4y3c

I304V 3D polymerase mutant of EMCV

Method: X-RAY DIFFRACTION

▼

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

3D polymerase

Mengo encephalomyocarditis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	GLYCEROL × 4 CHLORIDE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	GLYCEROL × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_ENMGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1834–2293 Author chain B； PDBConstruct 1–460； UniProt 1834–2293 Author chain C； PDBConstruct 1–460； UniProt 1834–2293 Author chain D； PDBConstruct 1–460； UniProt 1834–2293 Author chain E； PDBConstruct 1–460； UniProt 1834–2293 Author chain F； PDBConstruct 1–460； UniProt 1834–2293

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4y3c
Deposition date deposition_date	2015-02-10
Structure title title	I304V 3D polymerase mutant of EMCV
Keywords keywords	RNA dependent RNA polymerase Cardiovirus Inhibitor resistance, viral protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4y3c__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4y3c__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4y3c__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	24.24 Å
Rg (electron density)	23.12 Å
Total Rg	23.99 Å
Atom count	3680
Residues	460
Excluded volume	65720 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4y3c__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4y3c__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4y3c__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4y3c__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4y3c__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4y3c__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	3D polymerase
Molecular weight formula_weight	52230.5 kDa
EC 编号 ec_number	3.6.1.15,3.4.22.28,2.7.7.48
Mutation mutation	I304V
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	22220

GALERLPDGPRIHVPRKTALRPTVARQVFQPAFAPAVLSKFDPRTDADVDEVAFSKHTSNQETLPPVFRMVAREYANRVFALLGRDNGRLSVKQALDGLEGMDPMDKNTSPGLPYTTLGMRRTDVVDWETATLIPFAAERLEKMNNKDFSDIVYQTFLKDELRPIEKVQAAKTRIVDVPPFEHCILGRQLLGKFASKFQTQPGLELGSAIGCDPDVHWTAFGVAMQGFERVYDVDYSNFDSTHSVAMFRLLAEEFFSEENGFDPLVKDYLESLAISKHAYEEKRYLITGGLPSGCAATSMLNTVMNNIIIRAGLYLTYKNFEFDDVKVLSYGDDLLVATNYQLNFDRVRTSLAKTGYKITPANKTSTFPLESTLEDVVFLKRKFKKEGPLYRPVMNREALEAMLSYYRPGTLSEKLTSITMLAVHSGKQEYDRLFAPFREVGVIVPTFESVEYRWRSLFW

Source Source

Source organism organism	Mengo encephalomyocarditis virus
NCBI taxonomy ID ncbi_taxonomy_id	12107
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	71

▼

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4y3cA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cA03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4y3cB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cB03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4y3cC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cC03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4y3cD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cD03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4y3cE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cE03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	4y3cF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4y3cF03
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	232.332 Å
Unit-cell length b length_b	140.775 Å
Unit-cell length c length_c	171.838 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	126.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	138.960 Å
R factor r_factor	0.2215
R_work r_work	0.2200
R_free r_free	0.2498

I304V 3D polymerase mutant of EMCV

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

3D polymerase

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

4y3c__assembly_3__model_1

4y3c__assembly_3__model_1 | I(q)

4y3c__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

I304V 3D polymerase mutant of EMCV

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

3D polymerase

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

4y3c__assembly_3__model_1

4y3c__assembly_3__model_1 | I(q)

4y3c__assembly_3__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)