SAXSdb — 5j40

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

Large T antigen

JC polyomavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 6 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 6 SULFATE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LT_POVJC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–372； UniProt 261–628

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	5j40
Deposition date deposition_date	2016-03-31
Structure title title	The X-ray structure of JCV Helicase
Keywords keywords	Helicase, hexamer, Zn, ATP, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
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.

5j40__assembly_1__model_1

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

Download this curve (.dat)

5j40__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j40__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.32 Å
Rg (electron density)	40.80 Å
Total Rg	41.29 Å
Atom count	17226
Residues	2148
Excluded volume	308110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j40__assembly_1__model_1`	hexameric （6）	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 (5)

Entity 1 Entity 1 polymer

Description description	Large T antigen
Molecular weight formula_weight	42389.0 kDa
EC 编号 ec_number	3.6.4.-
Mutation mutation	E280A, D295N, N299A, Q301A, Q302A, K304A, K305A, E307A, K308A, K309A, I354L, D408E, R624A
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	3164

GSHMEEPEETKQVSWKLVTQYALDTKCEDVFLLMGMYLNFQEAPAACAACAAADQPNHFNHHEKHYYNAQIFADSKNQKSICQQAVDTVAAKQRVDSLHMTREEMLVERFNFLLDKMDLIFGAHGNAVLEQYMAGVAWIHCLLPQMDTVIYEFLKCIVLNIPKKRYWLFKGPIDSGKTTLAAALLDLCGGKSLNVNMPLERLNFELGVGIDQFMVVFEDVKGTGAESRDLPSGHGISNLDCLRDYLDGSVKVNLERKHQNKRTQVFPPGIVTMNEYSVPRTLQARFVRQIDFRPKAYLRKSLSCSEYLLEKRILQSGMTLLLLLIWFRPVADFAAAIHERIVQWKERLDLEISMYTFSTMKANVGMGAPILD

Source Source

Source organism organism	JC polyomavirus
Common name common_name	JCPyV
NCBI taxonomy ID ncbi_taxonomy_id	10632
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	288

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5j40a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.20 — Extended AAA-ATPase domain

CATH v4.4 (3 domains)

Domain ID domain_id	5j40A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	510 — Zinc finger, large T-antigen D1 domain

Domain ID domain_id	5j40A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	70 — Large T antigen, SV40, domain 3

Domain ID domain_id	5j40A03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	109.910 Å
Unit-cell length b length_b	109.910 Å
Unit-cell length c length_c	67.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 6
Space-group number int_tables_number	168
Crystal system crystal_system	—

Resolution resolution	2.170 Å
Low-resolution limit resolution_low	38.970 Å
R factor r_factor	0.1720
R_work r_work	0.1690
R_free r_free	0.2280

The X-ray structure of JCV Helicase

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

Large T antigen

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

5j40__assembly_1__model_1

5j40__assembly_1__model_1 | I(q)

5j40__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

The X-ray structure of JCV Helicase

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

Large T antigen

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

5j40__assembly_1__model_1

5j40__assembly_1__model_1 | I(q)

5j40__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)