SAXSdb — 3win

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

HA3

Clostridium botulinum B

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	17 kD hemagglutinin component × 3 （Q45841） HA1 × 6 （Q33CP6） water × 15	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q33CP8_CLOBO
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain D； PDBConstruct 25–194； UniProt 19–188 Author chain E； PDBConstruct 1–431； UniProt 196–626

17 kD hemagglutinin component

Clostridium botulinum B

UniProt Q45841

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	HA3 × 3 （Q33CP8） HA3 × 3 （Q33CP8） HA1 × 6 （Q33CP6） water × 15	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q45841_CLOBO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 24–168； UniProt 2–146

HA1

Clostridium botulinum B

UniProt Q33CP6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 15	HA3 × 3 （Q33CP8） HA3 × 3 （Q33CP8） 17 kD hemagglutinin component × 3 （Q45841） water × 15	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q33CP6_CLOBO
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 29–316； UniProt 7–294 Author chain B； PDBConstruct 29–316； UniProt 7–294

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	3win
Deposition date deposition_date	2013-09-19
Structure title title	Clostridium botulinum Hemagglutinin
Keywords keywords	;bacterial pathogenesis, bacterial toxins, carbohydrate-binding protein, E-cadherin, epithelial cell, protein complexes, botulinum toxin, hemagglutinin, Beta-trefoil, TOXIN ;; TOXIN
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.

3win__assembly_1__model_1

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

Download this curve (.dat)

3win__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3win__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	92.48 Å
Rg (electron density)	92.96 Å
Total Rg	92.54 Å
Atom count	31416
Residues	3897
Excluded volume	557560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3win__assembly_1__model_1`	pentadecameric （15）	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 (5)

Entity 1 Entity 1 polymer

Description description	HA3
Molecular weight formula_weight	22295.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D
Atom count atom_count	10522

MASWSHPQFEKGALEVLFQGPGYQYSDTIDLADGNYVVSRGDGWILSRQNQILGGSVISNGSTGIVGDLRVNDNAIPYYYPTPSFNEEYIKNNIQTVFANFTEANQIPIGFEFSKTAPSNKNLYMYLQYTYIRYEIIKVLQHEIIERAVLYVPSLGYVKSIEFNPGEKINKDFYFLTNDKCILNEQFLYKKILE

Source Source

Source organism organism	Clostridium botulinum B
NCBI taxonomy ID ncbi_taxonomy_id	36827
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	HA3
Molecular weight formula_weight	48762.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

NNIFNSKVSSTQRVLPYSNGLYVINKGDGYIRTNDKDLIGTLLIEAGSSGSIIQPRLRNTTRPLFTTSNDAKFSQQYTEERLKDAFNVQLFNTSTSLFKFVEEAPSNKNICIKAYNTYEKYELIDYQNGSIVNKAEYYLPSLGYCEVTNAPSPESEVVKTQVAEDGFIQNGPEEEIVVGVIDPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIYEAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIENQIKFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDTSNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLNLLNSTKSIRLLNGAIYILKVEVTELNNYNIKLHIDITN

Source Source

Source organism organism	Clostridium botulinum B
NCBI taxonomy ID ncbi_taxonomy_id	36827
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	17 kD hemagglutinin component
Molecular weight formula_weight	19248.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSSGLVPRGSHMASSAERTFLPNGNYNIKSIFSGSLYLSPVSGSLTFSNESSANNQKWNVEYMAENRCFKISNVAEPNKYLSYDNFGFISLDSLSNRCYWFPIKIAVNTYIMLSLNKVNELDYAWDIYDTNENILSQPLLLLPNFDIYNSNQMFKLEKI

Source Source

Source organism organism	Clostridium botulinum B
NCBI taxonomy ID ncbi_taxonomy_id	36827
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	HA1
Molecular weight formula_weight	36059.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MASWSHPQFEKGALEVLFQGPGYPDDDDIQNSLNDKIVTISCKANTDLFFYQVPGNGNVSLFQQTRNYLERWRIIYDSNKAAYKIKSMNIYNTNLVLTWNAPTHNISAQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYADTVARNLKLSTLNNSSYIKFIIEDYVISDFKNFTCRISPILAGGKVVQQVSMTNLAVNLYIWNNDLNQKWTIIYNEEKAAYQFFNKILSNGVLTWIFSDGNTVRVSSSAQNNDAQYWLINPVSDNYDRYTITNLRDKTKVLDLYGGQTADGTTIQVFNSNGGDNQIWTMSNP

Source Source

Source organism organism	Clostridium botulinum B
NCBI taxonomy ID ncbi_taxonomy_id	36827
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	50

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	3winA01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3winA02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3winB01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3winB02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3winC00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	3winD00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3winE01
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	15 — Proaerolysin; Chain A, domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3winE03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	1090 —

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Unit-cell length a length_a	324.726 Å
Unit-cell length b length_b	324.726 Å
Unit-cell length c length_c	117.588 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	24

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	48.430 Å
R factor r_factor	0.2025
R_work r_work	0.1999
R_free r_free	0.2512

Clostridium botulinum Hemagglutinin

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

HA3

State in the Current Structure

Other States of the Same Protein in the Database

17 kD hemagglutinin component

State in the Current Structure

Other States of the Same Protein in the Database

HA1

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

3win__assembly_1__model_1

3win__assembly_1__model_1 | I(q)

3win__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Clostridium botulinum Hemagglutinin

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

HA3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

17 kD hemagglutinin component

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

HA1

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

3win__assembly_1__model_1

3win__assembly_1__model_1 | I(q)

3win__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 (5)

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

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)