8uk9

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog

Method: X-RAY DIFFRACTION

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

Sliding-clamp-loader small subunit

Tequatrovirus T4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader large subunit × 4 （P04526） Sliding clamp × 3 （P04525） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader large subunit × 4 （P04526） Sliding clamp × 3 （P04525） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LOADS_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–187； UniProt 1–187 Author chain Q； PDBConstruct 1–187； UniProt 1–187

Sliding-clamp-loader large subunit

Tequatrovirus T4

UniProt P04526

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader small subunit × 1 （P04527） Sliding clamp × 3 （P04525） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader small subunit × 1 （P04527） Sliding clamp × 3 （P04525） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LOADL_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–320； UniProt 1–319 Author chain C； PDBConstruct 2–320； UniProt 1–319 Author chain D； PDBConstruct 2–320； UniProt 1–319 Author chain E； PDBConstruct 2–320； UniProt 1–319 Author chain K； PDBConstruct 2–320； UniProt 1–319 Author chain L； PDBConstruct 2–320； UniProt 1–319 Author chain M； PDBConstruct 2–320； UniProt 1–319 Author chain N； PDBConstruct 2–320； UniProt 1–319

Sliding clamp

Tequatrovirus T4

UniProt P04525

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader small subunit × 1 （P04527） Sliding-clamp-loader large subunit × 4 （P04526） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 8 DNA 2	Sliding-clamp-loader small subunit × 1 （P04527） Sliding-clamp-loader large subunit × 4 （P04526） DNA template × 1 DNA primer × 1 ALUMINUM FLUORIDE × 3 ADENOSINE-5'-DIPHOSPHATE × 4 MAGNESIUM ION × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CLAMP_BPT4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain F； PDBConstruct 1–228； UniProt 1–228 Author chain G； PDBConstruct 1–228； UniProt 1–228 Author chain H； PDBConstruct 1–228； UniProt 1–228 Author chain R； PDBConstruct 1–228； UniProt 1–228 Author chain S； PDBConstruct 1–228； UniProt 1–228 Author chain T； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8uk9
Deposition date deposition_date	2023-10-12
Structure title title	Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog
Keywords keywords	DNA Replication, AAA+ ATPase, Bacteriophage, Complex, DNA, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8uk9__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8uk9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8uk9__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.75 Å
Rg (electron density)	40.85 Å
Total Rg	41.17 Å
Atom count	17755
Residues	2185
Excluded volume	314740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8uk9__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8uk9__assembly_2__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Sliding-clamp-loader small subunit
Molecular weight formula_weight	21391.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,Q
Atom count atom_count	35422

MSLFKDDIQLNEHQVAWYSKDWTAVQSAADSFKEKAENEFFEIIGAINNKTKCSIAQKDYSKFMVENALSQFPECMPAVYAMNLIGSGLSDEAHFNYLMAAVPRGKRYGKWAKLVEDSTEVLIIKLLAKRYQVNTNDAINYKSILTKNGKLPLVLKELKGLVTDDFLKEVTKNVKEQKQLKKLALEW

Source Source

Source organism organism	Tequatrovirus T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Sliding-clamp-loader large subunit
Molecular weight formula_weight	35909.4 kDa
Mutation mutation	D110C
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,D,E,K,L,M,N

SMITVNEKEHILEQKYRPSTIDECILPAFDKETFKSITSKGKIPHIILHSPSPGTGKTTVAKALCHDVNADMMFVNGSDCKIDFVRGPLTNFASAASFDGRQKVIVIDEFCRSGLAESQRHLRSFMEAYSSNCSIIITANNIDGIIKPLQSRCRVITFGQPTDEDKIEMMKQMIRRLTEICKHEGIAIADMKVVAALVKKNFPDFRKTIGELDSYSSKGVLDAGILSLVTNDRGAIDDVLESLKNKDVKQLRALAPKYAADYSWFVGKLAEEIYSRVTPQSIIRMYEIVGENNQYHGIAANTELHLAYLFIQLACEMQWK

Source Source

Source organism organism	Tequatrovirus T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Sliding clamp
Molecular weight formula_weight	24881.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H,R,S,T

MKLSKDTTALLKNFATINSGIMLKSGQFIMTRAVNGTTYAEANISDVIDFDVAIYDLNGFLGILSLVNDDAEISQSEDGNIKIADARSTIFWPAADPSTVVAPNKPIPFPVASAVTEIKAEDLQQLLRVSRGLQIDTIAITVKEGKIVINGFNKVEDSALTRVKYSLTLGDYDGENTFNFIINMANMKMQPGNYKLLLWAKGKQGAAKFEGEHANYVVALEADSTHDF

Source Source

Source organism organism	Tequatrovirus T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	DNA template
Molecular weight formula_weight	7347.7 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,O

TTTTTATGTACTCGTAGTGTCTGC

Entity 5 Entity 5 polymer

Description description	DNA primer
Molecular weight formula_weight	6136.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,P

GCAGACACTACGAGTACATA

Entity 6 Entity 6 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	8

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Unit-cell length a length_a	95.243 Å
Unit-cell length b length_b	231.991 Å
Unit-cell length c length_c	264.511 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	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	48.130 Å
R factor r_factor	0.2530
R_work r_work	0.2526
R_free r_free	0.2650

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog

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

Sliding-clamp-loader small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Sliding-clamp-loader large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8uk9__assembly_1__model_1

8uk9__assembly_1__model_1 | I(q)

8uk9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)

Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog

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

Sliding-clamp-loader small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sliding-clamp-loader large subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Sliding clamp

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8uk9__assembly_1__model_1

8uk9__assembly_1__model_1 | I(q)

8uk9__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

7. Citations (1)