SAXSdb — 7pa7

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

Major capsid protein VP1

Betapolyomavirus hominis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	scFv 29B1 antibody heavy chain × 5 water × 10	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 10	scFv 29B1 antibody heavy chain × 5 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP1_POVBK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain AAA； PDBConstruct 5–275； UniProt 31–301 Author chain BBB； PDBConstruct 5–275； UniProt 31–301 Author chain CCC； PDBConstruct 5–275； UniProt 31–301 Author chain DDD； PDBConstruct 5–275； UniProt 31–301 Author chain EEE； PDBConstruct 5–275； UniProt 31–301 Author chain MMM； PDBConstruct 5–275； UniProt 31–301 Author chain NNN； PDBConstruct 5–275； UniProt 31–301 Author chain OOO； PDBConstruct 5–275； UniProt 31–301 Author chain PPP； PDBConstruct 5–275； UniProt 31–301 Author chain QQQ； PDBConstruct 5–275； UniProt 31–301

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	7pa7
Deposition date deposition_date	2021-07-29
Structure title title	BK polyomavirus VP1 in complex with scFv 29B1
Keywords keywords	antibody, polyomavirus, VP1, neutralization, VIRAL PROTEIN; VIRAL PROTEIN
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.

7pa7__assembly_1__model_1

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

Download this curve (.dat)

7pa7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7pa7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.85 Å
Rg (electron density)	43.48 Å
Total Rg	43.79 Å
Atom count	18491
Residues	2433
Excluded volume	325140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7pa7__assembly_1__model_1`	decameric （10）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7pa7__assembly_2__model_1`	decameric （10）	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	scFv 29B1 antibody heavy chain
Molecular weight formula_weight	26947.7 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	eee,aaa,bbb,ccc,ddd,mmm,nnn,ooo,ppp,qqq
Atom count atom_count	37703

GSYVLTQPPSVSVAPGKTARITCGGNNIGSRSVHWYQHKPGQAPVMIISYDMNRPSGIPERVSGSNYGNTATLTISRVEAGDEADYYCQVWDSRSDHPYVFGTGTRVTVLGSTSGSGKPGSGEGSTKGEVQLVESGGGLVKPGGSLRLSCAASGITFQYYAMNWVRQAPGKGLEWVSSIGGRGDTTYYTDSVKGRFTISRDNSKSTLYLQMNSLRAEDTAVYYCAKEPFDSSGDHRGVFDYWGQGTLVTVSS

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Major capsid protein VP1
Molecular weight formula_weight	30261.0 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA,BBB,CCC,DDD,EEE,MMM,NNN,OOO,PPP,QQQ

GSHMGGVEVLEVKTGVDAITEVECFLNPEMGDPDENLRGFSLKLSAENDFSSDSPERKMLPCYSTARIPLPNLNEDLTCGNLLMWEAVTVQTEVIGITSMLNLHAGSQKVHEHGGGKPIQGSNFHFFAVGGDPLEMQGVLMNYRTKYPDGTITPKNPTAQSQVMNTDHKAYLDKNNAYPVECWVPDPSRNENTRYFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCKADSLYVSAADICGLFTNSSGTQQWRGLARYFKIRLRKRSVKNPYP

Source Source

Source organism organism	Betapolyomavirus hominis
NCBI taxonomy ID ncbi_taxonomy_id	1891762
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	726

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Unit-cell length a length_a	114.588 Å
Unit-cell length b length_b	114.614 Å
Unit-cell length c length_c	142.373 Å
Unit-cell angle α angle_alpha	92.31 °
Unit-cell angle β angle_beta	106.00 °
Unit-cell angle γ angle_gamma	111.41 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	48.444 Å
R factor r_factor	—
R_work r_work	0.2471
R_free r_free	0.2724

BK polyomavirus VP1 in complex with scFv 29B1

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

Major capsid protein VP1

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

7pa7__assembly_1__model_1

7pa7__assembly_1__model_1 | I(q)

7pa7__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 water

7. Citations (1)

BK polyomavirus VP1 in complex with scFv 29B1

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

Major capsid protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7pa7__assembly_1__model_1

7pa7__assembly_1__model_1 | I(q)

7pa7__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 water

7. Citations (1)