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6mid

Cryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195

Method: ELECTRON MICROSCOPY
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1. Protein Identity and Related Structures Protein Identity & Related Structures

E protein

OrganismNot specified

UniProt A0A024B7W1

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 480 其他Polymer 180 monoclonal antibody ZIKV-195 heavy chain × 60 monoclonal antibody ZIKV-195 light chain × 60 （A0A0B4J1U3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 180 Consistent with protein count
2 Other combination Heteromer Protein 8 其他Polymer 3 monoclonal antibody ZIKV-195 heavy chain × 1 monoclonal antibody ZIKV-195 light chain × 1 （A0A0B4J1U3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Consistent with protein count
3 Other combination Heteromer Protein 40 其他Polymer 15 monoclonal antibody ZIKV-195 heavy chain × 5 monoclonal antibody ZIKV-195 light chain × 5 （A0A0B4J1U3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 Consistent with protein count
4 Other combination Heteromer Protein 48 其他Polymer 18 monoclonal antibody ZIKV-195 heavy chain × 6 monoclonal antibody ZIKV-195 light chain × 6 （A0A0B4J1U3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 18 Consistent with protein count
5 Other combination Heteromer Protein 8 其他Polymer 3 monoclonal antibody ZIKV-195 heavy chain × 1 monoclonal antibody ZIKV-195 light chain × 1 （A0A0B4J1U3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5jmt 6ld1 6ld2 6ld3 6ld4 6ld5

6 assemblies

Homodimer
5iy3

1 assemblies

Homotetramer

None

Other homooligomers
6lnu 6lnu 6lnu 6lnu 6lnu

5 assemblies

Heteromeric or nucleic-acid complex
5gzr 5gzr 5gzr 5gzr 5gzr 5gzr 5h30 5h30 5h30 5h30 5h30 5h30

94 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POLG_ZIKVF
Isoform —
PDB entities 1, 2
Chains and sequence ranges Author chain A； PDBConstruct 1–504； UniProt 291–794 Author chain C； PDBConstruct 1–504； UniProt 291–794 Author chain E； PDBConstruct 1–504； UniProt 291–794 Author chain B； PDBConstruct 1–75； UniProt 216–290 Author chain D； PDBConstruct 1–75； UniProt 216–290 Author chain F； PDBConstruct 1–75； UniProt 216–290

monoclonal antibody ZIKV-195 light chain

OrganismNot specified

UniProt A0A0B4J1U3

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Heteromer Protein 480 其他Polymer 180 E protein × 180 （A0A024B7W1） M protein × 180 （A0A024B7W1） monoclonal antibody ZIKV-195 heavy chain × 60 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 180 Consistent with protein count
2 Other combination Heteromer Protein 8 其他Polymer 3 E protein × 3 （A0A024B7W1） M protein × 3 （A0A024B7W1） monoclonal antibody ZIKV-195 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Consistent with protein count
3 Other combination Heteromer Protein 40 其他Polymer 15 E protein × 15 （A0A024B7W1） M protein × 15 （A0A024B7W1） monoclonal antibody ZIKV-195 heavy chain × 5 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 Consistent with protein count
4 Other combination Heteromer Protein 48 其他Polymer 18 E protein × 18 （A0A024B7W1） M protein × 18 （A0A024B7W1） monoclonal antibody ZIKV-195 heavy chain × 6 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 18 Consistent with protein count
5 Other combination Heteromer Protein 8 其他Polymer 3 E protein × 3 （A0A024B7W1） M protein × 3 （A0A024B7W1） monoclonal antibody ZIKV-195 heavy chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6mid 6mid 6mid 6mid 6mid

5 assemblies

View Construct and Data Evidence
UniProt name LV136_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain L； PDBConstruct 1–96； UniProt 20–115

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_id6mid
Deposition date deposition_date2018-09-19
Structure title titleCryo-EM structure of the ZIKV virion in complex with Fab fragments of the potently neutralizing human monoclonal antibody ZIKV-195
Keywords keywordsvirus, monoclonal antibody, complex, VIRUS-IMMUNE SYSTEM complex; VIRUS/IMMUNE SYSTEM
Experimental Method methodELECTRON 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.

6mid__assembly_1__model_1

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

Download this curve (.dat)

6mid__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 1010 1011 1012 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6mid__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）0.00 Å
Rg (electron density)211.80 Å
Total Rg211.90 Å
Atom count903240
Residues117840
Excluded volume16079000 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6mid__assembly_1__model_1 480-meric （480） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6mid__assembly_2__model_1 octameric （8） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3 1 6mid__assembly_3__model_1 40-meric （40） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4 1 6mid__assembly_4__model_1 48-meric （48） Excluded — —
Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5 1 6mid__assembly_5__model_1 octameric （8） 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 (5)

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6. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id6midA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily10 — Tick-borne Encephalitis virus Glycoprotein, domain 1
Domain ID domain_id6midA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 2
Domain ID domain_id6midA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 3
Domain ID domain_id6midA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily350 —
Domain ID domain_id6midA05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily260 —
Domain ID domain_id6midB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily970 — Flavivirus envelope glycoprotein M-like
Domain ID domain_id6midC01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily10 — Tick-borne Encephalitis virus Glycoprotein, domain 1
Domain ID domain_id6midC02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 2
Domain ID domain_id6midC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 3
Domain ID domain_id6midC04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily350 —
Domain ID domain_id6midC05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily260 —
Domain ID domain_id6midD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily970 — Flavivirus envelope glycoprotein M-like
Domain ID domain_id6midE01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology98 — Tick-borne Encephalitis virus Glycoprotein; domain 1
Homologous superfamily homologous superfamily10 — Tick-borne Encephalitis virus Glycoprotein, domain 1
Domain ID domain_id6midE02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology67 — Viral Envelope Glycoprotein; domain 2
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 2
Domain ID domain_id6midE03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology387 — Viral Envelope Glycoprotein; domain 3
Homologous superfamily homologous superfamily10 — Viral Envelope Glycoprotein, domain 3
Domain ID domain_id6midE04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily350 —
Domain ID domain_id6midE05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily260 —
Domain ID domain_id6midF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily970 — Flavivirus envelope glycoprotein M-like
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7. Citations (1)