1jfi

Crystal Structure of the NC2-TBP-DNA Ternary Complex

Method: X-RAY DIFFRACTION D_max: 88.5 Å Quality: GOOD

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

Transcription Regulator NC2 alpha chain

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–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–77	Fragment：RESIDUES 1-77	5'-D(TPTPGPGPCPTPAPTPAPAPAPAPGPGPGPCPTPCPC)-3' × 1 5'-D(GGPAPGPCPCPCPTPTPTPTPAPTPAPGPCPCPAPA)-3' × 1 Transcription Regulator NC2 beta chain × 1 （Q01658） TATA-BOX-BINDING PROTEIN (TBP) × 1 （P20226）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.277

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	DRAP1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–77； UniProt 1–77

Transcription Regulator NC2 beta chain

Homo sapiens

UniProt Q01658

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–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain B； UniProt 1–176	Not recorded	5'-D(TPTPGPGPCPTPAPTPAPAPAPAPGPGPGPCPTPCPC)-3' × 1 5'-D(GGPAPGPCPCPCPTPTPTPTPAPTPAPGPCPCPAPA)-3' × 1 Transcription Regulator NC2 alpha chain × 1 （Q14919） TATA-BOX-BINDING PROTEIN (TBP) × 1 （P20226）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.277

Other States of the Same Protein in the Database

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

View Construct and Data Evidence

UniProt name	TBAP_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 4–179； UniProt 1–176

TATA-BOX-BINDING PROTEIN (TBP)

Homo sapiens

UniProt P20226

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–DNA Heteromer Protein × 3 DNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain C； UniProt 159–339	Fragment：RESIDUES 359-539	5'-D(TPTPGPGPCPTPAPTPAPAPAPAPGPGPGPCPTPCPC)-3' × 1 5'-D(GGPAPGPCPCPCPTPTPTPTPAPTPAPGPCPCPAPA)-3' × 1 Transcription Regulator NC2 alpha chain × 1 （Q14919） Transcription Regulator NC2 beta chain × 1 （Q01658）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；PEG 4000, sodium citrate, potassium chloride, magnesium chloride, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.62 Å R-free 0.277

