SAXSdb — 2mkr

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

RNA polymerase II transcription factor B subunit 1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–115	Not recorded	Epstein-Barr nuclear antigen 2 × 1 （P12978）	SOLUTION NMR NMR measurement conditions：pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.7 mM [U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition：0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-100% 15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT-24, 100% D2O \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2MKR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y5O NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH Deposited 2004-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–115（115 aa） Fragment：sequence database residues 1-115	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM SODIUM PHOSPHATE；Pressure AMBIENT NMR sample composition 1.2 MM TFB1 [UNLABELED], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O; 1.2 MM TFB1 [U-15N], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 90% H2O, 10% D2O; 1.2 MM TFB1 [U-15N,13C], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O	Resolution not provided
2GS0 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the activation domain of p53 Deposited 2006-04-25	Different mutation/modification Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa）	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate；Pressure ambient NMR sample composition 1.0 mM Tfb1 U-15N, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM Tfb1 U-15N,13C, 1.0 mM p53 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 \| 100% D20 NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM p53 U-15N, 1.0 mM Tfb1 unlabeled, 1.00 mM EDTA, 20 mM phosphate buffer; 100% D20 \| 100% D20	Resolution not provided
2K2U NMR Structure of the complex between Tfb1 subunit of TFIIH and the activation domain of VP16 Deposited 2008-04-11	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa） Fragment：PH domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure Ambient NMR sample composition 1.0 mM [U-99% 15N] Tfb1, 1.0 mM VP16, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Tfb1, 1.0 mM VP16, 100% D2O \| 100% D2O NMR sample composition 1.0 mM [U-99% 15N] VP16, 1.0 mM Tfb1, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] VP16, 1.0 mM Tfb1, 100% D2O \| 100% D2O	Resolution not provided
2L2I NMR Structure of the complex between the Tfb1 subunit of TFIIH and the activation domain of EKLF Deposited 2010-08-18	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：PH domain (UNP residues 2-115)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure ambient NMR sample composition 1 mM [U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 100% D2O \| 100% D2O NMR sample composition 0.6 mM [U-100% 13C; U-100% 15N] EKLF, 1.2 mM Tfb1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 2 mM EKLF, 100% D2O \| 100% D2O	Resolution not provided
2LOX NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad2 Deposited 2012-01-27	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad2, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2M14 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and Rad4 Deposited 2012-11-16	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 1 mM [U-100% 15N] Tfb1, 1.25 mM Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 13C; U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition 1.25 mM Tfb1, 1 mM [U-100% 15N] Rad4, 20 mM sodium phosphate, 1 mM EDTA, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N0Y NMR structure of the complex between the C-terminal domain of the Rift Valley fever virus protein NSs and the PH domain of the Tfb1 subunit of TFIIH Deposited 2015-03-18	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–115（115 aa） Fragment：Pleckstrin homology domain residues 1-115	Mutation：M1P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] RNA polymerase II transcription factor B subunit 1, 2 mM Non-structural protein NS-S, 100% D2O \| 100% D2O NMR sample composition 0.5 mM [U-15N] RNA polymerase II transcription factor B subunit 1, 1 mM Non-structural protein NS-S, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM RNA polymerase II transcription factor B subunit 1, 0.5 mM [U-13C; U-15N] Non-structural protein NS-S, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM RNA polymerase II transcription factor B subunit 1, 1 mM [U-13C; U-15N] Non-structural protein NS-S, 100% D2O \| 100% D2O NMR sample composition 0.4 mM RNA polymerase II transcription factor B subunit 1, 0.2 mM [U-15N] Non-structural protein NS-S, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N23 NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the N-terminal activation domain of EKLF (TAD1) Deposited 2015-04-27	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：Pleckstrin homology domain, UNP residues 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] RNA polymerase II transcription factor B subunit 1, 2 mM N-terminal transactivation domain of Krueppel-like factor 1, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] N-terminal transactivation domain of Krueppel-like factor 1, 2 mM RNA polymerase II transcription factor B subunit 1, 100% D2O \| 100% D2O	Resolution not provided
