SAXSdb — 9qcm

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

Botulinum neurotoxin type B

Clostridium botulinum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH × 1 （B1INP6） Hemagglutinin component HA70 × 3 （B1INQ0） Hemagglutinin component HA17 × 3 （B1INP9） Hemagglutinin component HA33 × 6 （B1INP8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BXB_CLOBK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–1292； UniProt 2–1291

Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH

Clostridium botulinum

UniProt B1INP6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Botulinum neurotoxin type B × 1 （B1INP5） Hemagglutinin component HA70 × 3 （B1INQ0） Hemagglutinin component HA17 × 3 （B1INP9） Hemagglutinin component HA33 × 6 （B1INP8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1INP6_CLOBK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1197； UniProt 1–1197

Hemagglutinin component HA70

Clostridium botulinum

UniProt B1INQ0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Botulinum neurotoxin type B × 1 （B1INP5） Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH × 1 （B1INP6） Hemagglutinin component HA17 × 3 （B1INP9） Hemagglutinin component HA33 × 6 （B1INP8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1INQ0_CLOBK
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–626； UniProt 1–626 Author chain D； PDBConstruct 1–626； UniProt 1–626 Author chain E； PDBConstruct 1–626； UniProt 1–626

Hemagglutinin component HA17

Clostridium botulinum

UniProt B1INP9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Botulinum neurotoxin type B × 1 （B1INP5） Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH × 1 （B1INP6） Hemagglutinin component HA70 × 3 （B1INQ0） Hemagglutinin component HA33 × 6 （B1INP8）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1INP9_CLOBK
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain F； PDBConstruct 1–146； UniProt 1–146 Author chain G； PDBConstruct 1–146； UniProt 1–146 Author chain H； PDBConstruct 1–146； UniProt 1–146

Hemagglutinin component HA33

Clostridium botulinum

UniProt B1INP8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 14	Botulinum neurotoxin type B × 1 （B1INP5） Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH × 1 （B1INP6） Hemagglutinin component HA70 × 3 （B1INQ0） Hemagglutinin component HA17 × 3 （B1INP9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B1INP8_CLOBK
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–294； UniProt 1–294 Author chain J； PDBConstruct 1–294； UniProt 1–294 Author chain K； PDBConstruct 1–294； UniProt 1–294 Author chain L； PDBConstruct 1–294； UniProt 1–294 Author chain M； PDBConstruct 1–294； UniProt 1–294 Author chain N； PDBConstruct 1–294； UniProt 1–294

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	9qcm
Deposition date deposition_date	2025-03-04
Last revision last_revision	2025-09-10
Structure title title	Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)
Keywords keywords	progenitor-toxin complex, botulinum neurotoxin, hemagglutinin, TOXIN; TOXIN
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.

9qcm__assembly_1__model_1

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

Download this curve (.dat)

9qcm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9qcm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	88.77 Å
Rg (electron density)	89.09 Å
Total Rg	88.67 Å
Atom count	47012
Residues	6207
Excluded volume	836970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9qcm__assembly_1__model_1`	14-meric （14）	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	Botulinum neurotoxin type B
Molecular weight formula_weight	152427.1 kDa
Mutation mutation	E232Q, H235Y
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	47012

MGPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHQLIYVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTEHHHHHHHHHH

