SAXSdb — 7faw

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

Transcription elongation factor S-II

Saccharomyces cerevisiae S288C

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 1–73	Fragment：LW domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris, pH 8.5, 25% PEG 3350	Resolution 2.44 Å R-free 0.240
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–73	Fragment：LW domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris, pH 8.5, 25% PEG 3350	Resolution 2.44 Å R-free 0.240
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–73	Fragment：LW domain	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；0.1M Tris, pH 8.5, 25% PEG 3350	Resolution 2.44 Å R-free 0.240

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 7FAW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ENW ELONGATION FACTOR TFIIS DOMAIN II Deposited 2000-03-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–240（110 aa） Fragment：DOMAIN II (RESIDUES 131-240)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；270 K；Ionic strength (raw mmCIF value) 50 mM；Pressure ambient NMR sample composition 2 mM TFIIS; 5mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM TFIIS; 5mM phosphate buffer; 99.996% D2O \| 99.996% D2O	Resolution not provided
1EO0 CONSERVED DOMAIN COMMON TO TRANSCRIPTION FACTORS TFIIS, ELONGIN A, CRSP70 Deposited 2000-03-21	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–77（77 aa） Fragment：DOMAIN I	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；273 K；Ionic strength (raw mmCIF value) 300 mM NaCl；Pressure ambient NMR sample composition 2 mM TFIIS1-111; 10 mM phosphate buffer; 90% H2O, 10%D2O \| 90% H2O/10% D2O	Resolution not provided
1PQV RNA polymerase II-TFIIS complex Deposited 2003-06-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain S 1–309（309 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；sodium-ammonium tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.80 Å
1Y1V Refined RNA Polymerase II-TFIIS complex Deposited 2004-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain S 131–309（179 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.80 Å R-free 0.294
1Y1Y RNA Polymerase II-TFIIS-DNA/RNA complex Deposited 2004-11-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain S 131–309（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.00 Å
3GTM Co-complex of Backtracked RNA polymerase II with TFIIS Deposited 2009-03-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: tetradecameric	Chain S 147–306（160 aa） Fragment：Transcription Factor IIS E291H mutation, UNP residues 147-309	Mutation：E291H	MG MAGNESIUM ION × 1 ZN ZINC ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；390mM (NH4)2HPO4/NaH2PO4, pH 6.0, 50mM Dioxane, 10mM DTT, 9-11% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.80 Å R-free 0.289
3PO3 Arrested RNA Polymerase II reactivation intermediate Deposited 2010-11-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain S 132–309（178 aa）	Mutation：D290A	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ACT ACETATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；4-7% PEG6000, 50mM HEPES pH 7.0, 200mM AMMONIUM ACETATE, 300mM SODIUM ACETATE, 5mM TCEP , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.189
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric	Chain 2 136–309（174 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,	Resolution 6.00 Å
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain S 1–309（309 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric	Chain S 1–309（309 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric	Chain AS 1–309（309 aa） Chain BS 1–309（309 aa）	Not recorded	ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain S 1–309（309 aa）	Not recorded	ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8UOT Composite map of PICdeltaTFIIK form1 Deposited 2023-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain S 1–309（309 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM HEPES PH 7.6 50 mM KOAc 5 mM DTT 2 mM MgOAc cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	TFS2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–73； UniProt 1–73 Author chain B； PDBConstruct 1–73； UniProt 1–73 Author chain C； PDBConstruct 1–73； UniProt 1–73

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	7faw
Deposition date deposition_date	2021-07-07
Structure title title	Structure of LW domain from Yeast
Keywords keywords	LW, Transcription, Paf1C; TRANSCRIPTION
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	22.20 Å
Radius of gyration Rg (electron density) rg_electron	21.75 Å
Forward intensity I(0) i0	12948100.00
Molecular weight molecular_weight	28075.0 kDa
Excluded volume excluded_volume	35673 Å³
Envelope volume envelope_volume	43053 Å³
Hydration-shell volume shell_volume	17804 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	26.97 Å
Envelope Rg envelope_rg	22.18 Å
Shape Rg shape_rg	21.79 Å
Total Rg total_rg	22.38 Å
Total atoms total_atoms	1977
Residues n_residues	252
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	81.0 Å
Rg (real space) rg_real	22.29 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	1.2950e+07
I(0) uncertainty (real space) i0_real_error	1.9380e+05
Rg (reciprocal space) rg_reciprocal	22.28 Å
I(0) (reciprocal space) i0_reciprocal	12950000.0000
Solution quality estimate total_estimate	0.7526
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.336
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3692000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.708; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.654; 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)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	7fawA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Domain ID domain_id	7fawB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

Domain ID domain_id	7fawC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	930 — Transcription Elongation Factor S-II; Chain A
Homologous superfamily homologous superfamily	10 — Conserved domain common to transcription factors TFIIS, elongin A, CRSP70

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8. Citations (1)

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Unit-cell length a length_a	32.014 Å
Unit-cell length b length_b	91.568 Å
Unit-cell length c length_c	118.068 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.438 Å
Low-resolution limit resolution_low	36.179 Å
R factor r_factor	0.2054
R_work r_work	0.2016
R_free r_free	0.2398

Description description	Transcription elongation factor S-II
Molecular weight formula_weight	9800.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2015

Structure of LW domain from Yeast

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

Transcription elongation factor S-II

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 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)

来源生物 organism	Saccharomyces cerevisiae S288C
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

fit	/app/data/saxs_computation/fa/7faw/7faw.fit
pddf	/app/data/pr_computation/fa/7faw/7faw.pr.out
profile	/app/data/saxs_computation/fa/7faw/7faw.dat