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1JFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 158–337（180 aa） Fragment：C-TERMINAL CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain F 158–337（180 aa） Fragment：C-TERMINAL CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain J 158–337（180 aa） Fragment：C-TERMINAL CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain N 158–337（180 aa） Fragment：C-TERMINAL CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.65 Å R-free 0.260
1C9B CRYSTAL STRUCTURE OF A HUMAN TBP CORE DOMAIN-HUMAN TFIIB CORE DOMAIN COMPLEX BOUND TO AN EXTENDED, MODIFIED ADENOVIRAL MAJOR LATE PROMOTER (ADMLP) Deposited 1999-08-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain R 158–337（180 aa） Fragment：C-TERMINAL CORE DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG 8000, TRIS.HCL, AMMONIUM ACETATE, MAGNESIUM CHLORIDE, POTASSIUM CHLORIDE, SODIUM CITRATE, DTT, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K	Resolution 2.65 Å R-free 0.260
1CDW HUMAN TBP CORE DOMAIN COMPLEXED WITH DNA Deposited 1996-04-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 159–337（179 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.258
1NVP HUMAN TFIIA/TBP/DNA COMPLEX Deposited 2003-02-04	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 159–339（181 aa） Fragment：C-TERMINAL 181 AMINO ACIDS	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；295 K；PEG6000, lithium nitrate, calcium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.247
1TGH TATA BINDING PROTEIN (TBP)/DNA COMPLEX Deposited 1996-02-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 113–297（185 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.90 Å R-free 0.294
4ROC Human TFIIB-related factor 2 (Brf2) and TBP bound to U6#2 promoter Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 159–339（181 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.215
4ROD Human TFIIB-related factor 2 (Brf2) and TBP bound to TRNAU1 promoter Deposited 2014-10-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 159–339（181 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.247
4ROE Human TFIIB-related factor 2 (Brf2) and TBP bound to RPPH1 promoter Deposited 2014-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain B 159–339（181 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；10-20% PEG 3350, 50-100 mM MgCl2, 2 mM DTT, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.222
5FUR Structure of human TFIID-IIA bound to core promoter DNA Deposited 2016-01-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain A 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40；pH 7.9；10 MM HEPES, 10 MM MGCL2, 50 MM KCL, 3% TREHALOSE 1 MM DTT, 0.0125% NP-40 cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE	Resolution 8.50 Å
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 3.90 Å
5IYC Human core-PIC in the initial transcribing state Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 11	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).	Resolution 3.90 Å
5N9G TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- Deposited 2017-02-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 159–339（181 aa） Fragment：UNP residues 159-339	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-16% PEG 8000, 150-200 mM KCl, 100 mM MES pH 6.5, 10-15 mM MgCl2, 1 mM TCEP	Resolution 2.70 Å R-free 0.234
5N9G TFIIIB -TBP/Brf2/DNA and SANT domain of Bdp1- Deposited 2017-02-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain G 159–339（181 aa） Fragment：UNP residues 159-339	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10-16% PEG 8000, 150-200 mM KCl, 100 mM MES pH 6.5, 10-15 mM MgCl2, 1 mM TCEP	Resolution 2.70 Å R-free 0.234
6MZD Human TFIID Lobe A canonical Deposited 2018-11-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain T 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N	Resolution 9.80 Å
6MZL Human TFIID canonical state Deposited 2018-11-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain T 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N	Resolution 23.00 Å
6MZM Human TFIID bound to promoter DNA and TFIIA Deposited 2018-11-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain T 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE；BT 4s; BF 15N	Resolution 7.50 Å
6O9L Human holo-PIC in the closed state Deposited 2019-03-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
7EDX p53-bound TFIID-based core PIC on HDM2 promoter Deposited 2021-03-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain P 1–339（339 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 4.50 Å
7EG7 TFIID-based core PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain P 1–339（339 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 6.20 Å
7EG8 TFIID-based core PIC on PUMA promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 37 PDB declaration: 39-meric	Chain P 1–339（339 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 7.40 Å
7EG9 TFIID-based intermediate PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
7EGA TFIID-based intermediate PIC on PUMA promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 39 PDB declaration: 41-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
7EGD SCP promoter-bound TFIID-TFIIA in initial TBP-loading state Deposited 2021-03-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.75 Å
7EGE TFIID in canonical conformation Deposited 2021-03-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.00 Å
7EGF TFIID lobe A subcomplex Deposited 2021-03-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
7EGI TFIID in rearranged conformation Deposited 2021-03-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.82 Å
7EGJ SCP promoter-bound TFIID-TFIIA in post TBP-loading state Deposited 2021-03-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain P 1–339（339 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.64 Å
7ENA TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED) Deposited 2021-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric	Chain DP 1–339（339 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
7ENC TFIID-based PIC-Mediator holo-complex in fully-assembled state (hPIC-MED) Deposited 2021-04-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 74 PDB declaration: 76-meric	Chain DP 1–339（339 aa）	Not recorded	ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.13 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain P 1–339（339 aa）	Not recorded	MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
7NVR Human Mediator with RNA Polymerase II Pre-initiation complex Deposited 2021-03-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 56 PDB declaration: 58-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 18 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7NVS RNA polymerase II core pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
7NVT RNA polymerase II core pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7NVU RNA polymerase II core pre-initiation complex with open promoter DNA Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7NVY RNA polymerase II pre-initiation complex with closed promoter DNA in proximal position Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
