SAXSdb — 6ilk

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

Complement decay-accelerating factor

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 300	Capsid protein VP1 × 60 Capsid protein VP2 × 60 Capsid protein VP3 × 60 Capsid protein VP4 × 60 SPHINGOSINE × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 SPHINGOSINE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 25	Capsid protein VP1 × 5 Capsid protein VP2 × 5 Capsid protein VP3 × 5 Capsid protein VP4 × 5 SPHINGOSINE × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 30	Capsid protein VP1 × 6 Capsid protein VP2 × 6 Capsid protein VP3 × 6 Capsid protein VP4 × 6 SPHINGOSINE × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 5	Capsid protein VP1 × 1 Capsid protein VP2 × 1 Capsid protein VP3 × 1 Capsid protein VP4 × 1 SPHINGOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DAF_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–192； UniProt 94–285

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	6ilk
Deposition date deposition_date	2018-10-18
Structure title title	Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4
Keywords keywords	Echovirus 6, CD55, Cryo-EM, virus-receptor complex, 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.

6ilk__assembly_1__model_1

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

Download this curve (.dat)

6ilk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ilk__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)	139.50 Å
Total Rg	139.50 Å
Atom count	481500
Residues	61140
Excluded volume	8505800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ilk__assembly_1__model_1`	300-meric （300）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6ilk__assembly_2__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`6ilk__assembly_3__model_1`	25-meric （25）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`6ilk__assembly_4__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`6ilk__assembly_5__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	31707.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8025

VVRVADTMPSGPSNSESIPALTAAETGHTSQVVPSDTIQTRHVRNFHVRSESSVENFLSRSACVYIVEYKTRDDTPDKMYDSWVINTRQVAQLRRKLEFFTYVRFDVEVTFVITSVQDDSTRQNTDTPALTHQIMYVPPGGPIPQAVDDYNWQTSTNPSVFWTEGNAPPRMSIPFMSVGNAYSNFYDGWSHFSQTGVYGFNTLNNMGKLYFRHVNDKTISPITSKVRIYFKPKHVKAWVPRPPRLCEYTHKDNVDFEPKGVTTSRTQLTISNSTHVEN

Entity 2 Entity 2 polymer

Description description	Capsid protein VP2
Molecular weight formula_weight	28064.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SDRVRSITLGNSTITTQESANVVVGYGVWPDYLSDEEATAEDQPTQPDVATCRFYTLDSVSWMKESQGWWWKFPDALRDMGLFGQNMQYHYLGRSGYTIHVQCNASKFHQGCLLVVCVPEAEMGAANINEKINREHLSNGEVANTFSGTKSSNTNDVQQAVFNAGMGVAVGNLTIFPHQWINLRTNNCATIVMPYINSVPMDNMFRHYNFTLMIIPFAKLDYAAGSSTYIPITVTVAPMCAEYNGLRLAGHQ

Entity 3 Entity 3 polymer

Description description	Capsid protein VP3
Molecular weight formula_weight	26378.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GLPVMNTPGSNQFLTSDDYQSPTAMPQFDVTPEMNIPGEVKNLMEIAEVDSVVPVNNVNENVNSLEAYRIPVHSVTETGAQVFGFTLQPGADTVMERTLLGEILNYYANWSGSIKLTFMYCGSAMATGKFLLAYSPPGAGVPKNRREAMLGTHIIWDIGLQSSCVLCVPWISQTHYRFVSKDIYTDAGFITCWYQTSIVVPAEVQNQSVILCFVSACNDFSVRLLRDSPFVRQTAFYQ

Entity 4 Entity 4 polymer

Description description	Capsid protein VP4
Molecular weight formula_weight	7338.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GAQVSTQKTGAHETSLSASGNSIIHYTNINYYKDAASNSANRQDFTQDPGKFTEPVKDIMVKSLPALN

Entity 5 Entity 5 polymer

Description description	Complement decay-accelerating factor
Molecular weight formula_weight	21308.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

CNRSCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWSTAVEFCKKKSCPNPGEIRNGQIDVPGGILFGATISFSCNTGYKLFGSTSSFCLISGSSVQWSDPLPECREIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRG

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 6 Entity 6 non-polymer

Description description	SPHINGOSINE
Molecular weight formula_weight	299.5 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d6ilka_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d6ilkc_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d6ilke1
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6ilke2
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

Domain ID domain_id	d6ilke3
Class class	g — Small proteins
Fold Fold fold	g.18 — Complement control module/SCR domain
Superfamily Superfamily superfamily	g.18.1 — Complement control module/SCR domain
Family Family family	g.18.1.0 — automated matches

CATH v4.4 (5 domains)

Domain ID domain_id	6ilkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6ilkB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6ilkC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6ilkE01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

Domain ID domain_id	6ilkE02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	70 — Complement Module; domain 1
Homologous superfamily homologous superfamily	10 — Complement Module, domain 1

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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	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	28528

Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4

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

Complement decay-accelerating factor

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

6ilk__assembly_1__model_1

6ilk__assembly_1__model_1 | I(q)

6ilk__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 (6)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Cryo-EM structure of Echovirus 6 complexed with its attachment receptor CD55 at PH 7.4

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

Complement decay-accelerating factor

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

6ilk__assembly_1__model_1

6ilk__assembly_1__model_1 | I(q)

6ilk__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 (6)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)