SAXSdb — 6diz

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

VP1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP2 × 60 （I6W7A3） VP3 × 60 （A0A0E3SXU7） VP4 × 60 （M4QLY4） SPHINGOSINE × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （I6W7A3） VP3 × 1 （A0A0E3SXU7） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP2 × 5 （I6W7A3） VP3 × 5 （A0A0E3SXU7） VP4 × 5 （M4QLY4） SPHINGOSINE × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP2 × 6 （I6W7A3） VP3 × 6 （A0A0E3SXU7） VP4 × 6 （M4QLY4） SPHINGOSINE × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP2 × 1 （I6W7A3） VP3 × 1 （A0A0E3SXU7） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D4QGA8_9ENTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–297； UniProt 566–862

VP2

OrganismNot specified

UniProt I6W7A3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP1 × 60 （D4QGA8） VP3 × 60 （A0A0E3SXU7） VP4 × 60 （M4QLY4） SPHINGOSINE × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP3 × 1 （A0A0E3SXU7） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （D4QGA8） VP3 × 5 （A0A0E3SXU7） VP4 × 5 （M4QLY4） SPHINGOSINE × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （D4QGA8） VP3 × 6 （A0A0E3SXU7） VP4 × 6 （M4QLY4） SPHINGOSINE × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP3 × 1 （A0A0E3SXU7） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I6W7A3_9ENTO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–245； UniProt 79–323

VP3

OrganismNot specified

UniProt A0A0E3SXU7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP1 × 60 （D4QGA8） VP2 × 60 （I6W7A3） VP4 × 60 （M4QLY4） SPHINGOSINE × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP2 × 1 （I6W7A3） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （D4QGA8） VP2 × 5 （I6W7A3） VP4 × 5 （M4QLY4） SPHINGOSINE × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （D4QGA8） VP2 × 6 （I6W7A3） VP4 × 6 （M4QLY4） SPHINGOSINE × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP2 × 1 （I6W7A3） VP4 × 1 （M4QLY4） SPHINGOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0E3SXU7_9ENTO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–242； UniProt 324–565

VP4

OrganismNot specified

UniProt M4QLY4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 240	VP1 × 60 （D4QGA8） VP2 × 60 （I6W7A3） VP3 × 60 （A0A0E3SXU7） SPHINGOSINE × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP2 × 1 （I6W7A3） VP3 × 1 （A0A0E3SXU7） SPHINGOSINE × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 20	VP1 × 5 （D4QGA8） VP2 × 5 （I6W7A3） VP3 × 5 （A0A0E3SXU7） SPHINGOSINE × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 24	VP1 × 6 （D4QGA8） VP2 × 6 （I6W7A3） VP3 × 6 （A0A0E3SXU7） SPHINGOSINE × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	VP1 × 1 （D4QGA8） VP2 × 1 （I6W7A3） VP3 × 1 （A0A0E3SXU7） SPHINGOSINE × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	M4QLY4_9ENTO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–78； UniProt 1–78

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	6diz
Deposition date deposition_date	2018-05-24
Structure title title	EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385
Keywords keywords	tryptophan dendrimers, EV-A71, 5-fold vertex, Cryo-EM, 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.

6diz__assembly_1__model_1

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

Download this curve (.dat)

6diz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6diz__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)	132.00 Å
Total Rg	132.00 Å
Atom count	392100
Residues	50520
Excluded volume	6964400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6diz__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6diz__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`6diz__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`6diz__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`6diz__assembly_5__model_1`	tetrameric （4）	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	VP1
Molecular weight formula_weight	32748.8 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	6535

GDRVADVIESSIGDSVSRALTQALPAPTGQNTQVSSHRLDTGEVPALQAAEIGASSNTSDESMIETRCVLNSHSTAETTLDSFFSRAGLVGEIDLPLEGTTNPNGYANWDIDITGYAQMRRKVELFTYMRFDAEFTFVACTPTGQVVPQLLQYMFVPPGAPKPESRESLAWQTATNPSVFVKLTDPPAQVSVPFMSPASAYQWFYDGYPTFGEHKQEKDLEYGACPNNMMGTFSVRTVGSSKSKYPLVVRIYMRMKHVRAWIPRPMRNQNYLFKANPNYAGNSIKPTGTSRSAITTL

Entity 2 Entity 2 polymer

Description description	VP2
Molecular weight formula_weight	26946.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SDRVAQLTIGNSTITTQEAANIIVGYGEWPSYCSDDDATAVDKPTRPDVSVNRFYTLDTKLWEKSSKGWYWKFPDVLTETGVFGQNAQFHYLYRSGFCIHVQCNASKFHQGALLVAILPEYVIGTVAGGTGTEDSHPPYKQTQPGADGFELQHPYVLDAGIPISQLTVCHHQRINLRTNNCATIIVPYMNTLPFDSALNHCNFGLLVVPISPLDFDQGATPVIPITITLAPMCSEFAGLRQAVTQ

Entity 3 Entity 3 polymer

Description description	VP3
Molecular weight formula_weight	26540.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GFPTELKPGTNQFLTTDDGVSAPILPNFHPTPCIHIPGEVRNLLELCQVETILEVNNVPTNATSLMERLRFPVSAQAGKGELCAVFRADPGRDGPWQSTMLGQLCGYYTQWSGSLEVTFMFTGSFMATGKMLIAYTPPGGPLPKDRATAMLGTHVIWDFGLQSSVTLVIPWISNTHYRAHARDGVFDYYTTGLVSIWYQTNYVVPIGAPNTAYIIALAAAQKNFTMKLCKDTSHILQTASIQ

Entity 4 Entity 4 polymer

Description description	VP4
Molecular weight formula_weight	8367.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MGSQVSTQRSGSHENSNSATEGSTINYTTINYYKDSYAATAGKQSLKQDPDKFANPVKDIFTEMAAPLKSPSAEACGY

Entity 5 Entity 5 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) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	6dizA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6dizB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	6dizC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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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	3.59 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	11813

EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385

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

VP1

State in the Current Structure

Other States of the Same Protein in the Database

VP2

State in the Current Structure

Other States of the Same Protein in the Database

VP3

State in the Current Structure

Other States of the Same Protein in the Database

VP4

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

6diz__assembly_1__model_1

6diz__assembly_1__model_1 | I(q)

6diz__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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385

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

VP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VP2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VP3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VP4

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

6diz__assembly_1__model_1

6diz__assembly_1__model_1 | I(q)

6diz__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

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)