7NVZ RNA polymerase II pre-initiation complex with closed promoter DNA in distal position Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
7NW0 RNA polymerase II pre-initiation complex with open promoter DNA Deposited 2021-03-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 30 PDB declaration: 32-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 15 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 BEF BERYLLIUM TRIFLUORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7ZWC Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZWD Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC) Deposited 2022-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 11 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ZX7 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) Deposited 2022-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 11 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7ZX8 Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 24-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 11 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7ZXE Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) Deposited 2022-05-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8BVW RNA polymerase II pre-initiation complex with the distal +1 nucleosome (PIC-Nuc18W) Deposited 2022-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 40 PDB declaration: 42-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
8BYQ RNA polymerase II pre-initiation complex with the proximal +1 nucleosome (PIC-Nuc10W) Deposited 2022-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric	Chain O 1–339（339 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
8BZ1 RNA polymerase II core pre-initiation complex with the proximal +1 nucleosome (cPIC-Nuc10W) Deposited 2022-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8GXQ PIC-Mediator in complex with +1 nucleosome (T40N) in MH-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain DP 1–339（339 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.04 Å
8GXS PIC-Mediator in complex with +1 nucleosome (T40N) in H-binding state Deposited 2022-09-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 83 PDB declaration: 87-meric	Chain DP 1–339（339 aa）	Not recorded	ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.16 Å
8ITY human RNA polymerase III pre-initiation complex closed DNA 1 Deposited 2023-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.90 Å
8IUE RNA polymerase III pre-initiation complex melting complex 1 Deposited 2023-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.10 Å
8IUH RNA polymerase III pre-initiation complex open complex 1 Deposited 2023-03-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.40 Å
8S51 RNA polymerase II core initially transcribing complex with an ordered RNA of 8 nt Deposited 2024-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8S52 RNA polymerase II core initially transcribing complex with an ordered RNA of 10 nt Deposited 2024-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8S5N RNA polymerase II core initially transcribing complex with an ordered RNA of 12 nt Deposited 2024-02-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric	Chain O 1–339（339 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8WAK Structure of transcribing complex 2 (TC2), the initially transcribing complex with Pol II positioned 2nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.47 Å
8WAL Structure of transcribing complex 3 (TC3), the initially transcribing complex with Pol II positioned 3nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.52 Å
8WAN Structure of transcribing complex 4 (TC4), the initially transcribing complex with Pol II positioned 4nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.07 Å
8WAO Structure of transcribing complex 5 (TC5), the initially transcribing complex with Pol II positioned 5nt downstream of TSS. Deposited 2023-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å
8WAP Structure of transcribing complex 6 (TC6), the initially transcribing complex with Pol II positioned 6nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.85 Å
8WAQ Structure of transcribing complex 7 (TC7), the initially transcribing complex with Pol II positioned 7nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.29 Å
8WAR Structure of transcribing complex 8 (TC8), the initially transcribing complex with Pol II positioned 8nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.20 Å
8WAS Structure of transcribing complex 9 (TC9), the initially transcribing complex with Pol II positioned 9nt downstream of TSS. Deposited 2023-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 48 PDB declaration: 51-meric	Chain P 1–339（339 aa）	Not recorded	ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 W0F [[(2~{S},3~{R},4~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-methoxy-4-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.13 Å
9FSO Human RNA Polymerase III Class III Open Pre-initiation Complex 1 (OC1) Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain R 159–339（181 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
9FSP RNA Polymerase III Class III Open Pre-initation Complex 2 (OC2) Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain R 159–339（181 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.39 Å
9FSQ RNA Polymerase III Class III Melting Pre-Initiation Complex (MC) Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain R 159–339（181 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.51 Å
9FSR RNA Polymerase III Class III Open Mini Pre-initiation Complex 1 (OC1-mini) Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain R 159–339（181 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.76 Å
9FSS RNA Polymerase III Class III Open Mini Pre-Initiation complex 2 (OC2-mini) Deposited 2024-06-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 23 PDB declaration: 25-meric	Chain R 159–339（181 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.14 Å
9K3B Human RNA Polymerase III de novo transcribing complex 10 overall (TC10-overall) Deposited 2024-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 6 MG MAGNESIUM ION × 1 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.80 Å
9K3U Human RNA Polymerase III de novo transcribing complex 5 (TC5) Deposited 2024-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.00 Å
9K3V Human RNA Polymerase III de novo transcribing complex 4 (TC4) Deposited 2024-10-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 7 3AT 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE × 1 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.50 Å
9LXN Human RNA Polymerase III de novo transcribing complex 5 (TC5)(without 3'dATP) Deposited 2025-02-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain U 1–339（339 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.30 Å

