[English] 日本語
Yorodumi
- PDB-4lo3: HA17-HA33-LacNac -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lo3
TitleHA17-HA33-LacNac
Components
  • HA-17
  • HA-33
KeywordsPROTEIN TRANSPORT / progenitor toxin complex / botulinum neurotoxin / botulism / neurotoxin associated protein / hemagglutinin / carbohydrate/sugar binding / secreted protein
Function / homology
Function and homology information


Toxicity of botulinum toxin type A (botA) / Toxicity of botulinum toxin type B (botB)
Similarity search - Function
Hemagglutinin component HA-17 / Clostridium botulinum HA-17 domain / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-lactosamine / HA-33 / HA-17
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsLee, K. / Gu, S. / Jin, L. / Le, T.T. / Cheng, L.W. / Strotmeier, J. / Kruel, A.M. / Yao, G. / Perry, K. / Rummel, A. / Jin, R.
CitationJournal: PLoS Pathog / Year: 2013
Title: Structure of a bimodular botulinum neurotoxin complex provides insights into its oral toxicity.
Authors: Kwangkook Lee / Shenyan Gu / Lei Jin / Thi Tuc Nghi Le / Luisa W Cheng / Jasmin Strotmeier / Anna Magdalena Kruel / Guorui Yao / Kay Perry / Andreas Rummel / Rongsheng Jin /
Abstract: Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the fatal disease botulism, a flaccid paralysis of the muscle. BoNTs are released together with several auxiliary ...Botulinum neurotoxins (BoNTs) are produced by Clostridium botulinum and cause the fatal disease botulism, a flaccid paralysis of the muscle. BoNTs are released together with several auxiliary proteins as progenitor toxin complexes (PTCs) to become highly potent oral poisons. Here, we report the structure of a ∼760 kDa 14-subunit large PTC of serotype A (L-PTC/A) and reveal insight into its absorption mechanism. Using a combination of X-ray crystallography, electron microscopy, and functional studies, we found that L-PTC/A consists of two structurally and functionally independent sub-complexes. A hetero-dimeric 290 kDa complex protects BoNT, while a hetero-dodecameric 470 kDa complex facilitates its absorption in the harsh environment of the gastrointestinal tract. BoNT absorption is mediated by nine glycan-binding sites on the dodecameric sub-complex that forms multivalent interactions with carbohydrate receptors on intestinal epithelial cells. We identified monosaccharides that blocked oral BoNT intoxication in mice, which suggests a new strategy for the development of preventive countermeasures for BoNTs based on carbohydrate receptor mimicry.
History
DepositionJul 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HA-33
C: HA-17
B: HA-33
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,9995
Polymers85,2333
Non-polymers7672
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-19 kcal/mol
Surface area30560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.216, 118.803, 162.536
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-258-

HOH

21B-459-

HOH

-
Components

#1: Protein HA-33 / HA-33 protein / HA34 / Non-toxin haemagglutinin HA34


Mass: 34081.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: HA-33, ha33, ha34 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45871
#2: Protein HA-17 / HA-17 protein / HA17 / Ha17 protein / Non-toxin haemagglutinin HA17


