SAXSdb — 8jj6

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

Negative elongation factor B

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–560	Not recorded	Negative elongation factor complex member C/D × 1 （H0UI80） NELF-E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M BICINE pH 8.5 and 20% v/v Polyethylene glycol 300	Resolution 2.72 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–560	Not recorded	Negative elongation factor complex member C/D × 1 （H0UI80） NELF-E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M BICINE pH 8.5 and 20% v/v Polyethylene glycol 300	Resolution 2.72 Å R-free 0.262

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 8JJ6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6GML Structure of paused transcription complex Pol II-DSIF-NELF Deposited 2018-05-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain V 42–580（539 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7PKS Structural basis of Integrator-mediated transcription regulation Deposited 2021-08-26	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: 31-meric	Chain V 1–580（580 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 10 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7YCX The structure of INTAC-PEC complex Deposited 2022-07-02	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 f 1–580（580 aa）	Not recorded	ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.18 Å
8RBX Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex Deposited 2023-12-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 43 PDB declaration: 46-meric	Chain v 1–580（580 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8UHA Structure of paused transcription complex Pol II-DSIF-NELF - tilted Deposited 2023-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain V 1–580（580 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 3.50 Å
8UHD Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated Deposited 2023-10-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain V 1–580（580 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 2.80 Å
8UHG Structure of paused transcription complex Pol II-DSIF-NELF - poised post-translocated Deposited 2023-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain V 1–554（554 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 2.70 Å
8UI0 Structure of poised transcription complex Pol II-DSIF-NELF - pre-translocated Deposited 2023-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric	Chain V 1–554（554 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 2.70 Å
8W8E human co-transcriptional RNA capping enzyme RNGTT Deposited 2023-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric	Chain V 1–580（580 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric	Chain V 1–580（580 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric	Chain V 1–580（580 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric	Chain V 1–580（580 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric	Chain f 1–580（580 aa）	Not recorded	ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å

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

View Construct and Data Evidence

UniProt name	NELFB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–560； UniProt 1–560 Author chain B； PDBConstruct 1–560； UniProt 1–560

Negative elongation factor complex member C/D

Homo sapiens

UniProt H0UI80

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 45–191	Not recorded	Negative elongation factor B × 1 （Q8WX92） NELF-E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M BICINE pH 8.5 and 20% v/v Polyethylene glycol 300	Resolution 2.72 Å R-free 0.262
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 45–191	Not recorded	Negative elongation factor B × 1 （Q8WX92） NELF-E × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；0.1M BICINE pH 8.5 and 20% v/v Polyethylene glycol 300	Resolution 2.72 Å R-free 0.262

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	H0UI80_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–147； UniProt 45–191 Author chain D； PDBConstruct 1–147； UniProt 45–191

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	8jj6
Deposition date deposition_date	2023-05-29
Structure title title	Structure of the NELF-BCE complex
Keywords keywords	transcription elongation factor, negative transcription elongation factor(NELF), TRANSCRIPTION; 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	52.35 Å
Radius of gyration Rg (electron density) rg_electron	52.74 Å
Forward intensity I(0) i0	386723000.00
Molecular weight molecular_weight	166770.0 kDa
Excluded volume excluded_volume	211100 Å³
Envelope volume envelope_volume	322970 Å³
Hydration-shell volume shell_volume	57124 Å³
Envelope diameter envelope_diameter	204.6 Å
Shell Rg shell_rg	47.13 Å
Envelope Rg envelope_rg	53.37 Å
Shape Rg shape_rg	52.80 Å
Total Rg total_rg	52.27 Å
Total atoms total_atoms	11726
Residues n_residues	1462
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	197.0 Å
Rg (real space) rg_real	52.87 Å
Rg uncertainty (real space) rg_real_error	2.44 Å
I(0) (real space) i0_real	3.8670e+08
I(0) uncertainty (real space) i0_real_error	8.2740e+06
Rg (reciprocal space) rg_reciprocal	51.94 Å
I(0) (reciprocal space) i0_reciprocal	386200000.0000
Solution quality estimate total_estimate	0.5729
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	65.7 Å
Skewness Skewness skewness	0.649
Kurtosis Kurtosis kurtosis	0.322
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0003
Highest regularization parameter α highest_alpha	21280000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.614; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.848; Smooth: 0.568

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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	Negative elongation factor B
Molecular weight formula_weight	63842.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11833

MFAGLQDLGVANGEDLKETLTNCTEPLKAIEQFQTENGVLLPSLQSALPFLDLHGTPRLEFHQSVFDELRDKLLERVSAIASEGKAEERYKKLEDLLEKSFSLVKMPSLQPVVMCVMKHLPKVPEKKLKLVMADKELYRACAVEVKRQIWQDNQALFGDEVSPLLKQYILEKESALFSTELSVLHNFFSPSPKTRRQGEVVQRLTRMVGKNVKLYDMVLQFLRTLFLRTRNVHYCTLRAELLMSLHDLDVGEICTVDPCHKFTWCLDACIRERFVDSKRARELQGFLDGVKKGQEQVLGDLSMILCDPFAINTLALSTVRHLQELVGQETLPRDSPDLLLLLRLLALGQGAWDMIDSQVFKEPKMEVELITRFLPMLMSFLVDDYTFNVDQKLPAEEKAPVSYPNTLPESFTKFLQEQRMACEVGLYYVLHITKQRNKNALLRLLPGLVETFGDLAFGDIFLHLLTGNLALLADEFALEDFCSSLFDGFFLTASPRKENVHRHALRLLIHLHPRVAPSKLEALQKALEPTGQSGEAVKELYSQLGEKLEQLDHRKPSPAQ

来源 Source

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Negative elongation factor complex member C/D
Molecular weight formula_weight	16887.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

EGEDDAEVQQECLHKFSTRDYIMEPSIFNTLKRYFQAGGSPENVIQLLSENYTAVAQTVNLLAEWLIQTGVEPVQVQETVENHLKSLLIKHFDPRKADSIFTEEGETPAWLEQMIAHTTWRDLFYKLAEAHPDCLMLNFTVKLISDA

来源 Source

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	Escherichia coli

Entity 3 Entity 3 polymer

Description description	NELF-E
Molecular weight formula_weight	5712.9 kDa
Mutation mutation	L8M, N20M, L30M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MLVIPPGMSEEEEALQKKFMKLKKKKKALMALKKQSSSSTTSQGGVKRSLY

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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8. Citations (1)

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Unit-cell length a length_a	156.614 Å
Unit-cell length b length_b	166.709 Å
Unit-cell length c length_c	75.025 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	2.720 Å
Low-resolution limit resolution_low	37.510 Å
R factor r_factor	0.2087
R_work r_work	0.2059
R_free r_free	0.2622

fit	/app/data/saxs_computation/jj/8jj6/8jj6.fit
pddf	/app/data/pr_computation/jj/8jj6/8jj6.pr.out
profile	/app/data/saxs_computation/jj/8jj6/8jj6.dat

Structure of the NELF-BCE complex

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

Negative elongation factor B

State in the Current Structure

Other States of the Same Protein in the Database

Negative elongation factor complex member C/D

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)