76 other PDB entries and 81 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TBP_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 5–185； UniProt 159–339

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1jfi
Deposition date deposition_date	2001-06-20
Structure title title	Crystal Structure of the NC2-TBP-DNA Ternary Complex
Keywords keywords	;Histone, H2A/H2B, TBP, TATA-DNA, transcription initiation, NC2, Negative Cofactor, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, TRANSCRIPTION-DNA COMPLEX ;; TRANSCRIPTION/DNA
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	25.69 Å
Radius of gyration Rg (electron density) rg_electron	25.63 Å
Forward intensity I(0) i0	58956500.00
Molecular weight molecular_weight	53845.0 kDa
Excluded volume excluded_volume	64980 Å³
Envelope volume envelope_volume	83575 Å³
Hydration-shell volume shell_volume	27779 Å³
Envelope diameter envelope_diameter	91.9 Å
Shell Rg shell_rg	32.07 Å
Envelope Rg envelope_rg	25.66 Å
Shape Rg shape_rg	25.66 Å
Total Rg total_rg	26.21 Å
Total atoms total_atoms	3734
Residues n_residues	417
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	88.5 Å
Rg (real space) rg_real	25.70 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	5.8960e+07
I(0) uncertainty (real space) i0_real_error	9.2830e+05
Rg (reciprocal space) rg_reciprocal	25.70 Å
I(0) (reciprocal space) i0_reciprocal	58960000.0000
Solution quality estimate total_estimate	0.8709
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.4 Å
Skewness Skewness skewness	0.381
Kurtosis Kurtosis kurtosis	-0.212
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9771000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPGPGPCPTPAPTPAPAPAPAPGPGPGPCPTPCP*C)-3'
Molecular weight formula_weight	5844.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D
Atom count atom_count	3743

TTGGCTATAAAAGGGCTCC

Entity 2 Entity 2 polymer

Description description	5'-D(GGPAPGPCPCPCPTPTPTPTPAPTPAPGPCPCPAP*A)-3'
Molecular weight formula_weight	5804.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GGAGCCCTTTTATAGCCAA

Entity 3 Entity 3 polymer

Description description	Transcription Regulator NC2 alpha chain
Molecular weight formula_weight	10813.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MPSKKKKYNARFPPARIKKIMQTDEEIGKVAAAVPVIISRALELFLESLLKKACQVTQSRNAKTMTTSHLKQCIELEGDPAANKARKEAELAAATAEQ

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 BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Transcription Regulator NC2 beta chain
Molecular weight formula_weight	19755.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPHMASSSGNDDDLTIPRAAINKMIKETLPNVRVANDARELVVNCCTEFIHLISSEANEICNKSEKKTISPEHVIQALESLGFGSYISEVKEVLQECKTVALKRRKASSRLENLGIPEEELLRQQQELFAKARQQQAELAQQEWLQMQQAAQQAQLAAASASASNQAGSSQDEEDDDDI

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 BL21(DE3)

Entity 5 Entity 5 polymer

Description description	TATA-BOX-BINDING PROTEIN (TBP)
Molecular weight formula_weight	20856.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSHMSGIVPQLQNIVSTVNLGCKLDLKTIALRARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEQSRLAARKYARVVQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHQQFSSYEPELFPGLIYRMIKPRIVLLIFVSGKVVLTGAKVRAEIYEAFENIYPILKGFRKTT

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 BL21(DE3)

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

▼

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1jfia_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.3 — TBP-associated factors, TAFs

Domain ID domain_id	d1jfib_
Class class	a — All alpha proteins
Fold Fold fold	a.22 — Histone-fold
Superfamily Superfamily superfamily	a.22.1 — Histone-fold
Family Family family	a.22.1.3 — TBP-associated factors, TAFs

Domain ID domain_id	d1jfic1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1jfic2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.1 — TATA-box binding protein (TBP), C-terminal domain

Domain ID domain_id	d1jfic3
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 (4 domains)

Domain ID domain_id	1jfiA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	1jfiB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	1jfiC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

Domain ID domain_id	1jfiC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	10 — TATA-Binding Protein

▶

8. Citations (1)

▶

Unit-cell length a length_a	76.684 Å
Unit-cell length b length_b	119.075 Å
Unit-cell length c length_c	155.076 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	19.840 Å
R factor r_factor	0.2360
R_work r_work	0.2330
R_free r_free	0.2770

fit	/app/data/saxs_computation/jf/1jfi/1jfi.fit
pddf	/app/data/pr_computation/jf/1jfi/1jfi.pr.out
profile	/app/data/saxs_computation/jf/1jfi/1jfi.dat

Crystal Structure of the NC2-TBP-DNA Ternary Complex

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

Transcription Regulator NC2 alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Transcription Regulator NC2 beta chain

State in the Current Structure

Other States of the Same Protein in the Database

TATA-BOX-BINDING PROTEIN (TBP)

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (5 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)