7d7d

CryoEM structure of gp45-dependent transcription activation complex

Method: ELECTRON MICROSCOPY D_max: 198.1 Å Quality: GOOD

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

DNA-directed RNA polymerase subunit alpha

Escherichia coli

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain A； UniProt 1–329 Chain B； UniProt 1–329	Not recorded	DNA-directed RNA polymerase subunit beta × 1 （A0A080FHH4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （D7Y6A2） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 RNA polymerase-associated protein Gp33 × 1 （P13338） DNA-directed RNA polymerase subunit omega × 1 （A0A070UPX4） DNA polymerase clamp × 3 （P04525） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

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 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain A 1–329（329 aa） Chain B 1–329（329 aa） Chain K 1–329（329 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.58 Å
7D7C CryoEM structure of gp55-dependent RNA polymerase-promoter open complex Deposited 2020-10-03	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–329（329 aa） Chain B 1–329（329 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	U9ZUN7_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 1–329 Author chain B； PDBConstruct 1–329； UniProt 1–329

DNA-directed RNA polymerase subunit beta

Escherichia coli 1-392-07_S4_C3

UniProt A0A080FHH4

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain C； UniProt 1–1342	Not recorded	DNA-directed RNA polymerase subunit alpha × 2 （U9ZUN7） ;DNA-directed RNA polymerase subunit beta' ; × 1 （D7Y6A2） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 RNA polymerase-associated protein Gp33 × 1 （P13338） DNA-directed RNA polymerase subunit omega × 1 （A0A070UPX4） DNA polymerase clamp × 3 （P04525） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7D7C CryoEM structure of gp55-dependent RNA polymerase-promoter open complex Deposited 2020-10-03	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain C 1–1342（1342 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A080FHH4_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt D7Y6A2

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain D； UniProt 1–1407	Not recorded	DNA-directed RNA polymerase subunit alpha × 2 （U9ZUN7） DNA-directed RNA polymerase subunit beta × 1 （A0A080FHH4） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 RNA polymerase-associated protein Gp33 × 1 （P13338） DNA-directed RNA polymerase subunit omega × 1 （A0A070UPX4） DNA polymerase clamp × 3 （P04525） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain D 1–1407（1407 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.58 Å
7D7C CryoEM structure of gp55-dependent RNA polymerase-promoter open complex Deposited 2020-10-03	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain D 1–1407（1407 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	D7Y6A2_ECOLX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1407； UniProt 1–1407

RNA polymerase-associated protein Gp33

Enterobacteria phage T4

UniProt P13338

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain K； UniProt 1–112	Not recorded	DNA-directed RNA polymerase subunit alpha × 2 （U9ZUN7） DNA-directed RNA polymerase subunit beta × 1 （A0A080FHH4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （D7Y6A2） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 DNA-directed RNA polymerase subunit omega × 1 （A0A070UPX4） DNA polymerase clamp × 3 （P04525） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3TBI Crystal structure of T4 gp33 bound to E. coli RNAP beta-flap domain Deposited 2011-08-06	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 × 2 PDB declaration: dimeric	Chain A 1–112（112 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；295 K；0.1 M triethylamine N-oxide, 20% PEG2000 MME, 0.1 M Tris, pH 8.5, VAPOR DIFFUSION, temperature 295K	Resolution 3.00 Å R-free 0.295

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VG33_BPT4
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain K； PDBConstruct 21–132； UniProt 1–112

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt A0A070UPX4

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain E； UniProt 1–91	Not recorded	DNA-directed RNA polymerase subunit alpha × 2 （U9ZUN7） DNA-directed RNA polymerase subunit beta × 1 （A0A080FHH4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （D7Y6A2） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 RNA polymerase-associated protein Gp33 × 1 （P13338） DNA polymerase clamp × 3 （P04525） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VYU Escherichia coli transcription-translation complex C2 (TTC-C2) containing a 27 nt long mRNA spacer Deposited 2020-02-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 56 PDB declaration: 65-meric	Chain AF 1–91（91 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.00 Å
7CHW Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) Deposited 2020-07-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain E 1–91（91 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9	Resolution 3.58 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A070UPX4_ECOLX
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain E； PDBConstruct 1–91； UniProt 1–91

DNA polymerase clamp

Enterobacteria phage T4

UniProt P04525

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 × 10 DNA 2 PDB declaration: dodecameric（12） Consistent with all polymer counts	Chain G； UniProt 1–228 Chain H； UniProt 1–228 Chain I； UniProt 1–228	Not recorded	DNA-directed RNA polymerase subunit alpha × 2 （U9ZUN7） DNA-directed RNA polymerase subunit beta × 1 （A0A080FHH4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （D7Y6A2） DNA (template strand) × 1 gp55 × 1 DNA (nontemplate strand) × 1 RNA polymerase-associated protein Gp33 × 1 （P13338） DNA-directed RNA polymerase subunit omega × 1 （A0A070UPX4） MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.9 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.50 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7D7D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CZD CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4 Deposited 1999-09-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；60 mM PIPES 200 mM CASO4 0.1 % 1,4 Dioxane 15% Glycerol 15% PEG MME 5000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.259
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	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 × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain P 1–228（228 aa） Chain Q 1–228（228 aa） Chain R 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U60 Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog Deposited 2011-10-11	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 × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K	Resolution 3.34 Å R-free 0.282
3U61 Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP Deposited 2011-10-11	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 × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.305
6DRT Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4 Deposited 2018-06-13	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350	Resolution 2.12 Å R-free 0.240
8UH7 Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-07	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 × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl	Resolution 2.63 Å R-free 0.244
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	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 F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain R 1–228（228 aa） Chain S 1–228（228 aa） Chain T 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UNF Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Deposited 2023-10-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8UNH Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Deposited 2023-10-19	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9E5Y T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1 Deposited 2024-10-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
9EA2 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 2 Deposited 2024-11-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9EA3 T4 bacteriophage replicative holoenzyme containing triple mutations D75R, Q430E, and K432E in the exonuclease-deficient polymerase Deposited 2024-11-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
9EA6 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 3 Deposited 2024-11-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	CA CALCIUM ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPA5_BPT4
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain G； PDBConstruct 1–228； UniProt 1–228 Author chain H； PDBConstruct 1–228； UniProt 1–228 Author chain I； PDBConstruct 1–228； UniProt 1–228