Mass: 17069.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ha17, HA-17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q45878
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.2
Details: 0.1 M MES, 0.1 M magnesium chloride, 5% PEG8000, pH 6.2, EVAPORATION, temperature 292.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97952 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. all: 49590 / Num. obs: 49357 / % possible obs: 99.53 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.5
Reflection shellResolution: 2.249→2.4 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→47.956 Å / SU ML: 0.73 / σ(F): 1.36 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 2505 5.08 %RANDOM
Rwork0.1791 ---
obs0.1808 49357 99.53 %-
all-49590 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.472 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.9113 Å2-0 Å2-0 Å2
2---10.3061 Å20 Å2
3----5.6052 Å2
Refinement stepCycle: LAST / Resolution: 2.249→47.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 52 217 6114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096037
X-RAY DIFFRACTIONf_angle_d1.0888240
X-RAY DIFFRACTIONf_dihedral_angle_d14.7962181
X-RAY DIFFRACTIONf_chiral_restr0.223931
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.249-2.29180.31641270.23322524X-RAY DIFFRACTION97
2.2918-2.33860.27311380.21132568X-RAY DIFFRACTION100
2.3386-2.38950.30521460.21212566X-RAY DIFFRACTION100
2.3895-2.44510.26891390.2172573X-RAY DIFFRACTION99
2.4451-2.50620.2711360.21072582X-RAY DIFFRACTION100
2.5062-2.5740.24111330.21852597X-RAY DIFFRACTION100
2.574-2.64970.29071290.21642573X-RAY DIFFRACTION99
2.6497-2.73520.261490.21262575X-RAY DIFFRACTION100
2.7352-2.8330.27171400.20292608X-RAY DIFFRACTION100
2.833-2.94640.23851530.18822576X-RAY DIFFRACTION100
2.9464-3.08040.21441590.18312599X-RAY DIFFRACTION100
3.0804-3.24280.22681290.18282604X-RAY DIFFRACTION100
3.2428-3.44590.22161380.18542597X-RAY DIFFRACTION99
3.4459-3.71190.19751370.17292634X-RAY DIFFRACTION100
3.7119-4.08530.19951430.16652627X-RAY DIFFRACTION100
4.0853-4.6760.17161280.13712643X-RAY DIFFRACTION100
4.676-5.88960.16991240.15042663X-RAY DIFFRACTION99
5.8896-47.96740.18221570.19292743X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14980.101-0.20173.76371.82474.20730.05280.0467-0.10860.0843-0.10160.07030.2873-0.0540.04680.16030.0027-0.01930.23030.01750.259836.5124-12.858847.8465
24.6727-0.19560.4623.68350.59174.85560.01090.73850.1061-0.36460.1835-0.29740.11640.4532-0.20620.3198-0.02320.00550.4361-0.01520.337245.309-25.368517.574
34.9533-0.39020.50934.21080.67215.51790.01170.39140.0616-0.28130.10710.22470.2138-0.3502-0.09960.4023-0.0479-0.06050.39580.01640.367336.0117-25.01517.0943
42.22380.4114-1.24952.9807-0.21524.3407-0.2371-0.50450.2060.5572-0.0914-0.2622-0.39580.89370.31260.4932-0.0737-0.12420.4794-0.00950.392449.816911.553881.4324
53.3210.2442-1.21844.3951.1365.74470.02150.04410.65820.19220.2545-0.6821-1.13970.7454-0.21650.4977-0.172-0.07910.37720.01740.405351.118619.634666.233
61.4231.4928-0.38022.4987-1.59395.81860.1116-0.31180.29210.5694-0.15250.2645-0.5821-0.12580.08230.49040.0814-0.12580.3287-0.04590.287140.749111.037782.7413
73.66081.0609-1.01562.001-3.97324.8843-0.3028-0.22160.36460.06330.35260.054-0.5013-0.4291-0.0780.5906-0.0043-0.04830.3813-0.05430.291342.302917.689977.1411
81.6710.73980.6072.10091.41955.0227-0.085-0.22240.38160.2528-0.1880.3591-0.9453-0.29510.2260.40950.0125-0.02080.2604-0.05220.314536.23916.295568.4944
92.7351-1.2897-0.06074.90690.11714.2643-0.0156-0.13820.14420.4769-0.0617-0.083-0.0264-0.12250.14510.30110.0041-0.00050.2710.00840.230740.67335.348472.5196
101.4849-0.1060.64944.066-0.97113.1918-0.22070.3460.0522-0.2609-0.0257-0.5508-0.00040.50140.25050.2373-0.0410.02350.40630.00680.328248.05645.654260.6328
112.65584.86873.56998.95986.57484.81950.0566-0.05790.29910.46690.0979-0.6029-0.00120.5756-0.18480.3526-0.0324-0.12060.48730.01740.451552.62798.965270.7717
123.5231-0.62141.14732.5215-0.45223.86130.03990.14240.1707-0.2019-0.11260.0604-0.5371-0.02770.05850.27680.04550.01040.17470.00750.243834.540115.497141.5702
135.6576-1.87110.9693.33981.042.59260.95121.2357-0.7376-0.9417-0.74770.45440.5585-0.0507-0.15220.69230.2805-0.18210.6888-0.17770.607211.020414.975717.6297
144.5458-2.51471.4692.49220.69742.6370.91221.6201-0.4578-1.2248-0.79580.03870.29020.3111-0.1331.14220.583-0.07671.0777-0.15360.767118.878913.033212.2975
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 9:150)
2X-RAY DIFFRACTION2chain 'A' and (resseq 151:222)
3X-RAY DIFFRACTION3chain 'A' and (resseq 223:294)
4X-RAY DIFFRACTION4chain 'C' and (resseq 3:17)
5X-RAY DIFFRACTION5chain 'C' and (resseq 18:44)
6X-RAY DIFFRACTION6chain 'C' and (resseq 45:54)
7X-RAY DIFFRACTION7chain 'C' and (resseq 55:63)
8X-RAY DIFFRACTION8chain 'C' and (resseq 64:79)
9X-RAY DIFFRACTION9chain 'C' and (resseq 80:113)
10X-RAY DIFFRACTION10chain 'C' and (resseq 114:136)
11X-RAY DIFFRACTION11chain 'C' and (resseq 137:146)
12X-RAY DIFFRACTION12chain 'B' and (resseq 10:150)
13X-RAY DIFFRACTION13chain 'B' and (resseq 151:219)
14X-RAY DIFFRACTION14chain 'B' and (resseq 220:294)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more