SAXSdb — 2db9

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

Paf1/RNA polymerase II complex component

Homo sapiens

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 307–442	Fragment：Plus-3 domain, Residues 8-143	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.73mM plus-3 domain U-15N,13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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 2DB9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BZE NMR Structure of human RTF1 PLUS3 domain. Deposited 2005-08-16	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 228–359（132 aa） Fragment：PLUS3, RESIDUES 228-359	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 200；Pressure 1.0 NMR sample composition 90% WATER/10% D2O	Resolution not provided
3U1U Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain Deposited 2011-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 347–482（136 aa） Fragment：unp residues 347-482 Chain B 347–482（136 aa） Fragment：unp residues 347-482	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 23	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop vapor diffusion；pH 5.5；291 K；25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K	Resolution 1.80 Å R-free 0.235
3U1U Crystal structure of RNA polymerase-associated protein RTF1 homolog Plus-3 domain Deposited 2011-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 347–482（136 aa） Fragment：unp residues 347-482 Chain B 347–482（136 aa） Fragment：unp residues 347-482	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 23	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop vapor diffusion；pH 5.5；291 K；25% PEG-3350, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 5.5, sitting drop vapor diffusion, temperature 291K	Resolution 1.80 Å R-free 0.235
4L1P Crystal Structure of Human Rtf1 Plus3 domain Deposited 2013-06-03	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 B 353–484（132 aa） Fragment：UNP residues 353-484	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Trisodium citrate, PEG 3000, pH 5.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.12 Å R-free 0.240
4L1P Crystal Structure of Human Rtf1 Plus3 domain Deposited 2013-06-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 353–484（132 aa） Fragment：UNP residues 353-484	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；Trisodium citrate, PEG 3000, pH 5.5, vapor diffusion, sitting drop, temperature 293K	Resolution 2.12 Å R-free 0.240
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	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 B 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	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 E 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
4L1U Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide Deposited 2013-06-03	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 353–484（132 aa） Fragment：Plus3, UNP residues 353-484	Not recorded	SO4 SULFATE ION × 7 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.2；293 K；Sodium acetate, Ammonium sulfate, pH 4.2, vapor diffusion, sitting drop, temperature 293K	Resolution 2.42 Å R-free 0.226
6TED Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1 Deposited 2019-11-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；2 microliters applied to both sides of grid. Sample incubated on grid for 10s prior to blotting. Blotting for 8.5s.	Resolution 3.10 Å
7UNC Pol II-DSIF-SPT6-PAF1c-TFIIS complex with rewrapped nucleosome Deposited 2022-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7UND Pol II-DSIF-SPT6-PAF1c-TFIIS-nucleosome complex (stalled at +38) Deposited 2022-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8A3Y Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex Deposited 2022-06-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 27 PDB declaration: 30-meric	Chain R 353–600（248 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9EGX RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-hexasome, bp +27 Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 29 PDB declaration: 32-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9EGY RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27 Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 12 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain R 353–600（248 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric	Chain R 1–710（710 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å

17 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RTF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–143； UniProt 307–442

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	2db9
Deposition date deposition_date	2005-12-15
Structure title title	Solution structure of the plus-3 domain of human KIAA0252 protein
Keywords keywords	;plus-3 domain; structural genomics, KIAA0252, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, STRUCTURAL GENOMICS, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	16.07 Å
Radius of gyration Rg (electron density) rg_electron	15.46 Å
Forward intensity I(0) i0	1595220000.00
Molecular weight molecular_weight	332580.0 kDa
Excluded volume excluded_volume	414040 Å³
Envelope volume envelope_volume	42948 Å³
Hydration-shell volume shell_volume	19193 Å³
Envelope diameter envelope_diameter	67.3 Å
Shell Rg shell_rg	25.19 Å
Envelope Rg envelope_rg	19.34 Å
Shape Rg shape_rg	15.44 Å
Total Rg total_rg	15.71 Å
Total atoms total_atoms	46720
Residues n_residues	2980
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	61.2 Å
Rg (real space) rg_real	16.01 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.5950e+09
I(0) uncertainty (real space) i0_real_error	1.9200e+07
Rg (reciprocal space) rg_reciprocal	16.02 Å
I(0) (reciprocal space) i0_reciprocal	1595000000.0000
Solution quality estimate total_estimate	0.8047
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.4 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.155
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	625600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.527; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.894; Smooth: 0.983

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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) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2db9a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.21 — Plus3-like
Family Family family	b.34.21.1 — Plus3

Domain ID domain_id	d2db9a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2db9a3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2db9A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	200 — Plus-3 domain

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8. Citations (1)

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Description description	Paf1/RNA polymerase II complex component
Molecular weight formula_weight	16665.0 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	46720

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cell free synthesis

fit	/app/data/saxs_computation/db/2db9/2db9.fit
pddf	/app/data/pr_computation/db/2db9/2db9.pr.out
profile	/app/data/saxs_computation/db/2db9/2db9.dat

Solution structure of the plus-3 domain of human KIAA0252 protein

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

Paf1/RNA polymerase II complex component

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)