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	7d7d
Deposition date deposition_date	2020-10-03
Structure title title	CryoEM structure of gp45-dependent transcription activation complex
Keywords keywords	Transcription, RNA polymerase; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	57.47 Å
Radius of gyration Rg (electron density) rg_electron	57.37 Å
Forward intensity I(0) i0	3571790000.00
Molecular weight molecular_weight	482100.0 kDa
Excluded volume excluded_volume	595930 Å³
Envelope volume envelope_volume	921780 Å³
Hydration-shell volume shell_volume	132150 Å³
Envelope diameter envelope_diameter	196.8 Å
Shell Rg shell_rg	61.07 Å
Envelope Rg envelope_rg	56.50 Å
Shape Rg shape_rg	57.39 Å
Total Rg total_rg	57.39 Å
Total atoms total_atoms	33755
Residues n_residues	4170
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	198.1 Å
Rg (real space) rg_real	57.37 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	3.5720e+09
I(0) uncertainty (real space) i0_real_error	6.7310e+07
Rg (reciprocal space) rg_reciprocal	57.53 Å
I(0) (reciprocal space) i0_reciprocal	3573000000.0000
Solution quality estimate total_estimate	0.8633
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.0 Å
Skewness Skewness skewness	0.313
Kurtosis Kurtosis kurtosis	-0.330
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	463400000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.830

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	36558.7 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	33755

MQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQPEVKEEKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIADE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	150820.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

来源 Source

来源生物 organism	Escherichia coli 1-392-07_S4_C3
NCBI Class编号 ncbi_taxonomy_id	1444275
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	155366.8 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	DNA (template strand)
Molecular weight formula_weight	18203.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

GGCTGCTTCAGTATCAGGAGTATTTATACTCTCAGTAATAGTGCTGAGCTCTTTATTAG

来源 Source

来源生物 organism	Escherichia virus T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia virus T4

Entity 5 Entity 5 polymer

Description description	gp55
Molecular weight formula_weight	21565.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSETKPKYNYVNNKELLQAIIDWKTELANNKDPNKVVRQNDTIGLAIMLIAEGLSKRFNFSGYTQSWKQEMIADGIEASIKGLHNFDETKYKNPHAYITQACFNAFVQRIKKERKEVAKKYSYFVHNVYDSRDDDMVALVDETFIQDIYDKMTHYEESTYRTPGAEKKSVVDDSPSLDFLYEAND

来源 Source

来源生物 organism	Escherichia virus T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA (nontemplate strand)
Molecular weight formula_weight	18155.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

CTAATAAAGAGCTCAGCACTATTACTGAGAGTATAAATACTCCTGATACTGAAGCAGCC

Entity 7 Entity 7 polymer

Description description	RNA polymerase-associated protein Gp33
Molecular weight formula_weight	15014.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MGSSHHHHHHSSGLVPRGSHMTQFSLNDIRPVDETGLSEKELSIKKEKDEIAKLLDRQENGFIIEKMVEEFGMSYLEATTAFLEENSIPETQFAKFIPSGIIEKIQSEAIDENLLRPSVVRCEKTNTLDFLL

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	10249.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	DNA polymerase clamp
Molecular weight formula_weight	25952.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H,I

MKLSKDTTALLKNFATINSGIMLKSGQFIMTRAVNGTTYAEANISDVIDFDVAIYDLNGFLGILSLVNDDAEISQSEDGNIKIADARSTIFWPAADPSTVVAPNKPIPFPVASAVTEIKAEDLQQLLRVSRGLQIDTIAITVKEGKIVINGFNKVEDSALTRVKYSLTLGDYDGENTFNFIINMANMKMQPGNYKLLLWAKGKQGAAKFEGEHANYVVALEADSTHDFLEHHHHHH

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 10 Entity 10 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	8981

fit	/app/data/saxs_computation/d7/7d7d/7d7d.fit
pddf	/app/data/pr_computation/d7/7d7d/7d7d.pr.out
profile	/app/data/saxs_computation/d7/7d7d/7d7d.dat

CryoEM structure of gp45-dependent transcription activation complex

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

DNA-directed RNA polymerase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

;DNA-directed RNA polymerase subunit beta' ;

State in the Current Structure

Other States of the Same Protein in the Database

RNA polymerase-associated protein Gp33

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase subunit omega

State in the Current Structure

Other States of the Same Protein in the Database

DNA polymerase clamp

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

来源 Source

Entity 8 Entity 8 polymer

Polymer Polymer

来源 Source

Entity 9 Entity 9 polymer

Polymer Polymer

来源 Source

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)