5h37

Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0

Method: ELECTRON MICROSCOPY

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

structural protein E

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 720	C10 IgG heavy chain variable region × 180 C10 IgG light chain variable region × 180 2-acetamido-2-deoxy-beta-D-glucopyranose × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 12	C10 IgG heavy chain variable region × 3 C10 IgG light chain variable region × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 60	C10 IgG heavy chain variable region × 15 C10 IgG light chain variable region × 15 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 72	C10 IgG heavy chain variable region × 18 C10 IgG light chain variable region × 18 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 12	C10 IgG heavy chain variable region × 3 C10 IgG light chain variable region × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 720	C10 IgG heavy chain variable region × 180 C10 IgG light chain variable region × 180 2-acetamido-2-deoxy-beta-D-glucopyranose × 60	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A024B7W1_ZIKV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–504； UniProt 291–794 Author chain B； PDBConstruct 1–504； UniProt 291–794 Author chain C； PDBConstruct 1–504； UniProt 291–794 Author chain D； PDBConstruct 1–75； UniProt 216–290 Author chain E； PDBConstruct 1–75； UniProt 216–290 Author chain F； PDBConstruct 1–75； UniProt 216–290

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	5h37
Deposition date deposition_date	2016-10-20
Structure title title	Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0
Keywords keywords	IgG NAG, VIRUS-IMMUNE SYSTEM complex; VIRUS/IMMUNE SYSTEM
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.

5h37__assembly_1__model_1

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

Download this curve (.dat)

5h37__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5h37__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)	216.40 Å
Total Rg	216.40 Å
Atom count	1111020
Residues	145500
Excluded volume	19731000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5h37__assembly_1__model_1`	720-meric （720）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5h37__assembly_2__model_1`	dodecameric （12）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`5h37__assembly_3__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`5h37__assembly_4__model_1`	72-meric （72）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`5h37__assembly_5__model_1`	dodecameric （12）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`5h37__assembly_6__model_1`	720-meric （720）	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)

Entity 1 Entity 1 polymer

Description description	structural protein E
Molecular weight formula_weight	54444.1 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B
Atom count atom_count	18517

IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTIGKAFEATVRGAKRMAVLGDTAWDFGSVGGALNSLGKGIHQIFGAAFKSLFGGMSWFSQILIGTLLMWLGLNTKNGSISLMCLALGGVLIFLSTAVSA

Entity 2 Entity 2 polymer

Description description	strutural protein M
Molecular weight formula_weight	8496.9 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

AVTLPSHSTRKLQTRSQTWLESREYTKHLIRVENWIFRNPGFALAAAAIAWLLGSSTSQKVIYLVMILLIAPAYS

Entity 3 Entity 3 polymer

Description description	C10 IgG heavy chain variable region
Molecular weight formula_weight	14487.1 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,K,I

EVQLVESGAEVKKPGASVKVSCKASGYTFTSYAMHWVRQAPGQRLEWMGWINAGNGNTKYSQKFQDRVTITRDTSASTAYMELSSLRSEDTAIYYCARDKVDDYGDYWFPTLWYFDYWGQGTLVTVS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	C10 IgG light chain variable region
Molecular weight formula_weight	11298.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

SALTQPASVSGSPGQSITISCTGTSSDVGGFNYVSWFQQHPGKAPKLMLYDVTSRPSGVSSRFSGSKSGNTASLTISGLQAEDEADYYCSSHTSRGTWVFGGGTKLTVL

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

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	1

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	5h37A01
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	5h37A02
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	5h37A03
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	5h37A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5h37A05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5h37B01
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	5h37B02
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	5h37B03
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	5h37B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5h37B05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5h37C01
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	5h37C02
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	5h37C03
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	5h37C04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5h37C05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	260 —

Domain ID domain_id	5h37D00
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	5h37E00
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	5h37F00
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	5h37G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h37H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h37I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h37K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h37L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5h37M00
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	4.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	49100

Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0

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

structural protein E

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

5h37__assembly_1__model_1

5h37__assembly_1__model_1 | I(q)

5h37__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Cryo-EM structure of zika virus complexed with Fab C10 at pH 8.0

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

structural protein E

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

5h37__assembly_1__model_1

5h37__assembly_1__model_1 | I(q)

5h37__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)