5o6a

The cryo-EM structure of Tick-borne encephalitis virus mature particle

Method: ELECTRON MICROSCOPY

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

Envelope protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 360	2-acetamido-2-deoxy-beta-D-glucopyranose × 180	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 30	2-acetamido-2-deoxy-beta-D-glucopyranose × 15	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 36	2-acetamido-2-deoxy-beta-D-glucopyranose × 18	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 6	2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_TBEVH
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–496； UniProt 281–776 Author chain B； PDBConstruct 1–496； UniProt 281–776 Author chain C； PDBConstruct 1–496； UniProt 281–776 Author chain D； PDBConstruct 1–75； UniProt 206–280 Author chain E； PDBConstruct 1–75； UniProt 206–280 Author chain F； PDBConstruct 1–75； UniProt 206–280

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	5o6a
Deposition date deposition_date	2017-06-06
Structure title title	The cryo-EM structure of Tick-borne encephalitis virus mature particle
Keywords keywords	tick-borne encephalitis virus, mature particle, cryo-EM, VIRUS; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

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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.

5o6a__assembly_1__model_1

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

Download this curve (.dat)

5o6a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o6a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	212.00 Å
Total Rg	212.00 Å
Atom count	776520
Residues	101340
Excluded volume	13893000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o6a__assembly_1__model_1`	360-meric （360）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5o6a__assembly_2__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`5o6a__assembly_3__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`5o6a__assembly_4__model_1`	36-meric （36）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`5o6a__assembly_5__model_1`	hexameric （6）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Envelope protein
Molecular weight formula_weight	53667.4 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	12942

SRCTHLENRDFVTGTQGTTRVTLVLELGGCVTITAEGKPSMDVWLDAIYQENPAQTREYCLHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDRGWGNHCGLFGKGSIVACVKAACEAKKKATGHVYDANKIVYTVKVEPHTGDYVAANETHSGRKTASFTVSSEKTILTMGEYGDVSLLCRVASGVDLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGARNWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTKYHLKSGHVTCEVGLEKLKMKGLTYTMCDKTKFTWKRAPTDSGHDTVVMEVTFSGTKPCRIPVRAVAHGSPDVNVAMLITPNPTIENNGGGFIEMQLPPGDNIIYVGELSYQWFQKGSSIGRVFQKTKKGIERLTVIGEHAWDFGSAGGFLSSIGKALHTVLGGAFNSIFGGVGFLPKLLLGVALAWLGLNMRNPTMSMSFLLAGVLVLAMTLGVGA

Entity 2 Entity 2 polymer

Description description	Small envelope protein M
Molecular weight formula_weight	8339.9 kDa
EC 编号 ec_number	3.4.21.91,3.6.1.15,3.6.4.13,2.1.1.56,2.1.1.57,2.7.7.48
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

SVLIPSHAQGELTGRGHKWLEGDSLRTHLTRVEGWVWKNRLLALAMVTVVWLTLESVVTRVAVLVVLLCLAPVYA

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id	5o6aA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Tick-borne Encephalitis virus Glycoprotein, domain 1

Domain ID domain_id	5o6aA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 2

Domain ID domain_id	5o6aA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 3

Domain ID domain_id	5o6aA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6aA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6aB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Tick-borne Encephalitis virus Glycoprotein, domain 1

Domain ID domain_id	5o6aB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 2

Domain ID domain_id	5o6aB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 3

Domain ID domain_id	5o6aB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6aB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6aC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily	10 — Tick-borne Encephalitis virus Glycoprotein, domain 1

Domain ID domain_id	5o6aC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 2

Domain ID domain_id	5o6aC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily	10 — Viral Envelope Glycoprotein, domain 3

Domain ID domain_id	5o6aC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6aC05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6aD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	970 — Flavivirus envelope glycoprotein M-like

Domain ID domain_id	5o6aE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	970 — Flavivirus envelope glycoprotein M-like

Domain ID domain_id	5o6aF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	970 — Flavivirus envelope glycoprotein M-like

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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	1

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

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	522.000 Å
R factor r_factor	0.3590
R_work r_work	0.3590
R_free r_free	—

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	11882

The cryo-EM structure of Tick-borne encephalitis virus mature particle

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

Envelope protein

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

5o6a__assembly_1__model_1

5o6a__assembly_1__model_1 | I(q)

5o6a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)

The cryo-EM structure of Tick-borne encephalitis virus mature particle

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

Envelope protein

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

5o6a__assembly_1__model_1

5o6a__assembly_1__model_1 | I(q)

5o6a__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

7. Citations (1)