SAXSdb — 5ukb

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

Anti-vesicular stomatitis virus N VHH

Vicugna pacos

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	Nucleocapsid × 10 （A6H4P1） RNA (45-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A192B6J5_VICPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain a； PDBConstruct 3–124； UniProt 3–124 Author chain b； PDBConstruct 3–124； UniProt 3–124 Author chain c； PDBConstruct 3–124； UniProt 3–124 Author chain d； PDBConstruct 3–124； UniProt 3–124 Author chain e； PDBConstruct 3–124； UniProt 3–124

Nucleocapsid

Vesicular stomatitis Indiana virus

UniProt A6H4P1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 20 RNA 2	Anti-vesicular stomatitis virus N VHH × 10 （A0A192B6J5） RNA (45-MER) × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A6H4P1_9RHAB
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 3–423； UniProt 2–422 Author chain B； PDBConstruct 3–423； UniProt 2–422 Author chain C； PDBConstruct 3–423； UniProt 2–422 Author chain D； PDBConstruct 3–423； UniProt 2–422 Author chain E； PDBConstruct 3–423； UniProt 2–422

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	5ukb
Deposition date deposition_date	2017-01-20
Structure title title	VSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004
Keywords keywords	VESICULAR STOMATITIS VIRUS, NUCLEOPROTEIN, INHIBITORY VHH, ANTIVIRAL, Viral Protein-RNA-Immune System complex; Viral Protein/RNA/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.

5ukb__assembly_1__model_1

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

Download this curve (.dat)

5ukb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5ukb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.64 Å
Rg (electron density)	66.79 Å
Total Rg	66.73 Å
Atom count	44420
Residues	5500
Excluded volume	784100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5ukb__assembly_1__model_1`	22-meric （22）	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	Anti-vesicular stomatitis virus N VHH
Molecular weight formula_weight	15094.7 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d,c,b,a,e
Atom count atom_count	22210

QVQLVESGGGLVQAGGSLTLSCVASGRPFRNYRLGWFRQAPGKEREFVAAINWGGVITNYADSVKGRFTISRDDAKNTVYLQMNSLKPEETAVYYCAAFDSTGSPIVRDNYEYWGQGTQVTVSSGGLPETGGHHHHHH

Source Source

Source organism organism	Vicugna pacos
Common name common_name	Alpaca
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nucleocapsid
Molecular weight formula_weight	47535.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

MASVTVKRIIDNTVIVPKLPANEDPVEYPADYFRKSKEIPLYINTTKSLSDLRGYVYQGLKSGNVSIIHVNSYLYGALKDIRGKLDKDWSSFGINIGKAGDTIGIFDLVSLKALDGVLPDGVSDASRTSADDKWLPLYLLGLYRVGRTQMPEYRKKLMDGLTNQCKMINEQFEPLVPEGRDIFDVWGNDSNYTKIVAAVDMFFHMFKKHECASFRYGTIVSRFKDCAALATFGHLCKITGMSTEDVTTWILNREVADEMVQMMLPGQEIDKADSYMPYLIDFGLSSKSPYSSVKNPAFHFWGQLTALLLRSTRARNARQPDDIEYTSLTTAGLLYAYAVGSSADLAQQFCVGDNKYTPDDSTGGLTTNAPPQGRDVVEWLGWFEDQNRKPTPDMMQYAKRAVMSLQGLREKTIGKYAKSEFDK

Source Source

Source organism organism	Vesicular stomatitis Indiana virus
NCBI taxonomy ID ncbi_taxonomy_id	11277
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	RNA (45-MER)
Molecular weight formula_weight	13732.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

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Unit-cell length a length_a	240.117 Å
Unit-cell length b length_b	335.497 Å
Unit-cell length c length_c	75.899 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	20

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	5.473 Å
Low-resolution limit resolution_low	137.515 Å
R factor r_factor	0.3365
R_work r_work	0.3364
R_free r_free	0.3375

VSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004

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

Anti-vesicular stomatitis virus N VHH

State in the Current Structure

Other States of the Same Protein in the Database

Nucleocapsid

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

5ukb__assembly_1__model_1

5ukb__assembly_1__model_1 | I(q)

5ukb__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 (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

7. Citations (1)

VSV N PROTEIN IN COMPLEX WITH INHIBITORY NANOBODY 1004

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

Anti-vesicular stomatitis virus N VHH

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nucleocapsid

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

5ukb__assembly_1__model_1

5ukb__assembly_1__model_1 | I(q)

5ukb__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 (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

7. Citations (1)