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11	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 × 29 PDB declaration: 31-meric	Chain 1 1–218（218 aa） Chain 1 250–295（46 aa） Chain 1 537–642（106 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE BLOTTED FOR 8 S AND PLUNGE-FROZEN IN LIQUID ETHANE.	Resolution 4.70 Å
5OQM STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH AND CORE MEDIATOR Deposited 2017-08-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric	Chain 1 1–121（121 aa） Chain 1 176–218（43 aa） Chain 1 250–295（46 aa） Chain 1 522–642（121 aa）	Not recorded	ZN ZINC ION × 16 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Grids were blotted for 8 s and plunge-frozen in liquid ethane.	Resolution 5.80 Å
5URN NMR structure of the complex between the PH domain of the Tfb1 subunit from TFIIH and the transactivation domain 1 of p65 Deposited 2017-02-11	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–115（114 aa） Fragment：PLECKSTRIN HOMOLOGY DOMAIN, UNP RESIDUES 2-115	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0；Pressure AMBIENT NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 1.6 mM TRANSCRIPTION FACTOR P65, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] TRANSCRIPTION FACTOR P65, 1.6 mM RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 1, 100% D2O \| 100% D2O	Resolution not provided
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain 1 1–218（218 aa） Chain 1 250–295（46 aa） Chain 1 537–642（106 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 16 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.70 Å
7K01 Structure of TFIIH in TFIIH/Rad4-Rad23-Rad33 DNA opening complex Deposited 2020-09-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 5 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Sample dialyzed for 30 minutes into above buffer prior to grid making cryo-EM vitrification conditions Cryogen ETHANE；Grids were manually blotted for 2-3 seconds prior to plunge freezing	Resolution 3.90 Å
7K04 Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening Deposited 2020-09-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain 1 2–642（641 aa）	Not recorded	CA CALCIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted by Leica EM CPC	Resolution 9.25 Å
7M2U Nucleotide Excision Repair complex TFIIH Rad4-33 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 × 9 PDB declaration: undecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 5 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.20 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06	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 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7O4J Yeast RNA polymerase II transcription pre-initiation complex (consensus) Deposited 2021-04-06	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 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7O4K Yeast TFIIH in the contracted state within the pre-initiation complex Deposited 2021-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 10 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7O4L Yeast TFIIH in the expanded state within the pre-initiation complex Deposited 2021-04-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: heptadecameric	Chain 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 11 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12	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 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O73 Yeast RNA polymerase II transcription pre-initiation complex with closed distorted promoter DNA Deposited 2021-04-12	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 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7O75 Yeast RNA polymerase II transcription pre-initiation complex with open promoter DNA Deposited 2021-04-13	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 1 1–642（642 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 17 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7ZSA Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP (complex B) Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7ZSB Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C Deposited 2022-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric	Chain 1 1–642（642 aa）	Not recorded	ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 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 1 1–642（642 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 1 1–642（642 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

