6iw2

Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state

Method: X-RAY DIFFRACTION

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

Envelope protein E

Yellow fever virus (strain 17D vaccine)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Heavy chain of monoclonal antibody 5A × 2 Light chain of monoclonal antibody 5A × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Heavy chain of monoclonal antibody 5A × 2 Light chain of monoclonal antibody 5A × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 6	Heavy chain of monoclonal antibody 5A × 2 Light chain of monoclonal antibody 5A × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_YEFV1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 286–680 Author chain D； PDBConstruct 1–395； UniProt 286–680 Author chain G； PDBConstruct 1–395； UniProt 286–680 Author chain J； PDBConstruct 1–395； UniProt 286–680 Author chain M； PDBConstruct 1–395； UniProt 286–680 Author chain P； PDBConstruct 1–395； UniProt 286–680

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	6iw2
Deposition date deposition_date	2018-12-04
Structure title title	Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state
Keywords keywords	;Yellow fever virus, Neutralizing monoclonal antibody, Envelope protein, Flavivirus, VIRAL PROTEIN, VIRAL PROTEIN-IMMUNE SYSTEM complex ;; VIRAL PROTEIN/IMMUNE SYSTEM
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.

6iw2__assembly_2__model_1

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

Download this curve (.dat)

6iw2__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6iw2__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	42.75 Å
Rg (electron density)	43.20 Å
Total Rg	43.45 Å
Atom count	9496
Residues	1228
Excluded volume	168420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6iw2__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6iw2__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6iw2__assembly_3__model_1`	hexameric （6）	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	Envelope protein E
Molecular weight formula_weight	43234.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G,J,M,P
Atom count atom_count	28516

AHCIGITDRDFIEGVHGGTWVSATLEQDKCVTVMAPDKPSLDISLETVAIDRPAEVRKVCYNAVLTHVKINDKCPSTGEAHLAEENEGDNACKRTYSDRGWGNGCGLFGKGSIVACAKFTCAKSMSLFEVDQTKIQYVIRAQLHVGAKQENWNTDIKTLKFDALSGSQEVEFIGYGKATLECQVQTAVDFGNSYIAEMETESWIVDRQWAQDLTLPWQSGSGGVWREMHHLVEFEPPHAATIRVLALGNQEGSLKTALTGAMRVTKDTNDNNLYKLHGGHVSCRVKLSALTLKGTSYKICTDKMFFVKNPTDTGHGTVVMQVKVSKGAPCRIPVIVADDLTAAINKGILVTVNPIASTNDDEVLIEVNPPFGDSYIIVGRGDSRLTYQWHKEGSS

Source Source

Source organism organism	Yellow fever virus (strain 17D vaccine)
Common name common_name	YFV
NCBI taxonomy ID ncbi_taxonomy_id	11090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Heavy chain of monoclonal antibody 5A
Molecular weight formula_weight	13543.0 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E,H,K,N,Q

EVQLVESGPRLVKPSETLSLTCTVSGGSTYNHHWSWIRQPPGRGLEWIGYISYSGKSNYNPSLKSRVTISLEPSTTQFSLKLNSLTAADTAVYYCAREYRDDTNYYYYSLDVWGPGTMVT

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Light chain of monoclonal antibody 5A
Molecular weight formula_weight	11700.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I,L,O,R

QIVMTQSPSTLSASVGDRVTITCRASQSIGSWLAWYQQKPGKAPKLLIYKASSLESGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCQQYNNYSYTFGPGTKLEIK

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d6iw2a1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2a2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2b_
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	d6iw2c_
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	d6iw2d1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2d2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2e_
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	d6iw2f_
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	d6iw2g1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2g2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2h_
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	d6iw2i_
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	d6iw2j1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2j2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2k_
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	d6iw2l_
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	d6iw2m1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2m2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2n_
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	d6iw2o_
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	d6iw2p1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.10 — Viral glycoprotein, central and dimerisation domains
Superfamily Superfamily superfamily	f.10.1 — Viral glycoprotein, central and dimerisation domains
Family Family family	f.10.1.0 — automated matches

Domain ID domain_id	d6iw2p2
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.1.18.0 — automated matches

Domain ID domain_id	d6iw2q_
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	d6iw2r_
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)

CATH v4.4 (24 domains)

Domain ID domain_id	6iw2A01
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	6iw2A02
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	6iw2A03
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	6iw2A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6iw2D01
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	6iw2D02
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	6iw2D03
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	6iw2D04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6iw2G01
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	6iw2G02
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	6iw2G03
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	6iw2G04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6iw2J01
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	6iw2J02
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	6iw2J03
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	6iw2J04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6iw2M01
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	6iw2M02
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	6iw2M03
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	6iw2M04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	6iw2P01
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	6iw2P02
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	6iw2P03
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	6iw2P04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

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Unit-cell length a length_a	95.967 Å
Unit-cell length b length_b	99.244 Å
Unit-cell length c length_c	123.099 Å
Unit-cell angle α angle_alpha	96.39 °
Unit-cell angle β angle_beta	94.90 °
Unit-cell angle γ angle_gamma	100.36 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	48.695 Å
R factor r_factor	0.2392
R_work r_work	0.2375
R_free r_free	0.2720

Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state

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

Envelope 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

6iw2__assembly_2__model_1

6iw2__assembly_2__model_1 | I(q)

6iw2__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of 5A ScFv in complex with YFV-17D sE in prefusion state

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

Envelope 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

6iw2__assembly_2__model_1

6iw2__assembly_2__model_1 | I(q)

6iw2__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) 48 domains

SCOP 2.08 (24 domains)

CATH v4.4 (24 domains)

7. Citations (1)