6uta

Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII

Method: X-RAY DIFFRACTION

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

Z004 iGL Fab heavy chain

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab light chain × 1 （P0DOX7） Env × 1 （A0A1X9PPI0）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab light chain × 1 （P0DOX7） Env × 1 （A0A1X9PPI0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S6C4S0_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 109–229； UniProt 129–249 Author chain H； PDBConstruct 109–229； UniProt 129–249

Z004 iGL Fab light chain

Homo sapiens

UniProt P0DOX7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab heavy chain × 1 （S6C4S0） Env × 1 （A0A1X9PPI0）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab heavy chain × 1 （S6C4S0） Env × 1 （A0A1X9PPI0）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IGK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 109–214； UniProt 109–214 Author chain L； PDBConstruct 109–214； UniProt 109–214

Env

Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013

UniProt A0A1X9PPI0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab heavy chain × 1 （S6C4S0） Z004 iGL Fab light chain × 1 （P0DOX7）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Z004 iGL Fab heavy chain × 1 （S6C4S0） Z004 iGL Fab light chain × 1 （P0DOX7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A1X9PPI0_ZIKV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 2–110； UniProt 299–407 Author chain E； PDBConstruct 2–110； UniProt 299–407

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	6uta
Deposition date deposition_date	2019-10-29
Structure title title	Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII
Keywords keywords	VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

6uta__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6uta__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6uta__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.88 Å
Rg (electron density)	28.63 Å
Total Rg	29.24 Å
Atom count	4013
Residues	529
Excluded volume	71212 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6uta__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6uta__assembly_2__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Z004 iGL Fab heavy chain
Molecular weight formula_weight	24819.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A
Atom count atom_count	8038

EVQLLESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRGPRGVGELFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

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 2 Entity 2 polymer

Description description	Z004 iGL Fab light chain
Molecular weight formula_weight	23515.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNSYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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 3 Entity 3 polymer

Description description	Env
Molecular weight formula_weight	11935.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,C

MRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTI

Source Source

Source organism organism	Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013
Common name common_name	ZIKV
NCBI taxonomy ID ncbi_taxonomy_id	2043570
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6utaa_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6utab1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6utab2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6utac_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.4 — Class II viral fusion proteins C-terminal domain

Domain ID domain_id	d6utae_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.4 — Class II viral fusion proteins C-terminal domain

Domain ID domain_id	d6utah_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6utal1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d6utal2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (10 domains)

Domain ID domain_id	6utaA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6utaE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6utaH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6utaL02
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	85.907 Å
Unit-cell length b length_b	85.907 Å
Unit-cell length c length_c	327.458 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	tetragonal

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	38.420 Å
R factor r_factor	0.2751
R_work r_work	0.2743
R_free r_free	0.2912

Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII

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

Z004 iGL Fab heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Z004 iGL Fab light chain

State in the Current Structure

Other States of the Same Protein in the Database

Env

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

6uta__assembly_2__model_1

6uta__assembly_2__model_1 | I(q)

6uta__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII

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

Z004 iGL Fab heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Z004 iGL Fab light chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Env

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

6uta__assembly_2__model_1

6uta__assembly_2__model_1 | I(q)

6uta__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

7. Citations (1)