SAXSdb — 2mow

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–153	Fragment：CID (UNP residues 1-153)	Poly(A) RNA polymerase protein 2 × 1 （P53632）	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

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 2MOW	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 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
2M88 NMR structure of a two-domain RNA-binding fragment of Nrd1 Deposited 2013-05-08	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 307–491（185 aa） Fragment：UNP residues 307-491	Not recorded	No recorded non-water small molecule	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
3CLJ Structure of the RNA polymerase II CTD-interacting domain of Nrd1 Deposited 2008-03-19	Different construct Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 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 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 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 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 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 1–153； UniProt 1–153

Poly(A) RNA polymerase protein 2

OrganismNot specified

UniProt P53632

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 573–584	Fragment：NIM (UNP residues 573-584)	Protein NRD1 × 1 （P53617）	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

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 2MOW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3NYB Structure and function of the polymerase core of TRAMP, a RNA surveillance complex Deposited 2010-07-14	Different construct Different mutation/modification 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 161–481（321 aa） Fragment：central and catalytic domains of Trf4p (UNP residues 161-481)	Mutation：D293A	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；100 mM sodium citrate at pH 5.8, 200 mM sodium acetate, 11% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.258
4U4C The molecular architecture of the TRAMP complex reveals the organization and interplay of its two catalytic activities Deposited 2014-07-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: Dimeric	Chain B 111–160（50 aa） Fragment：UNP residues 1-62,UNP residues 111-160,UNP residues 1-62,UNP residues 111-160	Not recorded	SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 2 CL CHLORIDE ION × 2 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；285.15 K；0.1 M Tris pH 8.2, 0.15 M Li2SO4, 32% PEG 400	Resolution 2.40 Å R-free 0.240

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PAP2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 573–584

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	2mow
Deposition date deposition_date	2014-05-06
Structure title title	Structure of Nrd1p CID - Trf4p NIM complex
Keywords keywords	transcription termination, RNA degradation, RNAP II CTD, protein-protein interaction, TRANSCRIPTION; TRANSCRIPTION
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	17.32 Å
Radius of gyration Rg (electron density) rg_electron	16.32 Å
Forward intensity I(0) i0	2296750000.00
Molecular weight molecular_weight	393220.0 kDa
Excluded volume excluded_volume	486130 Å³
Envelope volume envelope_volume	51908 Å³
Hydration-shell volume shell_volume	21518 Å³
Envelope diameter envelope_diameter	78.9 Å
Shell Rg shell_rg	27.36 Å
Envelope Rg envelope_rg	21.09 Å
Shape Rg shape_rg	16.32 Å
Total Rg total_rg	16.51 Å
Total atoms total_atoms	54440
Residues n_residues	3460
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	65.8 Å
Rg (real space) rg_real	17.30 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	2.2970e+09
I(0) uncertainty (real space) i0_real_error	3.3710e+07
Rg (reciprocal space) rg_reciprocal	17.30 Å
I(0) (reciprocal space) i0_reciprocal	2297000000.0000
Solution quality estimate total_estimate	0.6939
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	22.5 Å
Skewness Skewness skewness	0.387
Kurtosis Kurtosis kurtosis	0.121
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	979900.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.407; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 0.883; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein NRD1
Molecular weight formula_weight	18315.7 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	54440

MQQDDDFQNFVATLESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSIGRAYLDETRSNSNSSSNKPGTCAHAINTLGEVIQELLSDAIAKSNQDHKEKIRMLLDIWDRSGLFQKSYLNAIRSKCFAMDLEHHHHHH

来源 Source

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	Saccharomyces cerevisiae

Entity 2 Entity 2 polymer

Description description	Poly(A) RNA polymerase protein 2
Molecular weight formula_weight	1416.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DDDEDGYNPYTL

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2mowA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

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8. Citations (1)

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fit	/app/data/saxs_computation/mo/2mow/2mow.fit
pddf	/app/data/pr_computation/mo/2mow/2mow.pr.out
profile	/app/data/saxs_computation/mo/2mow/2mow.dat

Structure of Nrd1p CID - Trf4p NIM complex

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

Poly(A) RNA polymerase protein 2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)