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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P29055 New Search
35PDB entries
35Biological assembly
37chain/assembly records
Main Difference Dimensions in This Set
Different construct Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3K7A Crystal Structure of an RNA polymerase II-TFIIB complex Deposited 2009-10-12 Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric（11） Consistent with protein count
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.9；295 K；1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 3.80 Å R-free 0.313
4BBR Structure of RNA polymerase II-TFIIB complex Deposited 2012-09-27 Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric（13） Consistent with protein count
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.40 Å R-free 0.211
4BBS Structure of an initially transcribing RNA polymerase II-TFIIB complex Deposited 2012-09-27 Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric（16） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.60 Å R-free 0.225
4V1N Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric（19） Consistent with all polymers
Chain M 1–345（345 aa）
Chain Q 1–734（734 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 7.80 Å
4V1O Architecture of the RNA polymerase II-Mediator core transcription initiation complex Deposited 2014-09-29 Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 180 MM POTASSIUM ACETATE, 5 % GLYCEROL, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；GRIDS WERE GLOW- DISCHARGED FOR 20 S BEFORE DEPOSITION OF 4 MICROLITERS SAMPLE AND INCUBATED FOR 30 S. GRIDS WERE WASHED TWICE WITH 4 MICROLITERS DISTILLED WATER, BLOTTED, AND VITRIFIED BY PLUNGING INTO LIQUID ETHANE WITH A MANUAL PLUNGER.
Resolution 9.70 Å
5FMF the P-lobe of RNA polymerase II pre-initiation complex Deposited 2015-11-03 Assembly 1 Protein–DNA Heteromer；Protein × 25 PDB declaration: 27-meric（27） Consistent with all polymers
Chain P 1–345（345 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC；pH 7.6；20 MM HEPES (PH7.6), 5 MM DTT, 2 MM MG(OAC)2,AND 40 MM KOAC
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK III,
Resolution 6.00 Å
5FYW Transcription initiation complex structures elucidate DNA opening (OC) Deposited 2016-03-10 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；CRYOGEN - ETHANE. INSTRUMENT - FEI VITROBOT MARK IV. QUANTIFOIL R 3.5- 1 HOLEY CARBON GRIDS WERE GLOW-DISCHARGED BEFORE DEPOSITION OF 4.5 MICROLITERS OF SAMPLE. GRIDS WERE THEN BLOTTED FOR 8.5 S AND PLUNGE- FROZEN IN LIQUID ETHANE.
Resolution 4.35 Å
5FZ5 Transcription initiation complex structures elucidate DNA opening (CC) Deposited 2016-03-10 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer 25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT；pH 7.5；25 MM HEPES-KOH PH 7.5, 150 MM POTASSIUM ACETATE, 2 MM MGCL2, 5 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；LIQUID ETHANE
Resolution 8.80 Å
5OQJ STRUCTURE OF YEAST TRANSCRIPTION PRE-INITIATION COMPLEX WITH TFIIH Deposited 2017-08-11 Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric（31） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Insufficient information Heteromer；Protein × 44 PDB declaration: 46-meric（46） Consistent with all polymers
Chain M 1–345（345 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
5SVA Mediator-RNA Polymerase II Pre-Initiation Complex Deposited 2016-08-05 Assembly 1 Protein–DNA Heteromer；Protein × 38 PDB declaration: 40-meric（40） Consistent with all polymers
Chain c 1–345（345 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 15.30 Å
6GYK Structure of a yeast closed complex (core CC1) Deposited 2018-06-30 Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: eicosameric（20） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.10 Å
6GYL Structure of a yeast closed complex with distorted DNA (core CCdist) Deposited 2018-06-30 Assembly 1 Protein–DNA Heteromer；Protein × 20 PDB declaration: 22-meric（22） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6GYM Structure of a yeast closed complex with distorted DNA (CCdist) Deposited 2018-06-30 Assembly 1 Protein–DNA Heteromer；Protein × 29 PDB declaration: 31-meric（31） Consistent with all polymers
Chain M 1–345（345 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
7ML0 RNA polymerase II pre-initiation complex (PIC1) Deposited 2021-04-27 Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric（28） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7ML1 RNA polymerase II pre-initiation complex (PIC2) Deposited 2021-04-27 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 19 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7ML2 RNA polymerase II pre-initiation complex (PIC3) Deposited 2021-04-27 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 17 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7ML4 RNA polymerase II initially transcribing complex (ITC) Deposited 2021-04-27 Assembly 1 Other combination Heteromer；Protein × 28 PDB declaration: 31-meric（31） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 1 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O4I Yeast RNA polymerase II transcription pre-initiation complex with initial transcription bubble Deposited 2021-04-06 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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
7O72 Yeast RNA polymerase II transcription pre-initiation complex with closed promoter DNA Deposited 2021-04-12 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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
7UI9 Core Mediator-PICearly (Copy A) Deposited 2022-03-28 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain M 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7UIF Mediator-PIC Early (Core B) Deposited 2022-03-29 Assembly 1 Protein heterocomplex Heteromer；Protein × 33 PDB declaration: 33-meric（33） Consistent with protein count
Chain M 1–345（345 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7UIO Mediator-PIC Early (Composite Model) Deposited 2022-03-29 Assembly 1 Protein–DNA Heteromer；Protein × 78 PDB declaration: 80-meric（80） Consistent with all polymers
Chain AM 1–345（345 aa）
Chain BM 1–345（345 aa）
Not recorded ZN ZINC ION × 4 THR THREONINE × 1 ALA ALANINE × 1 ASP ASPARTIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7ZS9 Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome (complex A) Deposited 2022-05-06 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 36 PDB declaration: 38-meric（38） Consistent with all polymers
Chain M 1–345（345 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
8CEN Yeast RNA polymerase II transcription pre-initiation complex with core Mediator Deposited 2023-02-02 Assembly 1 Protein–DNA Heteromer；Protein × 44 PDB declaration: 46-meric（46） Consistent with all polymers
Chain M 1–345（345 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 3.00 Å
8CEO Yeast RNA polymerase II transcription pre-initiation complex with core Mediator and the +1 nucleosome Deposited 2023-02-02 Assembly 1 Protein–DNA Heteromer；Protein × 52 PDB declaration: 54-meric（54） Consistent with all polymers
Chain M 1–345（345 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 3.60 Å
8UMH Consensus map of PICdeltaTFIIK form2 Deposited 2023-10-17 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 aa）
Not recorded ZN ZINC ION × 15 MG MAGNESIUM ION × 2 SF4 IRON/SULFUR CLUSTER × 1 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 4.10 Å
8UMI consensus map of PICdeltaTFIIK form1 Deposited 2023-10-17 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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
8UOQ Composite map of PIC_delta_TFIIK form2 Deposited 2023-10-20 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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 Assembly 1 Protein–DNA Heteromer；Protein × 28 PDB declaration: 30-meric（30） Consistent with all polymers
Chain M 1–345（345 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

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.