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TFB1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–115； UniProt 1–115

Epstein-Barr nuclear antigen 2

Human herpesvirus 4

UniProt P12978

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 453–465	Not recorded	RNA polymerase II transcription factor B subunit 1 × 1 （P32776）	SOLUTION NMR NMR measurement conditions：pH 6.5；300 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition：0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.7 mM [U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.7 mM [U-13C; U-15N] Tfb1, 2.1 mM EBNA2, 20 mM sodium phosphate, 1 mM DTT, 100% D2O \| 100% D2O NMR sample composition：0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-100% 15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM [U-13C; U-15N] EBNA2, 1.5 mM Tfb1, 20 mM sodium phosphate, 1 mM DTT-24, 100% D2O \| 100% D2O	Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2MKR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2N2J Solution structure of the EBNA-2 N-terminal Dimerization (END) domain from the Epstein-barr virus Deposited 2015-05-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–58（58 aa） Fragment：END DOMAIN (UNP RESIDUES 1-58) Chain B 1–58（58 aa） Fragment：END DOMAIN (UNP RESIDUES 1-58)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；323 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition 1 mM [U-13C; U-15N] EPSTEIN-BARR NUCLEAR ANTIGEN 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.1-0.5 mM [U-15N] EPSTEIN-BARR NUCLEAR ANTIGEN 2, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
5HDA Crystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif Deposited 2016-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 381–389（9 aa） Fragment：UNP Residues 381-389 Chain D 381–389（9 aa） Fragment：UNP Residues 381-389	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；21% PEGMME 350, 0.1M Tris-HCl pH 8.0, 6% Methanol, Hanging Drop Vapor Diffusion, Temperature 277K	Resolution 2.39 Å R-free 0.262
9D95 TRAV35/TRBV20 TCR - HLA-B38 complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 14–23（10 aa）	Not recorded	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4	Resolution 2.80 Å R-free 0.235
9D95 TRAV35/TRBV20 TCR - HLA-B38 complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 14–23（10 aa）	Not recorded	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4	Resolution 2.80 Å R-free 0.235
9D95 TRAV35/TRBV20 TCR - HLA-B38 complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain M 14–23（10 aa）	Not recorded	SO4 SULFATE ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4	Resolution 2.80 Å R-free 0.235
9D95 TRAV35/TRBV20 TCR - HLA-B38 complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 14–23（10 aa）	Not recorded	SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M Bis-Tris, pH6.5, 22%PEG3350, 0.2M (NH4)2SO4	Resolution 2.80 Å R-free 0.235
9D96 KIR3DL1 - HLA-B38-YHL complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 14–23（10 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；15% PEG 3350, 2% Tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6	Resolution 2.40 Å R-free 0.238
9D96 KIR3DL1 - HLA-B38-YHL complex Deposited 2024-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 14–23（10 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；15% PEG 3350, 2% Tacsimate, pH 5.0, and 0.1 M trisodium citrate, pH 5.6	Resolution 2.40 Å R-free 0.238

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EBNA2_EBVB9
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–13； UniProt 453–465

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	2mkr
Deposition date deposition_date	2014-02-12
Structure title title	Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH.
Keywords keywords	EBV, EBNA2, TFIIH, TFB1, ACTIVATION, TRANSCRIPTION, PH DOMAIN, VIRAL PROTEIN-TRANSCRIPTION complex; VIRAL PROTEIN/TRANSCRIPTION
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	16.58 Å
Radius of gyration Rg (electron density) rg_electron	15.84 Å
Forward intensity I(0) i0	1226290000.00
Molecular weight molecular_weight	289930.0 kDa
Excluded volume excluded_volume	360300 Å³
Envelope volume envelope_volume	44781 Å³
Hydration-shell volume shell_volume	19704 Å³
Envelope diameter envelope_diameter	62.6 Å
Shell Rg shell_rg	25.71 Å
Envelope Rg envelope_rg	19.65 Å
Shape Rg shape_rg	15.83 Å
Total Rg total_rg	16.05 Å
Total atoms total_atoms	40580
Residues n_residues	2560
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	57.0 Å
Rg (real space) rg_real	16.54 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	1.2260e+09
I(0) uncertainty (real space) i0_real_error	1.5380e+07
Rg (reciprocal space) rg_reciprocal	16.55 Å
I(0) (reciprocal space) i0_reciprocal	1226000000.0000
Solution quality estimate total_estimate	0.8798
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	460000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	RNA polymerase II transcription factor B subunit 1
Molecular weight formula_weight	12903.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	40580

PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEVVPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD

来源 Source

来源生物 organism	Saccharomyces cerevisiae S288c
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Epstein-Barr nuclear antigen 2
Molecular weight formula_weight	1633.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DLDESWDYIFETT

来源 Source

来源生物 organism	Human herpesvirus 4
通用名 common_name	HHV-4
NCBI Class编号 ncbi_taxonomy_id	10377
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2mkra_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.9 — TFIIH domain

CATH v4.4 (1 domains)

Domain ID domain_id	2mkrA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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fit	/app/data/saxs_computation/mk/2mkr/2mkr.fit
pddf	/app/data/pr_computation/mk/2mkr/2mkr.pr.out
profile	/app/data/saxs_computation/mk/2mkr/2mkr.dat

Structural Characterization of a Complex Between the Acidic Transactivation Domain of EBNA2 and the Tfb1/p62 subunit of TFIIH.

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

RNA polymerase II transcription factor B subunit 1

State in the Current Structure

Other States of the Same Protein in the Database

Epstein-Barr nuclear antigen 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)