5o6v

The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786

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 heterocomplex	Heteromer	Protein 600	Fab 19/1786 - Heavy chain × 120 Fab 19/1786 - Light chain × 120 2-acetamido-2-deoxy-beta-D-glucopyranose × 180	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	5o6v
Deposition date deposition_date	2017-06-07
Structure title title	The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786
Keywords keywords	tick-borne encephalitis virus, Fab 19/1786, 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.

5o6v__assembly_1__model_1

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

Download this curve (.dat)

5o6v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5o6v__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)	224.80 Å
Total Rg	224.70 Å
Atom count	1160760
Residues	151740
Excluded volume	20673000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5o6v__assembly_1__model_1`	600-meric （600）	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	Envelope protein
Molecular weight formula_weight	53667.4 kDa
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	19346

SRCTHLENRDFVTGTQGTTRVTLVLELGGCVTITAEGKPSMDVWLDAIYQENPAQTREYCLHAKLSDTKVAARCPTMGPATLAEEHQGGTVCKRDQSDRGWGNHCGLFGKGSIVACVKAACEAKKKATGHVYDANKIVYTVKVEPHTGDYVAANETHSGRKTASFTVSSEKTILTMGEYGDVSLLCRVASGVDLAQTVILELDKTVEHLPTAWQVHRDWFNDLALPWKHEGARNWNNAERLVEFGAPHAVKMDVYNLGDQTGVLLKALAGVPVAHIEGTKYHLKSGHVTCEVGLEKLKMKGLTYTMCDKTKFTWKRAPTDSGHDTVVMEVTFSGTKPCRIPVRAVAHGSPDVNVAMLITPNPTIENNGGGFIEMQLPPGDNIIYVGELSYQWFQKGSSIGRVFQKTKKGIERLTVIGEHAWDFGSAGGFLSSIGKALHTVLGGAFNSIFGGVGFLPKLLLGVALAWLGLNMRNPTMSMSFLLAGVLVLAMTLGVGA

Entity 2 Entity 2 polymer

Description description	Small envelope protein M
Molecular weight formula_weight	8339.9 kDa
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 polymer

Description description	Fab 19/1786 - Heavy chain
Molecular weight formula_weight	22730.4 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

EVKLEESGGGLVQPGGSLKLSCAASGFTFSSYGMSWVRQTPDKRLELVAATNSDGDSTYYPDSVKGRFTISRDRAKNTLYLQMSSLKSEDTAMYYCTRVLYDYDGEFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSKTWPSETVTCNVAHPASSTK

Entity 4 Entity 4 polymer

Description description	Fab 19/1786 - Light chain
Molecular weight formula_weight	22847.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

DIVMTQSQKFMSTSVGDRVTVTCKASQNVGTNVAWYQQKPGQSPKGLIYSASYRYSGVPDRFIGSGSGTDFTLTISNVQSGDLAEYFCQQYNNHPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQDGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKS

Entity 5 Entity 5 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) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	5o6vA01
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	5o6vA02
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	5o6vA03
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	5o6vA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6vA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6vB01
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	5o6vB02
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	5o6vB03
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	5o6vB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6vB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6vC01
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	5o6vC02
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	5o6vC03
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	5o6vC04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5o6vC05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5o6vD00
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	5o6vE00
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	5o6vF00
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	5o6vH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o6vI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o6vL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o6vL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o6vM01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5o6vM02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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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	580.000 Å
R factor r_factor	0.4058
R_work r_work	0.4058
R_free r_free	—

Resolution resolution	3.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	9797

The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786

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

5o6v__assembly_1__model_1

5o6v__assembly_1__model_1 | I(q)

5o6v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

The cryo-EM structure of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786

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

5o6v__assembly_1__model_1

5o6v__assembly_1__model_1 | I(q)

5o6v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)