SAXSdb — 3cji

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

Polyprotein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 240	CALCIUM ION × 60 water × 240	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 1 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 20	CALCIUM ION × 5 water × 20	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 24	CALCIUM ION × 6 water × 24	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 1 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 160	CALCIUM ION × 40 water × 160	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q155Z9_9PICO
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 674–936 Author chain B； PDBConstruct 1–239； UniProt 435–673 Author chain C； PDBConstruct 1–284； UniProt 151–434 Author chain D； PDBConstruct 1–71； UniProt 80–150

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	3cji
Deposition date deposition_date	2008-03-13
Structure title title	Structure of Seneca Valley Virus-001
Keywords keywords	;virus capsid protein structure, ATP-binding, Cytoplasm, Cytoplasmic vesicle, Helicase, Hydrolase, Membrane, Nucleotide-binding, Nucleotidyltransferase, Phosphoprotein, Protease, RNA replication, RNA-binding, RNA-directed RNA polymerase, Thiol protease, Transferase, Virion, icosahedral virus, virus ;; VIRUS
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.

3cji__assembly_1__model_1

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

Download this curve (.dat)

3cji__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cji__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)	133.60 Å
Total Rg	133.60 Å
Atom count	375192
Residues	47940
Excluded volume	6657200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cji__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cji__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3cji__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3cji__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3cji__assembly_5__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`3cji__assembly_6__model_1`	160-meric （160）	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	Polyprotein
Molecular weight formula_weight	29092.8 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	6521

STDNAETGVIEAGNTDTDFSGELAAPGSNHTNVKFLFDRSRLLNVIKVLEKDAVFPRPFPTQEGAQQDDGYFCLLTPRPTVASRPATRFGLYANPSGSGVLANTSLDFNFYSLACFTYFRSDLEVTVVSLEPDLEFAVGWFPSGSEYQASSFVYDQLHVPFHFTGRTPRAFASKGGKVSFVLPWNSVSSVLPVRWGGASKLSSATRGLPAHADWGTIYAFVPRPNEKKSTAVKHVAVYIRYKNARAWCPSMLPFRSYKQKMLM

Entity 2 Entity 2 polymer

Description description	Polyprotein
Molecular weight formula_weight	26492.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPIPTAPRENSLMFLSTLPDDTVPAYGNVRTPPVNYLPGEITDLLQLARIPTLMAFERVPEPVPASDTYVPYVAVPTQFDDRPLISFPITLSDPVYQNTLVGAISSNFANYRGCIQITLTFCGPMMARGKFLLSYSPPNGTQPQTLSEAMQCTYSIWDIGLNSSWTFVVPYISPSDYRETRAITNSVYSADGWFSLHKLTKITLPPDCPQSPCILFFASAGEDYTLRLPVDCNPSYVFH

Entity 3 Entity 3 polymer

Description description	Polyprotein
Molecular weight formula_weight	31732.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DHNTEEMENSADRVTTQTAGNTAINTQSSLGVLCAYVEDPTKSDPPSSSTDQPTTTFTAIDRWYTGRLNSWTKAVKTFSFQAVPLPGAFLSRQGGLNGGAFTATLHRHFLMKCGWQVQVQCNLTQFHQGALLVAMVPETTLDVKPDGKAKSLQELNEEQWVEMSDDYRTGKNMPFQSLGTYYRPPNWTWGPNFINPYQVTVFPHQILNARTSTSVDINVPYIGETPTQSSETQNSWTLLVMVLVPLDYKEGATTDPEITFSVRPTSPYFNGLRNRYTAGTDEEQ

Entity 4 Entity 4 polymer

Description description	Polyprotein
Molecular weight formula_weight	7393.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GNVQTTSKNDFDSRGNNGNMTFNYYANTYQNSVDFSTSSSASGAGPGNSRGGLAGLLTNFSGILNPLGYLK

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cjia_
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.121.4.0 — automated matches

Domain ID domain_id	d3cjib_
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.121.4.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id	3cjiA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3cjiB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3cjiC00
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	311.510 Å
Unit-cell length b length_b	311.510 Å
Unit-cell length c length_c	1526.401 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	360

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	88.560 Å
R factor r_factor	0.2580
R_work r_work	0.2580
R_free r_free	0.2600

Structure of Seneca Valley Virus-001

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

Polyprotein

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

3cji__assembly_1__model_1

3cji__assembly_1__model_1 | I(q)

3cji__assembly_1__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 (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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of Seneca Valley Virus-001

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

Polyprotein

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

3cji__assembly_1__model_1

3cji__assembly_1__model_1 | I(q)

3cji__assembly_1__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 (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 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)