 mM [U-13C; U-15N; U-2H] Nrd1, 50 mM sodium phosphate, 300 mM sodium chloride, 10 mM beta-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2M88	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LO6 Structure of Nrd1 CID bound to phosphorylated RNAP II CTD Deposited 2012-01-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa） Fragment：CID domain residues 1-154	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；293 K；Ionic strength (raw mmCIF value) 100；Pressure ambient NMR sample composition 2 mM [U-100% 13C; U-100% 15N] Nrd1 polypeptide, 2.3 mM phosphopeptide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2MOW Structure of Nrd1p CID - Trf4p NIM complex Deposited 2014-05-06	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa） Fragment：CID (UNP residues 1-153)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 1.5 mM Trf4p, 1 mM [U-99% 13C; U-99% 15N] Nrd1p, 100 mM sodium chloride, 50 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3CLJ Structure of the RNA polymerase II CTD-interacting domain of Nrd1 Deposited 2008-03-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 6–151（146 aa） Fragment：CTD-interacting domain, unp residues 6-151	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；100 mM Na-citrate buffer, 1.4 M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.220
5O1T Solution structure of the RNA binding domain of Nrd1 Deposited 2017-05-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–468（179 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 59.1；Pressure 1 NMR sample composition 600 uM [U-100% 13C; U-100% 15N] Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 800 uM Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Phe and Leu residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Ile residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 400 uM [U-100% 13C; U-100% 15N] expect for Arg residues Nrd1, 25 mM potassium phosphate, 25 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5O1W Structure of Nrd1 RNA binding domain Deposited 2017-05-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 301–489（189 aa） Fragment：UNP residues 301-489	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；12% PEG 8000, 0.1 M Bicine pH 9	Resolution 2.30 Å R-free 0.233
5O1X Structure of Nrd1 RNA binding domain Deposited 2017-05-19	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 290–468（179 aa） Fragment：UNP residues 290-468	Not recorded	EDO 1,2-ETHANEDIOL × 7 SCN THIOCYANATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Potassium Thiocyanate, 23% PEG 3350	Resolution 1.60 Å R-free 0.208
5O1Y Structure of Nrd1 RNA binding domain in complex with RNA (GUAA) Deposited 2017-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 290–468（179 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4	Resolution 2.45 Å R-free 0.217
5O1Z Structure of Nrd1 RNA binding domain in complex with RNA (CGUAAA) Deposited 2017-05-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 290–468（179 aa） Fragment：UNP residues 290-468	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4	Resolution 3.40 Å R-free 0.216
5O20 Structure of Nrd1 RNA binding domain in complex with RNA (UUAGUAAUCC) Deposited 2017-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 290–468（179 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；1M Sodium Potassium Phosphate pH 7.4	Resolution 3.53 Å R-free 0.269
6GC3 Structure of Nrd1 CID - Sen1 NIM complex Deposited 2018-04-17	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–153（153 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；293 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] CTD-interacting domain of Nrd1, 1.5 mM ASP-ASP-ASP-GLU-ASP-ASP-TYR-THR-PRO-SER-ILE-SER, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6O3W Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–156（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 2.10 Å R-free 0.204
6O3W Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM1 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–156（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 2.10 Å R-free 0.204
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–156（151 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 1.99 Å R-free 0.226
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–156（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 1.99 Å R-free 0.226
6O3X Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM2 Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–156（151 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 1.99 Å R-free 0.226
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 6–156（151 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 2.80 Å R-free 0.300
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 6–156（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 2.80 Å R-free 0.300
6O3Y Crystal structure of yeast Nrd1 CID in complex with Sen1 NIM3 Deposited 2019-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–156（151 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；sodium citrate, lithium chloride, PEG 6000	Resolution 2.80 Å R-free 0.300

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NRD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–186； UniProt 307–491

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	2m88
Deposition date deposition_date	2013-05-08
Structure title title	NMR structure of a two-domain RNA-binding fragment of Nrd1
Keywords keywords	Nrd1 complex, RNA processing and degradation, RRM structure, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	SOLUTION NMR

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.49 Å
Radius of gyration Rg (electron density) rg_electron	29.26 Å
Forward intensity I(0) i0	2442020000.00
Molecular weight molecular_weight	411110.0 kDa
Excluded volume excluded_volume	512460 Å³
Envelope volume envelope_volume	309270 Å³
Hydration-shell volume shell_volume	59937 Å³
Envelope diameter envelope_diameter	192.1 Å
Shell Rg shell_rg	44.19 Å
Envelope Rg envelope_rg	51.64 Å
Shape Rg shape_rg	29.17 Å
Total Rg total_rg	29.98 Å
Total atoms total_atoms	57480
Residues n_residues	3700
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	76.3 Å
Rg (real space) rg_real	24.50 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	2.2840e+09
I(0) uncertainty (real space) i0_real_error	2.9110e+07
Rg (reciprocal space) rg_reciprocal	29.79 Å
I(0) (reciprocal space) i0_reciprocal	2441000000.0000
Solution quality estimate total_estimate	0.6568
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.9 Å
Skewness Skewness skewness	0.551
Kurtosis Kurtosis kurtosis	-0.110
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.7471
Highest regularization parameter α highest_alpha	3973000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.014; Oscil: 0.904; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2m88A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	330 — RRM (RNA recognition motif) domain

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8. Citations (1)

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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	1

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

Description description	Protein NRD1
Molecular weight formula_weight	21799.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	57480

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

NMR structure of a two-domain RNA-binding fragment of Nrd1

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

Protein NRD1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/m8/2m88/2m88.fit
pddf	/app/data/pr_computation/m8/2m88/2m88.pr.out
profile	/app/data/saxs_computation/m8/2m88/2m88.dat