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
Molecular weight formula_weight	138876.8 kDa
EC 编号 ec_number	3.4.24.69
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNINDNLSINSPVDNKNVVVVRARKTDTVFKAFKVAPNIWVAPERYYGESLSIDEEYKVDGGIYDSNFLSQDSEKDKFLQAIITLLKRINSTNAGEKLLSLISTAIPFPYGYIGGGYYAPNMITFGSAPKSNKKLNSLISSTIPFPYAGYRETNYLSSEDNKSFYASNIVIFGPGANIVENNTVFYKKEDAENGMGTMTEIWFQPFLTYKYDEFYIDPAIELIKCLIKSLYFLYGIKPSDDLVIPYRLRSELENIEYSQLNIVDLLVSGGIDPKFINTDPYWFTDNYFSNAKKVFEDHRNIYETQIEGNNAIGNDIKLRLKQKFRININDIWELNLNYFSKEFSIMMPDRFNNALKHFYRKQYYKIDYPENYSINGFVNGQINVQLSLSDRNQDIINKPEEIINLLNGNNVSLMRSNIYGDGLKSTVDDFYSNYKIPYNRAYEYHFNNSNDSSLDNVNIGVIDNIPEIIDVNPYKENCDKFSPVQKITSTREINTNIPWPINYLQAQNTNNEKFSLSSDFVEVVSSKDKSLVYSFLSNVMFYLDSIKDNSPIDTDKKYYLWLREIFRNYSFDITATQEINTDCGINKVVTWFGKALNILNTSDSFVEEFQNLGPISLINKKENLSMPIIEIYGIPNDMLGLPLNDLNEKLFNIYLKNILYFKKVYFNFLDQWWTEYYSQYFDLICMAKQSILAQEKLIKQIIQNKLQDLFKADISMDKLNLMNLATEKTFIDLSNESQIAINNINDFLNKSAICVFDTNIYPKFISFMEQCINSVNSNVTAFIQKCTNITEDEKLQLIKLNTFMNIDFEFFDIQSIKDLITSETDLIKEEKESDYNLFLFTLQEDNNKVIEDISGKNTLVKYSDSISLVYGVNGDALYLKEPDESVSFSNKAFENGLTNSFSICFWLRNLGEDIITSKLIENKADNCGWEIYFENNGLVFSIVDCNGNEENIYLSDVISKNWYYISISIDRLRNQLLIFINDKLIANQSIEQILNIYSSNTISLVNENNPIYIEGLSILNRSITSEEVVNNYFSYLNNSYIRDISGERLEYNKTYELYNYVFPENSLYEVTENNNIYLSIKDTNNLNIQGAKFKLINIDANKQYVQKWDEGVVCLLGDEEKYVDISSENNRIQLVNSKDTAKRIIFNNDIFMPNCLTFAYNNKYLSLSLRDRNYNWMICNNNDNIPKAAHLWALKGI

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Hemagglutinin component HA70
Molecular weight formula_weight	71249.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MNSSIKKIYNHIQEKVINYSDTIDLADGNYVVSRGDGWILSRQNQILGGSVISNGSTGIVGDLRVNDNAIPYYYPTPSFNEEYIKNNIQTVFANFTEANQIPIGFEFSKTAPSNKNLYMYLQYTYIRYEIIKVLQHEIIERAVLYVPSLGYVKSIEFNPGEKINKDFYFLTNDKCILNEQFLYKKILETTKNIPTNNIFNSKVSSTQRVLPYSNGLYVINKGDGYIRTNDKDLIGTLLIEAGSSGSIIQPRLRNTTRPLFTTSNDAKFSQQYTEERLKDAFNVQLFNTSTSLFKFVEEAPSNKNICIKAYNTYEKYELIDYQNGSIVNKAEYYLPSLGYCEVTNAPSPESEVVKTQVAEDGFIQNGPEEEIVVGVIDPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIYEAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIENQIKFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDTSNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLNLLNSTKSIRLLNGAIYILKVEVTELNNYNIKLHIDITN

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Hemagglutinin component HA17
Molecular weight formula_weight	16919.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,G,H

MSAERTFLPNGNYNIKSIFSGSLYLSPVSGSLTFSNESSANNQKWNVEYMAENRCFKISNVAEPNKYLSYDNFGFISLDSLSNRCYWFPIKIAVNTYIMLSLNKVNELDYAWDIYDTNENILSQPLLLLPNFDIYNSNQMFKLEKI

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Hemagglutinin component HA33
Molecular weight formula_weight	33687.6 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N

MEHYSTIQNSLNDKIVTISCKANTDLFFYQVPGNGNVSLFQQTRNYLERWRIIYDSNKAAYKIKSMNIYNTNLVLTWNAPTHNISAQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYADTVARNLKLSTLNNSSYIKFIIEDYVISDFKNFTCRISPILAGGKVVQQVSMTNLAVNLYIWNNDLNQKWTIIYNEEKAAYQFFNKILSNGVLTWIFSDGNTVRVSSSAQNNDAQYWLINPVSDNYDRYTITNLRDKTKVLDLYGGQTADGTTIQVFNSNGGDNQIWTMSNP

Source Source

Source organism organism	Clostridium botulinum
NCBI taxonomy ID ncbi_taxonomy_id	1491
Host organism host_organism	Escherichia coli

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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	—

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

Resolution resolution	2.90 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	139594

Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)

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

Botulinum neurotoxin type B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin component HA70

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin component HA17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Hemagglutinin component HA33

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

9qcm__assembly_1__model_1

9qcm__assembly_1__model_1 | I(q)

9qcm__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

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 polymer

Polymer Polymer

Source Source

7. Citations (1)