SAXSdb — 3nyb

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

Poly(A) RNA polymerase protein 2

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 161–481	Fragment：central and catalytic domains of Trf4p (UNP residues 161-481) Mutation：D293A	Protein AIR2 × 1 （Q12476） 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

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 3NYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MOW Structure of Nrd1p CID - Trf4p NIM complex Deposited 2014-05-06	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 B 573–584（12 aa） Fragment：NIM (UNP residues 573-584)	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
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 mutation/modification Different oligomeric state Different ligand/ion 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–323； UniProt 161–481

Protein AIR2

Saccharomyces cerevisiae

UniProt Q12476

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 118–198	Fragment：fourth and fifth zinc knuckles of Air2p (UNP residues 118-198)	Poly(A) RNA polymerase protein 2 × 1 （P53632） 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

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 3NYB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2LLI Low resolution structure of RNA-binding subunit of the TRAMP complex Deposited 2011-11-10	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 57–180（124 aa） Fragment：UNP residues 57-180	Not recorded	ZN ZINC ION × 5	SOLUTION NMR NMR measurement conditions pH 8；293 K；Ionic strength (raw mmCIF value) 0.5；Pressure ambient NMR sample composition 100 uM uM [U-99% 13C; U-99% 15N] protein_1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
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 conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: Dimeric	Chain B 1–62（62 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	AIR2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–83； UniProt 118–198

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	3nyb
Deposition date deposition_date	2010-07-14
Structure title title	Structure and function of the polymerase core of TRAMP, a RNA surveillance complex
Keywords keywords	;polyA RNA polymerase, zinc knuckle protein, RNA surveillance, Mtr4p binds to Trf4p/Air2p heterodimer, TRANSFERASE-RNA BINDING PROTEIN complex ;; TRANSFERASE/RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	24.01 Å
Radius of gyration Rg (electron density) rg_electron	22.84 Å
Forward intensity I(0) i0	32001500.00
Molecular weight molecular_weight	43723.0 kDa
Excluded volume excluded_volume	54880 Å³
Envelope volume envelope_volume	66759 Å³
Hydration-shell volume shell_volume	24846 Å³
Envelope diameter envelope_diameter	83.6 Å
Shell Rg shell_rg	29.58 Å
Envelope Rg envelope_rg	23.07 Å
Shape Rg shape_rg	22.79 Å
Total Rg total_rg	23.87 Å
Total atoms total_atoms	3081
Residues n_residues	387
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	83.5 Å
Rg (real space) rg_real	23.98 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	3.2000e+07
I(0) uncertainty (real space) i0_real_error	4.0710e+05
Rg (reciprocal space) rg_reciprocal	23.99 Å
I(0) (reciprocal space) i0_reciprocal	32000000.0000
Solution quality estimate total_estimate	0.8694
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.340
Kurtosis Kurtosis kurtosis	-0.309
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6065000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Poly(A) RNA polymerase protein 2
Molecular weight formula_weight	36459.5 kDa
EC 编号 ec_number	2.7.7.-
Mutation mutation	D293A
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	3139

GSYPWILNHDHSKQKEISDWLTFEIKDFVAYISPSREEIEIRNQTISTIREAVKQLWPDADLHVFGSYSTDLYLPGSDIDCVVTSELGGKESRNNLYSLASHLKKKNLATEVEVVAKARVPIIKFVEPHSGIHIAVSFERTNGIEAAKLIREWLDDTPGLRELVLIVKQFLHARRLNNVHTGGLGGFSIICLVFSFLHMHPRIITNEIDPKDNLGVLLIEFFELYGKNFGYDDVALGSSDGYPVYFPKSTWSAIQPIKNPFSLAIQDPGDESNNISRGSFNIRDIKKAFAGAFDLLTNRCFELHSATFKDRLGKSILGNVIKY

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Protein AIR2
Molecular weight formula_weight	9399.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSWKKVQCTLCKSKKHSKERCPSIWRAYILVDDNEKAKPKVLPFHTIYCYNCGGKGHFGDDCKEKRSSRVPNEDGSAFTGSNL

来源 Source

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

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	58

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3nybA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1410 — Poly(a)-polymerase, middle domain
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3nybA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	3nybB00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	60 — HIV-1 Nucleocapsid Protein
Homologous superfamily homologous superfamily	10 — Zinc finger, CCHC-type

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8. Citations (1)

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Unit-cell length a length_a	92.720 Å
Unit-cell length b length_b	92.720 Å
Unit-cell length c length_c	103.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3 2 1
Space-group number int_tables_number	150
Crystal system crystal_system	—

Resolution resolution	2.701 Å
Low-resolution limit resolution_low	24.656 Å
R factor r_factor	0.1982
R_work r_work	0.1935
R_free r_free	0.2581

fit	/app/data/saxs_computation/ny/3nyb/3nyb.fit
pddf	/app/data/pr_computation/ny/3nyb/3nyb.pr.out
profile	/app/data/saxs_computation/ny/3nyb/3nyb.dat

Structure and function of the polymerase core of TRAMP, a RNA surveillance complex

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

Poly(A) RNA polymerase protein 2

State in the Current Structure

Other States of the Same Protein in the Database

Protein AIR2

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

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)